Development and validation of a complementary map to enhance the existing 1998 to 2008 Abbreviated Injury Scale map

PubMed Central

2011-01-01

Introduction Many trauma registries have used the Abbreviated Injury Scale 1990 Revision Update 98 (AIS98) to classify injuries. In the current AIS version (Abbreviated Injury Scale 2005 Update 2008 - AIS08), injury classification and specificity differ substantially from AIS98, and the mapping tools provided in the AIS08 dictionary are incomplete. As a result, data from different AIS versions cannot currently be compared. The aim of this study was to develop an additional AIS98 to AIS08 mapping tool to complement the current AIS dictionary map, and then to evaluate the completed map (produced by combining these two maps) using double-coded data. The value of additional information provided by free text descriptions accompanying assigned codes was also assessed. Methods Using a modified Delphi process, a panel of expert AIS coders established plausible AIS08 equivalents for the 153 AIS98 codes which currently have no AIS08 map. A series of major trauma patients whose injuries had been double-coded in AIS98 and AIS08 was used to assess the maps; both of the AIS datasets had already been mapped to another AIS version using the AIS dictionary maps. Following application of the completed (enhanced) map with or without free text evaluation, up to six AIS codes were available for each injury. Datasets were assessed for agreement in injury severity measures, and the relative performances of the maps in accurately describing the trauma population were evaluated. Results The double-coded injuries sustained by 109 patients were used to assess the maps. For data conversion from AIS98, both the enhanced map and the enhanced map with free text description resulted in higher levels of accuracy and agreement with directly coded AIS08 data than the currently available dictionary map. Paired comparisons demonstrated significant differences between direct coding and the dictionary maps, but not with either of the enhanced maps. Conclusions The newly-developed AIS98 to AIS08 complementary map enabled transformation of the trauma population description given by AIS98 into an AIS08 estimate which was statistically indistinguishable from directly coded AIS08 data. It is recommended that the enhanced map should be adopted for dataset conversion, using free text descriptions if available. PMID:21548991

Development and validation of a complementary map to enhance the existing 1998 to 2008 Abbreviated Injury Scale map.

PubMed

Palmer, Cameron S; Franklyn, Melanie; Read-Allsopp, Christine; McLellan, Susan; Niggemeyer, Louise E

2011-05-08

Many trauma registries have used the Abbreviated Injury Scale 1990 Revision Update 98 (AIS98) to classify injuries. In the current AIS version (Abbreviated Injury Scale 2005 Update 2008 - AIS08), injury classification and specificity differ substantially from AIS98, and the mapping tools provided in the AIS08 dictionary are incomplete. As a result, data from different AIS versions cannot currently be compared. The aim of this study was to develop an additional AIS98 to AIS08 mapping tool to complement the current AIS dictionary map, and then to evaluate the completed map (produced by combining these two maps) using double-coded data. The value of additional information provided by free text descriptions accompanying assigned codes was also assessed. Using a modified Delphi process, a panel of expert AIS coders established plausible AIS08 equivalents for the 153 AIS98 codes which currently have no AIS08 map. A series of major trauma patients whose injuries had been double-coded in AIS98 and AIS08 was used to assess the maps; both of the AIS datasets had already been mapped to another AIS version using the AIS dictionary maps. Following application of the completed (enhanced) map with or without free text evaluation, up to six AIS codes were available for each injury. Datasets were assessed for agreement in injury severity measures, and the relative performances of the maps in accurately describing the trauma population were evaluated. The double-coded injuries sustained by 109 patients were used to assess the maps. For data conversion from AIS98, both the enhanced map and the enhanced map with free text description resulted in higher levels of accuracy and agreement with directly coded AIS08 data than the currently available dictionary map. Paired comparisons demonstrated significant differences between direct coding and the dictionary maps, but not with either of the enhanced maps. The newly-developed AIS98 to AIS08 complementary map enabled transformation of the trauma population description given by AIS98 into an AIS08 estimate which was statistically indistinguishable from directly coded AIS08 data. It is recommended that the enhanced map should be adopted for dataset conversion, using free text descriptions if available.

Generation of Plausible Hurricane Tracks for Preparedness Exercises

DTIC Science & Technology

2017-04-25

wind extents are simulated by Poisson regression and temporal filtering . The un-optimized MATLAB code runs in less than a minute and is integrated into...of real hurricanes. After wind radii have been simulated for the entire track, median filtering , attenuation over land, and smoothing clean up the wind

The Coding Question.

PubMed

Gallistel, C R

2017-07-01

Recent electrophysiological results imply that the duration of the stimulus onset asynchrony in eyeblink conditioning is encoded by a mechanism intrinsic to the cerebellar Purkinje cell. This raises the general question - how is quantitative information (durations, distances, rates, probabilities, amounts, etc.) transmitted by spike trains and encoded into engrams? The usual assumption is that information is transmitted by firing rates. However, rate codes are energetically inefficient and computationally awkward. A combinatorial code is more plausible. If the engram consists of altered synaptic conductances (the usual assumption), then we must ask how numbers may be written to synapses. It is much easier to formulate a coding hypothesis if the engram is realized by a cell-intrinsic molecular mechanism. Copyright © 2017 Elsevier Ltd. All rights reserved.

Metastable neural dynamics mediates expectation

NASA Astrophysics Data System (ADS)

Mazzucato, Luca; La Camera, Giancarlo; Fontanini, Alfredo

Sensory stimuli are processed faster when their presentation is expected compared to when they come as a surprise. We previously showed that, in multiple single-unit recordings from alert rat gustatory cortex, taste stimuli can be decoded faster from neural activity if preceded by a stimulus-predicting cue. However, the specific computational process mediating this anticipatory neural activity is unknown. Here, we propose a biologically plausible model based on a recurrent network of spiking neurons with clustered architecture. In the absence of stimulation, the model neural activity unfolds through sequences of metastable states, each state being a population vector of firing rates. We modeled taste stimuli and cue (the same for all stimuli) as two inputs targeting subsets of excitatory neurons. As observed in experiment, stimuli evoked specific state sequences, characterized in terms of `coding states', i.e., states occurring significantly more often for a particular stimulus. When stimulus presentation is preceded by a cue, coding states show a faster and more reliable onset, and expected stimuli can be decoded more quickly than unexpected ones. This anticipatory effect is unrelated to changes of firing rates in stimulus-selective neurons and is absent in homogeneous balanced networks, suggesting that a clustered organization is necessary to mediate the expectation of relevant events. Our results demonstrate a novel mechanism for speeding up sensory coding in cortical circuits. NIDCD K25-DC013557 (LM); NIDCD R01-DC010389 (AF); NSF IIS-1161852 (GL).

Stimulated Mirror Instability From the Interplay of Anisotropic Protons and Electrons, and their Suprathermal Populations

NASA Astrophysics Data System (ADS)

Shaaban, S. M.; Lazar, M.; Astfalk, P.; Poedts, S.

2018-03-01

Mirror instability driven by the temperature anisotropy of protons can offer a plausible explanation for the mirror-like fluctuations observed in planetary magnetosheaths. In the present paper we invoke a realistic kinetic approach which can reproduce nonthermal features of plasma particles reported by the observations, i.e., temperature anisotropies and suprathermal populations. Seeking accuracy, a numerical analysis is performed using an advanced code named DSHARK, recently proposed to resolve the linear dispersion and stability for an arbitrary propagation in bi-Kappa distributed electron-proton plasmas. The stimulating effect of the anisotropic bi-Maxwellian electrons reported in Remya et al. (2013, https://doi.org/10.1002/jgra.50091) is markedly enhanced in the presence of suprathermal electrons described by the bi-Kappa distribution functions. The influence of suprathermal protons is more temperate, but overall, present results demonstrate that these sources of free energy provide natural conditions for a stimulated mirror instability, more efficient than predicted before and capable to compete with other instabilities (e.g., the electromagnetic ion-cyclotron instability) and mechanisms of relaxation.

Spatial Learning and Action Planning in a Prefrontal Cortical Network Model

PubMed Central

Martinet, Louis-Emmanuel; Sheynikhovich, Denis; Benchenane, Karim; Arleo, Angelo

2011-01-01

The interplay between hippocampus and prefrontal cortex (PFC) is fundamental to spatial cognition. Complementing hippocampal place coding, prefrontal representations provide more abstract and hierarchically organized memories suitable for decision making. We model a prefrontal network mediating distributed information processing for spatial learning and action planning. Specific connectivity and synaptic adaptation principles shape the recurrent dynamics of the network arranged in cortical minicolumns. We show how the PFC columnar organization is suitable for learning sparse topological-metrical representations from redundant hippocampal inputs. The recurrent nature of the network supports multilevel spatial processing, allowing structural features of the environment to be encoded. An activation diffusion mechanism spreads the neural activity through the column population leading to trajectory planning. The model provides a functional framework for interpreting the activity of PFC neurons recorded during navigation tasks. We illustrate the link from single unit activity to behavioral responses. The results suggest plausible neural mechanisms subserving the cognitive “insight” capability originally attributed to rodents by Tolman & Honzik. Our time course analysis of neural responses shows how the interaction between hippocampus and PFC can yield the encoding of manifold information pertinent to spatial planning, including prospective coding and distance-to-goal correlates. PMID:21625569

Numerical algorithm comparison for the accurate and efficient computation of high-incidence vortical flow

NASA Technical Reports Server (NTRS)

Chaderjian, Neal M.

1991-01-01

Computations from two Navier-Stokes codes, NSS and F3D, are presented for a tangent-ogive-cylinder body at high angle of attack. Features of this steady flow include a pair of primary vortices on the leeward side of the body as well as secondary vortices. The topological and physical plausibility of this vortical structure is discussed. The accuracy of these codes are assessed by comparison of the numerical solutions with experimental data. The effects of turbulence model, numerical dissipation, and grid refinement are presented. The overall efficiency of these codes are also assessed by examining their convergence rates, computational time per time step, and maximum allowable time step for time-accurate computations. Overall, the numerical results from both codes compared equally well with experimental data, however, the NSS code was found to be significantly more efficient than the F3D code.

What the success of brain imaging implies about the neural code.

PubMed

Guest, Olivia; Love, Bradley C

2017-01-19

The success of fMRI places constraints on the nature of the neural code. The fact that researchers can infer similarities between neural representations, despite fMRI's limitations, implies that certain neural coding schemes are more likely than others. For fMRI to succeed given its low temporal and spatial resolution, the neural code must be smooth at the voxel and functional level such that similar stimuli engender similar internal representations. Through proof and simulation, we determine which coding schemes are plausible given both fMRI's successes and its limitations in measuring neural activity. Deep neural network approaches, which have been forwarded as computational accounts of the ventral stream, are consistent with the success of fMRI, though functional smoothness breaks down in the later network layers. These results have implications for the nature of the neural code and ventral stream, as well as what can be successfully investigated with fMRI.

First Identification of Foreshock Plasma Populations at Mercury

NASA Astrophysics Data System (ADS)

Glass, A. N.; Tracy, P. J.; Raines, J. M.

2018-05-01

Observations of foreshock populations at Mercury are presented for the first time utilizing measurements from the Fast Imaging Plasma Spectrometer (FIPS) aboard MESSENGER, and plausible energization mechanisms are suggested and evaluated.

Understanding asteroid collisional history through experimental and numerical studies

NASA Technical Reports Server (NTRS)

Davis, Donald R.; Ryan, Eileen V.; Weidenschilling, S. J.

1991-01-01

Asteroids can lose angular momentum due to so called splash effect, the analog to the drain effect for cratering impacts. Numerical code with the splash effect incorporated was applied to study the simultaneous evolution of asteroid sized and spins. Results are presented on the spin changes of asteroids due to various physical effects that are incorporated in the described model. The goal was to understand the interplay between the evolution of sizes and spins over a wide and plausible range of model parameters. A single starting population was used both for size distribution and the spin distribution of asteroids and the changes in the spins were calculated over solar system history for different model parameters. It is shown that there is a strong coupling between the size and spin evolution, that the observed relative spindown of asteroids approximately 100 km diameter is likely to be the result of the angular momentum splash effect.

Understanding asteroid collisional history through experimental and numerical studies

NASA Astrophysics Data System (ADS)

Davis, Donald R.; Ryan, Eileen V.; Weidenschilling, S. J.

1991-06-01

Asteroids can lose angular momentum due to so called splash effect, the analog to the drain effect for cratering impacts. Numerical code with the splash effect incorporated was applied to study the simultaneous evolution of asteroid sized and spins. Results are presented on the spin changes of asteroids due to various physical effects that are incorporated in the described model. The goal was to understand the interplay between the evolution of sizes and spins over a wide and plausible range of model parameters. A single starting population was used both for size distribution and the spin distribution of asteroids and the changes in the spins were calculated over solar system history for different model parameters. It is shown that there is a strong coupling between the size and spin evolution, that the observed relative spindown of asteroids approximately 100 km diameter is likely to be the result of the angular momentum splash effect.

Modular neuron-based body estimation: maintaining consistency over different limbs, modalities, and frames of reference

PubMed Central

Ehrenfeld, Stephan; Herbort, Oliver; Butz, Martin V.

2013-01-01

This paper addresses the question of how the brain maintains a probabilistic body state estimate over time from a modeling perspective. The neural Modular Modality Frame (nMMF) model simulates such a body state estimation process by continuously integrating redundant, multimodal body state information sources. The body state estimate itself is distributed over separate, but bidirectionally interacting modules. nMMF compares the incoming sensory and present body state information across the interacting modules and fuses the information sources accordingly. At the same time, nMMF enforces body state estimation consistency across the modules. nMMF is able to detect conflicting sensory information and to consequently decrease the influence of implausible sensor sources on the fly. In contrast to the previously published Modular Modality Frame (MMF) model, nMMF offers a biologically plausible neural implementation based on distributed, probabilistic population codes. Besides its neural plausibility, the neural encoding has the advantage of enabling (a) additional probabilistic information flow across the separate body state estimation modules and (b) the representation of arbitrary probability distributions of a body state. The results show that the neural estimates can detect and decrease the impact of false sensory information, can propagate conflicting information across modules, and can improve overall estimation accuracy due to additional module interactions. Even bodily illusions, such as the rubber hand illusion, can be simulated with nMMF. We conclude with an outlook on the potential of modeling human data and of invoking goal-directed behavioral control. PMID:24191151

Experimental QR code optical encryption: noise-free data recovering.

PubMed

Barrera, John Fredy; Mira-Agudelo, Alejandro; Torroba, Roberto

2014-05-15

We report, to our knowledge for the first time, the experimental implementation of a quick response (QR) code as a "container" in an optical encryption system. A joint transform correlator architecture in an interferometric configuration is chosen as the experimental scheme. As the implementation is not possible in a single step, a multiplexing procedure to encrypt the QR code of the original information is applied. Once the QR code is correctly decrypted, the speckle noise present in the recovered QR code is eliminated by a simple digital procedure. Finally, the original information is retrieved completely free of any kind of degradation after reading the QR code. Additionally, we propose and implement a new protocol in which the reception of the encrypted QR code and its decryption, the digital block processing, and the reading of the decrypted QR code are performed employing only one device (smartphone, tablet, or computer). The overall method probes to produce an outcome far more attractive to make the adoption of the technique a plausible option. Experimental results are presented to demonstrate the practicality of the proposed security system.

What the success of brain imaging implies about the neural code

PubMed Central

Guest, Olivia; Love, Bradley C

2017-01-01

The success of fMRI places constraints on the nature of the neural code. The fact that researchers can infer similarities between neural representations, despite fMRI’s limitations, implies that certain neural coding schemes are more likely than others. For fMRI to succeed given its low temporal and spatial resolution, the neural code must be smooth at the voxel and functional level such that similar stimuli engender similar internal representations. Through proof and simulation, we determine which coding schemes are plausible given both fMRI’s successes and its limitations in measuring neural activity. Deep neural network approaches, which have been forwarded as computational accounts of the ventral stream, are consistent with the success of fMRI, though functional smoothness breaks down in the later network layers. These results have implications for the nature of the neural code and ventral stream, as well as what can be successfully investigated with fMRI. DOI: http://dx.doi.org/10.7554/eLife.21397.001 PMID:28103186

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

Côté, Benoit; Belczynski, Krzysztof; Fryer, Chris L.

The role of compact binary mergers as the main production site of r-process elements is investigated by combining stellar abundances of Eu observed in the Milky Way, galactic chemical evolution (GCE) simulations, and binary population synthesis models, and gravitational wave measurements from Advanced LIGO. We compiled and reviewed seven recent GCE studies to extract the frequency of neutron star–neutron star (NS–NS) mergers that is needed in order to reproduce the observed [Eu/Fe] versus [Fe/H] relationship. We used our simple chemical evolution code to explore the impact of different analytical delay-time distribution functions for NS–NS mergers. We then combined our metallicity-dependent population synthesis models with our chemical evolution code to bring their predictions, for both NS–NS mergers and black hole–neutron star mergers, into a GCE context. Finally, we convolved our results with the cosmic star formation history to provide a direct comparison with current and upcoming Advanced LIGO measurements. When assuming that NS–NS mergers are the exclusive r-process sites, and that the ejected r-process mass per merger event is 0.01 Mmore » $${}_{\\odot }$$, the number of NS–NS mergers needed in GCE studies is about 10 times larger than what is predicted by standard population synthesis models. Here, these two distinct fields can only be consistent with each other when assuming optimistic rates, massive NS–NS merger ejecta, and low Fe yields for massive stars. For now, population synthesis models and GCE simulations are in agreement with the current upper limit (O1) established by Advanced LIGO during their first run of observations. Upcoming measurements will provide an important constraint on the actual local NS–NS merger rate, will provide valuable insights on the plausibility of the GCE requirement, and will help to define whether or not compact binary mergers can be the dominant source of r-process elements in the universe.« less

Advanced LIGO constraints on neutron star mergers and r-process sites

DOE PAGES

Côté, Benoit; Belczynski, Krzysztof; Fryer, Chris L.; ...

2017-02-20

The role of compact binary mergers as the main production site of r-process elements is investigated by combining stellar abundances of Eu observed in the Milky Way, galactic chemical evolution (GCE) simulations, and binary population synthesis models, and gravitational wave measurements from Advanced LIGO. We compiled and reviewed seven recent GCE studies to extract the frequency of neutron star–neutron star (NS–NS) mergers that is needed in order to reproduce the observed [Eu/Fe] versus [Fe/H] relationship. We used our simple chemical evolution code to explore the impact of different analytical delay-time distribution functions for NS–NS mergers. We then combined our metallicity-dependent population synthesis models with our chemical evolution code to bring their predictions, for both NS–NS mergers and black hole–neutron star mergers, into a GCE context. Finally, we convolved our results with the cosmic star formation history to provide a direct comparison with current and upcoming Advanced LIGO measurements. When assuming that NS–NS mergers are the exclusive r-process sites, and that the ejected r-process mass per merger event is 0.01 Mmore » $${}_{\\odot }$$, the number of NS–NS mergers needed in GCE studies is about 10 times larger than what is predicted by standard population synthesis models. Here, these two distinct fields can only be consistent with each other when assuming optimistic rates, massive NS–NS merger ejecta, and low Fe yields for massive stars. For now, population synthesis models and GCE simulations are in agreement with the current upper limit (O1) established by Advanced LIGO during their first run of observations. Upcoming measurements will provide an important constraint on the actual local NS–NS merger rate, will provide valuable insights on the plausibility of the GCE requirement, and will help to define whether or not compact binary mergers can be the dominant source of r-process elements in the universe.« less

Modeling development of natural multi-sensory integration using neural self-organisation and probabilistic population codes

NASA Astrophysics Data System (ADS)

Bauer, Johannes; Dávila-Chacón, Jorge; Wermter, Stefan

2015-10-01

Humans and other animals have been shown to perform near-optimally in multi-sensory integration tasks. Probabilistic population codes (PPCs) have been proposed as a mechanism by which optimal integration can be accomplished. Previous approaches have focussed on how neural networks might produce PPCs from sensory input or perform calculations using them, like combining multiple PPCs. Less attention has been given to the question of how the necessary organisation of neurons can arise and how the required knowledge about the input statistics can be learned. In this paper, we propose a model of learning multi-sensory integration based on an unsupervised learning algorithm in which an artificial neural network learns the noise characteristics of each of its sources of input. Our algorithm borrows from the self-organising map the ability to learn latent-variable models of the input and extends it to learning to produce a PPC approximating a probability density function over the latent variable behind its (noisy) input. The neurons in our network are only required to perform simple calculations and we make few assumptions about input noise properties and tuning functions. We report on a neurorobotic experiment in which we apply our algorithm to multi-sensory integration in a humanoid robot to demonstrate its effectiveness and compare it to human multi-sensory integration on the behavioural level. We also show in simulations that our algorithm performs near-optimally under certain plausible conditions, and that it reproduces important aspects of natural multi-sensory integration on the neural level.

Giant impactors - Plausible sizes and populations

NASA Technical Reports Server (NTRS)

Hartmann, William K.; Vail, S. M.

1986-01-01

The largest sizes of planetesimals required to explain spin properties of planets are investigated in the context of the impact-trigger hypothesis of lunar origin. Solar system models with different large impactor sources are constructed and stochastic variations in obliquities and rotation periods resulting from each source are studied. The present study finds it highly plausible that earth was struck by a body of about 0.03-0.12 earth masses with enough energy and angular momentum to dislodge mantle material and form the present earth-moon system.

PRANAS: A New Platform for Retinal Analysis and Simulation.

PubMed

Cessac, Bruno; Kornprobst, Pierre; Kraria, Selim; Nasser, Hassan; Pamplona, Daniela; Portelli, Geoffrey; Viéville, Thierry

2017-01-01

The retina encodes visual scenes by trains of action potentials that are sent to the brain via the optic nerve. In this paper, we describe a new free access user-end software allowing to better understand this coding. It is called PRANAS (https://pranas.inria.fr), standing for Platform for Retinal ANalysis And Simulation. PRANAS targets neuroscientists and modelers by providing a unique set of retina-related tools. PRANAS integrates a retina simulator allowing large scale simulations while keeping a strong biological plausibility and a toolbox for the analysis of spike train population statistics. The statistical method (entropy maximization under constraints) takes into account both spatial and temporal correlations as constraints, allowing to analyze the effects of memory on statistics. PRANAS also integrates a tool computing and representing in 3D (time-space) receptive fields. All these tools are accessible through a friendly graphical user interface. The most CPU-costly of them have been implemented to run in parallel.

Loci Contributing to Boric Acid Toxicity in Two Reference Populations of Drosophila melanogaster

PubMed Central

Najarro, Michael A.; Hackett, Jennifer L.; Macdonald, Stuart J.

2017-01-01

Populations maintain considerable segregating variation in the response to toxic, xenobiotic compounds. To identify variants associated with resistance to boric acid, a commonly-used household insecticide with a poorly understood mechanism of action, we assayed thousands of individuals from hundreds of strains. Using the Drosophila Synthetic Population Resource (DSPR), a multi-parental population (MPP) of inbred genotypes, we mapped six QTL to short genomic regions containing few protein-coding genes (3–188), allowing us to identify plausible candidate genes underlying resistance to boric acid toxicity. One interval contains multiple genes from the cytochrome P450 family, and we show that ubiquitous RNAi of one of these genes, Cyp9b2, markedly reduces resistance to the toxin. Resistance to boric acid is positively correlated with caffeine resistance. The two phenotypes additionally share a pair of QTL, potentially suggesting a degree of pleiotropy in the genetic control of resistance to these two distinct xenobiotics. Finally, we screened the Drosophila Genetic Reference Panel (DGRP) in an attempt to identify sequence variants within mapped QTL that are associated with boric acid resistance. The approach was largely unsuccessful, with only one QTL showing any associations at QTL-specific 20% False Discovery Rate (FDR) thresholds. Nonetheless, these associations point to a potential candidate gene that can be targeted in future validation efforts. Although the mapping data resulting from the two reference populations do not clearly overlap, our work provides a starting point for further genetic dissection of the processes underlying boric acid toxicity in insects. PMID:28592646

Loci Contributing to Boric Acid Toxicity in Two Reference Populations of Drosophila melanogaster.

PubMed

Najarro, Michael A; Hackett, Jennifer L; Macdonald, Stuart J

2017-06-07

Populations maintain considerable segregating variation in the response to toxic, xenobiotic compounds. To identify variants associated with resistance to boric acid, a commonly-used household insecticide with a poorly understood mechanism of action, we assayed thousands of individuals from hundreds of strains. Using the Drosophila Synthetic Population Resource (DSPR), a multi-parental population (MPP) of inbred genotypes, we mapped six QTL to short genomic regions containing few protein-coding genes (3-188), allowing us to identify plausible candidate genes underlying resistance to boric acid toxicity. One interval contains multiple genes from the cytochrome P450 family, and we show that ubiquitous RNAi of one of these genes, Cyp9b2 , markedly reduces resistance to the toxin. Resistance to boric acid is positively correlated with caffeine resistance. The two phenotypes additionally share a pair of QTL, potentially suggesting a degree of pleiotropy in the genetic control of resistance to these two distinct xenobiotics. Finally, we screened the Drosophila Genetic Reference Panel (DGRP) in an attempt to identify sequence variants within mapped QTL that are associated with boric acid resistance. The approach was largely unsuccessful, with only one QTL showing any associations at QTL-specific 20% False Discovery Rate (FDR) thresholds. Nonetheless, these associations point to a potential candidate gene that can be targeted in future validation efforts. Although the mapping data resulting from the two reference populations do not clearly overlap, our work provides a starting point for further genetic dissection of the processes underlying boric acid toxicity in insects. Copyright © 2017 Najarro et al.

Phylogeographic Differentiation of Mitochondrial DNA in Han Chinese

PubMed Central

Yao, Yong-Gang; Kong, Qing-Peng; Bandelt, Hans-Jürgen; Kivisild, Toomas; Zhang, Ya-Ping

2002-01-01

To characterize the mitochondrial DNA (mtDNA) variation in Han Chinese from several provinces of China, we have sequenced the two hypervariable segments of the control region and the segment spanning nucleotide positions 10171–10659 of the coding region, and we have identified a number of specific coding-region mutations by direct sequencing or restriction-fragment–length–polymorphism tests. This allows us to define new haplogroups (clades of the mtDNA phylogeny) and to dissect the Han mtDNA pool on a phylogenetic basis, which is a prerequisite for any fine-grained phylogeographic analysis, the interpretation of ancient mtDNA, or future complete mtDNA sequencing efforts. Some of the haplogroups under study differ considerably in frequencies across different provinces. The southernmost provinces show more pronounced contrasts in their regional Han mtDNA pools than the central and northern provinces. These and other features of the geographical distribution of the mtDNA haplogroups observed in the Han Chinese make an initial Paleolithic colonization from south to north plausible but would suggest subsequent migration events in China that mainly proceeded from north to south and east to west. Lumping together all regional Han mtDNA pools into one fictive general mtDNA pool or choosing one or two regional Han populations to represent all Han Chinese is inappropriate for prehistoric considerations as well as for forensic purposes or medical disease studies. PMID:11836649

The emergence of DNA in the RNA world: an in silico simulation study of genetic takeover.

PubMed

Ma, Wentao; Yu, Chunwu; Zhang, Wentao; Wu, Sanmao; Feng, Yu

2015-12-07

It is now popularly accepted that there was an "RNA world" in early evolution of life. This idea has a direct consequence that later on there should have been a takeover of genetic material - RNA by DNA. However, since genetic material carries genetic information, the "source code" of all living activities, it is actually reasonable to question the plausibility of such a "revolutionary" transition. Due to our inability to model relevant "primitive living systems" in reality, it is as yet impossible to explore the plausibility and mechanisms of the "genetic takeover" by experiments. Here we investigated this issue by computer simulation using a Monte-Carlo method. It shows that an RNA-by-DNA genetic takeover may be triggered by the emergence of a nucleotide reductase ribozyme with a moderate activity in a pure RNA system. The transition is unstable and limited in scale (i.e., cannot spread in the population), but can get strengthened and globalized if certain parameters are changed against RNA (i.e., in favor of DNA). In relation to the subsequent evolution, an advanced system with a larger genome, which uses DNA as genetic material and RNA as functional material, is modeled - the system cannot sustain if the nucleotide reductase ribozyme is "turned off" (thus, DNA cannot be synthesized). Moreover, the advanced system cannot sustain if only DNA's stability, template suitability or replication fidelity (any of the three) is turned down to the level of RNA's. Genetic takeover should be plausible. In the RNA world, such a takeover may have been triggered by the emergence of some ribozyme favoring the formation of deoxynucleotides. The transition may initially have been "weak", but could have been reinforced by environmental changes unfavorable to RNA (such as temperature or pH rise), and would have ultimately become irreversible accompanying the genome's enlargement. Several virtues of DNA (versus RNA) - higher stability against hydrolysis, greater suitability as template and higher fidelity in replication, should have, each in its own way, all been significant for the genetic takeover in evolution. This study enhances our understandings of the relationship between information and material in the living world.

Spike train generation and current-to-frequency conversion in silicon diodes

NASA Technical Reports Server (NTRS)

Coon, D. D.; Perera, A. G. U.

1989-01-01

A device physics model is developed to analyze spontaneous neuron-like spike train generation in current driven silicon p(+)-n-n(+) devices in cryogenic environments. The model is shown to explain the very high dynamic range (0 to the 7th) current-to-frequency conversion and experimental features of the spike train frequency as a function of input current. The devices are interesting components for implementation of parallel asynchronous processing adjacent to cryogenically cooled focal planes because of their extremely low current and power requirements, their electronic simplicity, and their pulse coding capability, and could be used to form the hardware basis for neural networks which employ biologically plausible means of information coding.

A Method to Estimate the Size and Characteristics of HIV-positive Populations Using an Individual-based Stochastic Simulation Model.

PubMed

Nakagawa, Fumiyo; van Sighem, Ard; Thiebaut, Rodolphe; Smith, Colette; Ratmann, Oliver; Cambiano, Valentina; Albert, Jan; Amato-Gauci, Andrew; Bezemer, Daniela; Campbell, Colin; Commenges, Daniel; Donoghoe, Martin; Ford, Deborah; Kouyos, Roger; Lodwick, Rebecca; Lundgren, Jens; Pantazis, Nikos; Pharris, Anastasia; Quinten, Chantal; Thorne, Claire; Touloumi, Giota; Delpech, Valerie; Phillips, Andrew

2016-03-01

It is important not only to collect epidemiologic data on HIV but to also fully utilize such information to understand the epidemic over time and to help inform and monitor the impact of policies and interventions. We describe and apply a novel method to estimate the size and characteristics of HIV-positive populations. The method was applied to data on men who have sex with men living in the UK and to a pseudo dataset to assess performance for different data availability. The individual-based simulation model was calibrated using an approximate Bayesian computation-based approach. In 2013, 48,310 (90% plausibility range: 39,900-45,560) men who have sex with men were estimated to be living with HIV in the UK, of whom 10,400 (6,160-17,350) were undiagnosed. There were an estimated 3,210 (1,730-5,350) infections per year on average between 2010 and 2013. Sixty-two percent of the total HIV-positive population are thought to have viral load <500 copies/ml. In the pseudo-epidemic example, HIV estimates have narrower plausibility ranges and are closer to the true number, the greater the data availability to calibrate the model. We demonstrate that our method can be applied to settings with less data, however plausibility ranges for estimates will be wider to reflect greater uncertainty of the data used to fit the model.

An engineer's view on genetic information and biological evolution.

PubMed

Battail, Gérard

2004-01-01

We develop ideas on genome replication introduced in Battail [Europhys. Lett. 40 (1997) 343]. Starting with the hypothesis that the genome replication process uses error-correcting means, and the auxiliary one that nested codes are used to this end, we first review the concepts of redundancy and error-correcting codes. Then we show that these hypotheses imply that: distinct species exist with a hierarchical taxonomy, there is a trend of evolution towards complexity, and evolution proceeds by discrete jumps. At least the first two features above may be considered as biological facts so, in the absence of direct evidence, they provide an indirect proof in favour of the hypothesized error-correction system. The very high redundancy of genomes makes it possible. In order to explain how it is implemented, we suggest that soft codes and replication decoding, to be briefly described, are plausible candidates. Experimentally proven properties of long-range correlation of the DNA message substantiate this claim.

Validation of a Case Definition for Pediatric Brain Injury Using Administrative Data.

PubMed

McChesney-Corbeil, Jane; Barlow, Karen; Quan, Hude; Chen, Guanmin; Wiebe, Samuel; Jette, Nathalie

2017-03-01

Health administrative data are a common population-based data source for traumatic brain injury (TBI) surveillance and research; however, before using these data for surveillance, it is important to develop a validated case definition. The objective of this study was to identify the optimal International Classification of Disease , edition 10 (ICD-10), case definition to ascertain children with TBI in emergency room (ER) or hospital administrative data. We tested multiple case definitions. Children who visited the ER were identified from the Regional Emergency Department Information System at Alberta Children's Hospital. Secondary data were collected for children with trauma, musculoskeletal, or central nervous system complaints who visited the ER between October 5, 2005, and June 6, 2007. TBI status was determined based on chart review. Sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were calculated for each case definition. Of 6639 patients, 1343 had a TBI. The best case definition was, "1 hospital or 1 ER encounter coded with an ICD-10 code for TBI in 1 year" (sensitivity 69.8% [95% confidence interval (CI), 67.3-72.2], specificity 96.7% [95% CI, 96.2-97.2], PPV 84.2% [95% CI 82.0-86.3], NPV 92.7% [95% CI, 92.0-93.3]). The nonspecific code S09.9 identified >80% of TBI cases in our study. The optimal ICD-10-based case definition for pediatric TBI in this study is valid and should be considered for future pediatric TBI surveillance studies. However, external validation is recommended before use in other jurisdictions, particularly because it is plausible that a larger proportion of patients in our cohort had milder injuries.

A ROTATIONALLY POWERED MAGNETAR NEBULA AROUND SWIFT J1834.9–0846

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

Torres, Diego F.

A wind nebula generating extended X-ray emission was recently detected surrounding Swift J1834.9–0846. This is the first magnetar for which such a wind nebula was found. Here, we investigate whether there is a plausible scenario where the pulsar wind nebula (PWN) can be sustained without the need of advocating for additional sources of energy other than rotational. We do this by using a detailed radiative and dynamical code that studies the evolution of the nebula and its particle population in time. We find that such a scenario indeed exists: Swift J1834.9–0846's nebula can be explained as being rotationally powered, asmore » all other known PWNe are, if it is currently being compressed by the environment. The latter introduces several effects, the most important of which is the appearance of adiabatic heating, being increasingly dominant over the escape of particles as reverberation goes by. The need of reverberation naturally explains why this is the only magnetar nebula detected and provides estimates for Swift 1834.9–0846's age.« less

The modular modality frame model: continuous body state estimation and plausibility-weighted information fusion.

PubMed

Ehrenfeld, Stephan; Butz, Martin V

2013-02-01

Humans show admirable capabilities in movement planning and execution. They can perform complex tasks in various contexts, using the available sensory information very effectively. Body models and continuous body state estimations appear necessary to realize such capabilities. We introduce the Modular Modality Frame (MMF) model, which maintains a highly distributed, modularized body model continuously updating, modularized probabilistic body state estimations over time. Modularization is realized with respect to modality frames, that is, sensory modalities in particular frames of reference and with respect to particular body parts. We evaluate MMF performance on a simulated, nine degree of freedom arm in 3D space. The results show that MMF is able to maintain accurate body state estimations despite high sensor and motor noise. Moreover, by comparing the sensory information available in different modality frames, MMF can identify faulty sensory measurements on the fly. In the near future, applications to lightweight robot control should be pursued. Moreover, MMF may be enhanced with neural encodings by introducing neural population codes and learning techniques. Finally, more dexterous goal-directed behavior should be realized by exploiting the available redundant state representations.

Four Frames Suffice. A Provisionary Model of Vision and Space,

DTIC Science & Technology

1982-09-01

0 * / Justifi ati AvailabilitY Codes 1. Introduction This paper is an attempt to specify’ a computationally and scientifically plausible model of how...abstract neural compuiting unit and a variety of construtions built of these units and their properties. All of this is part of the connectionist...chosen are inlerided to elucidate the nia’or scientific problems in intermediate level vision and would not be the best choice or a practical computer

Stimulants and sudden death: what is a physician to do?

PubMed

Wilens, Timothy E; Prince, Jefferson B; Spencer, Thomas J; Biederman, Joseph

2006-09-01

Recently, a US Food and Drug Administration advisory committee raised concerns about cardiovascular risks and sudden death in children and adolescents with attention-deficit/hyperactivity disorder who are receiving stimulants. We comment on the risk of sudden death in children/adolescents taking stimulants compared with population rates, biological plausibility, and known cardiovascular effects of stimulants to determine specific risk. There does not seem to be higher risk of sudden death in stimulant-treated individuals compared with the general population. Although there is evidence of biological plausibility, the known effects of the stimulants on cardiovascular electrophysiology and vital signs seem to be benign. There does not seem to be compelling findings of a medication-specific risk necessitating changes in our stimulant treatment of children and adolescents with attention-deficit/hyperactivity disorder. The use of existing guidelines on the use of stimulants (and psychotropic agents) may identify children, adolescents, and adults who are vulnerable to sudden death.

The primitive code and repeats of base oligomers as the primordial protein-encoding sequence.

PubMed Central

Ohno, S; Epplen, J T

1983-01-01

Even if the prebiotic self-replication of nucleic acids and the subsequent emergence of primitive, enzyme-independent tRNAs are accepted as plausible, the origin of life by spontaneous generation still appears improbable. This is because the just-emerged primitive translational machinery had to cope with base sequences that were not preselected for their coding potentials. Particularly if the primitive mitochondria-like code with four chain-terminating base triplets preceded the universal code, the translation of long, randomly generated, base sequences at this critical stage would have merely resulted in the production of short oligopeptides instead of long polypeptide chains. We present the base sequence of a mouse transcript containing tetranucleotide repeats conserved during evolution. Even if translated in accordance with the primitive mitochondria-like code, this transcript in its three reading frames can yield 245-, 246-, and 251-residue-long tetrapeptidic periodical polypeptides that are already acquiring longer periodicities. We contend that the first set of base sequences translated at the beginning of life were such oligonucleotide repeats. By quickly acquiring longer periodicities, their products must have soon gained characteristic secondary structures--alpha-helical or beta-sheet or both. PMID:6574491

Evaluating and improving count-based population inference: A case study from 31 years of monitoring Sandhill Cranes

USGS Publications Warehouse

Gerber, Brian D.; Kendall, William L.

2017-01-01

Monitoring animal populations can be difficult. Limited resources often force monitoring programs to rely on unadjusted or smoothed counts as an index of abundance. Smoothing counts is commonly done using a moving-average estimator to dampen sampling variation. These indices are commonly used to inform management decisions, although their reliability is often unknown. We outline a process to evaluate the biological plausibility of annual changes in population counts and indices from a typical monitoring scenario and compare results with a hierarchical Bayesian time series (HBTS) model. We evaluated spring and fall counts, fall indices, and model-based predictions for the Rocky Mountain population (RMP) of Sandhill Cranes (Antigone canadensis) by integrating juvenile recruitment, harvest, and survival into a stochastic stage-based population model. We used simulation to evaluate population indices from the HBTS model and the commonly used 3-yr moving average estimator. We found counts of the RMP to exhibit biologically unrealistic annual change, while the fall population index was largely biologically realistic. HBTS model predictions suggested that the RMP changed little over 31 yr of monitoring, but the pattern depended on assumptions about the observational process. The HBTS model fall population predictions were biologically plausible if observed crane harvest mortality was compensatory up to natural mortality, as empirical evidence suggests. Simulations indicated that the predicted mean of the HBTS model was generally a more reliable estimate of the true population than population indices derived using a moving 3-yr average estimator. Practitioners could gain considerable advantages from modeling population counts using a hierarchical Bayesian autoregressive approach. Advantages would include: (1) obtaining measures of uncertainty; (2) incorporating direct knowledge of the observational and population processes; (3) accommodating missing years of data; and (4) forecasting population size.

Cognitive components of picture naming.

PubMed

Johnson, C J; Paivio, A; Clark, J M

1996-07-01

A substantial research literature documents the effects of diverse item attributes, task conditions, and participant characteristics on the case of picture naming. The authors review what the research has revealed about 3 generally accepted stages of naming a pictured object: object identification, name activation, and response generation. They also show that dual coding theory gives a coherent and plausible account of these findings without positing amodal conceptual representations, and they identify issues and methods that may further advance the understanding of picture naming and related cognitive tasks.

[Retrospective analysis of Mexican National Addictions Survey, 2008. Bias identification and correction].

PubMed

Romero-Martínez, Martín; Téllez-Rojo Solís, Martha María; Sandoval-Zárate, América Andrea; Zurita-Luna, Juan Manuel; Gutiérrez-Reyes, Juan Pablo

2013-01-01

To determine the presence of bias on the estimation of the consumption sometime in life of alcohol, tobacco or illegal drugs and inhalable substances, and to propose a correction for this in the case it is present. Mexican National Addictions Surveys (NAS) 2002, 2008, and 2011 were analyzed to compare population estimations of consumption sometime in life of tobacco, alcohol or illegal drugs and inhalable substances. A couple of alternative approaches for bias correction were developed. Estimated national prevalences of consumption sometime in life of alcohol and tobacco in the NAS 2008 are not plausible. There was no evidence of bias on the consumption sometime in life of illegal drugs and inhalable substances. New estimations for tobacco and alcohol consumption sometime in life were made, which resulted in plausible values when compared to other data available. Future analyses regarding tobacco and alcohol using NAS 2008 data will have to rely on these newly generated data weights, that are able to reproduce the new (plausible) estimations.

DA white dwarfs from the LSS-GAC survey DR1: the preliminary luminosity and mass functions and formation rate

NASA Astrophysics Data System (ADS)

Rebassa-Mansergas, A.; Liu, X.-W.; Cojocaru, R.; Yuan, H.-B.; Torres, S.; García-Berro, E.; Xiang, M.-X.; Huang, Y.; Koester, D.; Hou, Y.; Li, G.; Zhang, Y.

2015-06-01

Modern large-scale surveys have allowed the identification of large numbers of white dwarfs. However, these surveys are subject to complicated target selection algorithms, which make it almost impossible to quantify to what extent the observational biases affect the observed populations. The LAMOST (Large Sky Area Multi-Object Fiber Spectroscopic Telescope) Spectroscopic Survey of the Galactic anticentre (LSS-GAC) follows a well-defined set of criteria for selecting targets for observations. This advantage over previous surveys has been fully exploited here to identify a small yet well-characterized magnitude-limited sample of hydrogen-rich (DA) white dwarfs. We derive preliminary LSS-GAC DA white dwarf luminosity and mass functions. The space density and average formation rate of DA white dwarfs we derive are 0.83 ± 0.16 × 10-3 pc-3 and 5.42 ± 0.08 × 10-13 pc-3 yr-1, respectively. Additionally, using an existing Monte Carlo population synthesis code we simulate the population of single DA white dwarfs in the Galactic anticentre, under various assumptions. The synthetic populations are passed through the LSS-GAC selection criteria, taking into account all possible observational biases. This allows us to perform a meaningful comparison of the observed and simulated distributions. We find that the LSS-GAC set of criteria is highly efficient in selecting white dwarfs for spectroscopic observations (80-85 per cent) and that, overall, our simulations reproduce well the observed luminosity function. However, they fail at reproducing an excess of massive white dwarfs present in the observed mass function. A plausible explanation for this is that a sizable fraction of massive white dwarfs in the Galaxy are the product of white dwarf-white dwarf mergers.

An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder.

PubMed

Werling, Donna M; Brand, Harrison; An, Joon-Yong; Stone, Matthew R; Zhu, Lingxue; Glessner, Joseph T; Collins, Ryan L; Dong, Shan; Layer, Ryan M; Markenscoff-Papadimitriou, Eirene; Farrell, Andrew; Schwartz, Grace B; Wang, Harold Z; Currall, Benjamin B; Zhao, Xuefang; Dea, Jeanselle; Duhn, Clif; Erdman, Carolyn A; Gilson, Michael C; Yadav, Rachita; Handsaker, Robert E; Kashin, Seva; Klei, Lambertus; Mandell, Jeffrey D; Nowakowski, Tomasz J; Liu, Yuwen; Pochareddy, Sirisha; Smith, Louw; Walker, Michael F; Waterman, Matthew J; He, Xin; Kriegstein, Arnold R; Rubenstein, John L; Sestan, Nenad; McCarroll, Steven A; Neale, Benjamin M; Coon, Hilary; Willsey, A Jeremy; Buxbaum, Joseph D; Daly, Mark J; State, Matthew W; Quinlan, Aaron R; Marth, Gabor T; Roeder, Kathryn; Devlin, Bernie; Talkowski, Michael E; Sanders, Stephan J

2018-05-01

Genomic association studies of common or rare protein-coding variation have established robust statistical approaches to account for multiple testing. Here we present a comparable framework to evaluate rare and de novo noncoding single-nucleotide variants, insertion/deletions, and all classes of structural variation from whole-genome sequencing (WGS). Integrating genomic annotations at the level of nucleotides, genes, and regulatory regions, we define 51,801 annotation categories. Analyses of 519 autism spectrum disorder families did not identify association with any categories after correction for 4,123 effective tests. Without appropriate correction, biologically plausible associations are observed in both cases and controls. Despite excluding previously identified gene-disrupting mutations, coding regions still exhibited the strongest associations. Thus, in autism, the contribution of de novo noncoding variation is probably modest in comparison to that of de novo coding variants. Robust results from future WGS studies will require large cohorts and comprehensive analytical strategies that consider the substantial multiple-testing burden.

Revisiting the operational RNA code for amino acids: Ensemble attributes and their implications.

PubMed

Shaul, Shaul; Berel, Dror; Benjamini, Yoav; Graur, Dan

2010-01-01

It has been suggested that tRNA acceptor stems specify an operational RNA code for amino acids. In the last 20 years several attributes of the putative code have been elucidated for a small number of model organisms. To gain insight about the ensemble attributes of the code, we analyzed 4925 tRNA sequences from 102 bacterial and 21 archaeal species. Here, we used a classification and regression tree (CART) methodology, and we found that the degrees of degeneracy or specificity of the RNA codes in both Archaea and Bacteria differ from those of the genetic code. We found instances of taxon-specific alternative codes, i.e., identical acceptor stem determinants encrypting different amino acids in different species, as well as instances of ambiguity, i.e., identical acceptor stem determinants encrypting two or more amino acids in the same species. When partitioning the data by class of synthetase, the degree of code ambiguity was significantly reduced. In cryptographic terms, a plausible interpretation of this result is that the class distinction in synthetases is an essential part of the decryption rules for resolving the subset of RNA code ambiguities enciphered by identical acceptor stem determinants of tRNAs acylated by enzymes belonging to the two classes. In evolutionary terms, our findings lend support to the notion that in the pre-DNA world, interactions between tRNA acceptor stems and synthetases formed the basis for the distinction between the two classes; hence, ambiguities in the ancient RNA code were pivotal for the fixation of these enzymes in the genomes of ancestral prokaryotes.

Revisiting the operational RNA code for amino acids: Ensemble attributes and their implications

PubMed Central

Shaul, Shaul; Berel, Dror; Benjamini, Yoav; Graur, Dan

2010-01-01

It has been suggested that tRNA acceptor stems specify an operational RNA code for amino acids. In the last 20 years several attributes of the putative code have been elucidated for a small number of model organisms. To gain insight about the ensemble attributes of the code, we analyzed 4925 tRNA sequences from 102 bacterial and 21 archaeal species. Here, we used a classification and regression tree (CART) methodology, and we found that the degrees of degeneracy or specificity of the RNA codes in both Archaea and Bacteria differ from those of the genetic code. We found instances of taxon-specific alternative codes, i.e., identical acceptor stem determinants encrypting different amino acids in different species, as well as instances of ambiguity, i.e., identical acceptor stem determinants encrypting two or more amino acids in the same species. When partitioning the data by class of synthetase, the degree of code ambiguity was significantly reduced. In cryptographic terms, a plausible interpretation of this result is that the class distinction in synthetases is an essential part of the decryption rules for resolving the subset of RNA code ambiguities enciphered by identical acceptor stem determinants of tRNAs acylated by enzymes belonging to the two classes. In evolutionary terms, our findings lend support to the notion that in the pre-DNA world, interactions between tRNA acceptor stems and synthetases formed the basis for the distinction between the two classes; hence, ambiguities in the ancient RNA code were pivotal for the fixation of these enzymes in the genomes of ancestral prokaryotes. PMID:19952117

An algebraic hypothesis about the primeval genetic code architecture.

PubMed

Sánchez, Robersy; Grau, Ricardo

2009-09-01

A plausible architecture of an ancient genetic code is derived from an extended base triplet vector space over the Galois field of the extended base alphabet {D,A,C,G,U}, where symbol D represents one or more hypothetical bases with unspecific pairings. We hypothesized that the high degeneration of a primeval genetic code with five bases and the gradual origin and improvement of a primeval DNA repair system could make possible the transition from ancient to modern genetic codes. Our results suggest that the Watson-Crick base pairing G identical with C and A=U and the non-specific base pairing of the hypothetical ancestral base D used to define the sum and product operations are enough features to determine the coding constraints of the primeval and the modern genetic code, as well as, the transition from the former to the latter. Geometrical and algebraic properties of this vector space reveal that the present codon assignment of the standard genetic code could be induced from a primeval codon assignment. Besides, the Fourier spectrum of the extended DNA genome sequences derived from the multiple sequence alignment suggests that the called period-3 property of the present coding DNA sequences could also exist in the ancient coding DNA sequences. The phylogenetic analyses achieved with metrics defined in the N-dimensional vector space (B(3))(N) of DNA sequences and with the new evolutionary model presented here also suggest that an ancient DNA coding sequence with five or more bases does not contradict the expected evolutionary history.

Theta-Gamma Coding Meets Communication-through-Coherence: Neuronal Oscillatory Multiplexing Theories Reconciled.

PubMed

McLelland, Douglas; VanRullen, Rufin

2016-10-01

Several theories have been advanced to explain how cross-frequency coupling, the interaction of neuronal oscillations at different frequencies, could enable item multiplexing in neural systems. The communication-through-coherence theory proposes that phase-matching of gamma oscillations between areas enables selective processing of a single item at a time, and a later refinement of the theory includes a theta-frequency oscillation that provides a periodic reset of the system. Alternatively, the theta-gamma neural code theory proposes that a sequence of items is processed, one per gamma cycle, and that this sequence is repeated or updated across theta cycles. In short, both theories serve to segregate representations via the temporal domain, but differ on the number of objects concurrently represented. In this study, we set out to test whether each of these theories is actually physiologically plausible, by implementing them within a single model inspired by physiological data. Using a spiking network model of visual processing, we show that each of these theories is physiologically plausible and computationally useful. Both theories were implemented within a single network architecture, with two areas connected in a feedforward manner, and gamma oscillations generated by feedback inhibition within areas. Simply increasing the amplitude of global inhibition in the lower area, equivalent to an increase in the spatial scope of the gamma oscillation, yielded a switch from one mode to the other. Thus, these different processing modes may co-exist in the brain, enabling dynamic switching between exploratory and selective modes of attention.

Is the population of Crotalus durissus (Serpentes, Viperidae) expanding in Brazil?

PubMed Central

2013-01-01

Crotalus durissus are found from Mexico to northern Argentina in a highly disjunct distribution. According to some studies, this species is prone to occupy areas disturbed by human activities and floods comprise a plausible method of dispersal as inferred for some North American rattlesnakes. Based on the literature, it seems plausible that Crotalus durissus expanded their natural distribution in Brazil due to floods, but only in a few municipalities in Rio de Janeiro State. Data entries of Butantan Institute, in São Paulo, Brazil, from 1998 to 2012 show a declining tendency of snakes brought by donors. In addition, research shows no evidence of Crotalus durissus being an expanding species in the Brazilian territory. PMID:24314146

Is the population of Crotalus durissus (Serpentes, Viperidae) expanding in Brazil?

PubMed

Duarte, Marcelo Ribeiro; Menezes, Frederico Alcântara

2013-12-05

Crotalus durissus are found from Mexico to northern Argentina in a highly disjunct distribution. According to some studies, this species is prone to occupy areas disturbed by human activities and floods comprise a plausible method of dispersal as inferred for some North American rattlesnakes. Based on the literature, it seems plausible that Crotalus durissus expanded their natural distribution in Brazil due to floods, but only in a few municipalities in Rio de Janeiro State. Data entries of Butantan Institute, in São Paulo, Brazil, from 1998 to 2012 show a declining tendency of snakes brought by donors. In addition, research shows no evidence of Crotalus durissus being an expanding species in the Brazilian territory.

The Boundaries of Genocide: Quantifying the Uncertainty of the Death Toll During the Pol Pot Regime (1975-1979)

PubMed Central

Heuveline, Patrick

2015-01-01

Estimates of excess deaths under Pol Pot's rule of Cambodia (1975-79) range from under one million to over three million. The more plausible among those, methodologically, still vary from one to two million deaths, but this range of independent point estimates has no particular statistical meaning. Stochastically reconstructing population dynamics in Cambodia from extant historical and demographic data yields interpretable distributions of the death toll and other demographic indicators. The resulting 95-percent simulation interval (1.2 to 2.8 million excess deaths) demonstrates substantial uncertainty with regards to the exact scale of mortality, yet still excludes nearly half of the previous death-toll estimates. The 1.5 to 2.25 million interval contains 69 per cent of the simulations for the actual number of excess death, more than the wider (one to two million) range of previous plausible estimates. The median value of 1.9 million excess deaths represents 21 percent of the population at risk. PMID:26218856

RNA catalysis and the origins of life

NASA Technical Reports Server (NTRS)

Orgel, Leslie E.

1986-01-01

The role of RNA catalysis in the origins of life is considered in connection with the discovery of riboszymes, which are RNA molecules that catalyze sequence-specific hydrolysis and transesterification reactions of RNA substrates. Due to this discovery, theories positing protein-free replication as preceding the appearance of the genetic code are more plausible. The scope of RNA catalysis in biology and chemistry is discussed, and it is noted that the development of methods to select (or predict) RNA sequences with preassigned catalytic functions would be a major contribution to the study of life's origins.

An Estimation of Turbulent Kinetic Energy and Energy Dissipation Rate Based on Atmospheric Boundary Layer Similarity Theory

NASA Technical Reports Server (NTRS)

Han, Jongil; Arya, S. Pal; Shaohua, Shen; Lin, Yuh-Lang; Proctor, Fred H. (Technical Monitor)

2000-01-01

Algorithms are developed to extract atmospheric boundary layer profiles for turbulence kinetic energy (TKE) and energy dissipation rate (EDR), with data from a meteorological tower as input. The profiles are based on similarity theory and scalings for the atmospheric boundary layer. The calculated profiles of EDR and TKE are required to match the observed values at 5 and 40 m. The algorithms are coded for operational use and yield plausible profiles over the diurnal variation of the atmospheric boundary layer.

Population and labour force projections for 27 European countries, 2002-052: impact of international migration on population ageing: Projections de population et de population active pour 27 pays européens 2002-052: impact de la migration internationale sur le vieillissement de la population.

PubMed

Bijak, Jakub; Kupiszewska, Dorota; Kupiszewski, Marek; Saczuk, Katarzyna; Kicinger, Anna

2007-03-01

Population and labour force projections are made for 27 selected European countries for 2002-052, focussing on the impact of international migration on population and labour force dynamics. Starting from single scenarios for fertility, mortality and economic activity, three sets of assumptions are explored regarding migration flows, taking into account probable policy developments in Europe following the enlargement of the EU. In addition to age structures, various support ratio indicators are analysed. The results indicate that plausible immigration cannot offset the negative effects of population and labour force ageing.

On the Evolution of the Standard Genetic Code: Vestiges of Critical Scale Invariance from the RNA World in Current Prokaryote Genomes

PubMed Central

José, Marco V.; Govezensky, Tzipe; García, José A.; Bobadilla, Juan R.

2009-01-01

Herein two genetic codes from which the primeval RNA code could have originated the standard genetic code (SGC) are derived. One of them, called extended RNA code type I, consists of all codons of the type RNY (purine-any base-pyrimidine) plus codons obtained by considering the RNA code but in the second (NYR type) and third (YRN type) reading frames. The extended RNA code type II, comprises all codons of the type RNY plus codons that arise from transversions of the RNA code in the first (YNY type) and third (RNR) nucleotide bases. In order to test if putative nucleotide sequences in the RNA World and in both extended RNA codes, share the same scaling and statistical properties to those encountered in current prokaryotes, we used the genomes of four Eubacteria and three Archaeas. For each prokaryote, we obtained their respective genomes obeying the RNA code or the extended RNA codes types I and II. In each case, we estimated the scaling properties of triplet sequences via a renormalization group approach, and we calculated the frequency distributions of distances for each codon. Remarkably, the scaling properties of the distance series of some codons from the RNA code and most codons from both extended RNA codes turned out to be identical or very close to the scaling properties of codons of the SGC. To test for the robustness of these results, we show, via computer simulation experiments, that random mutations of current genomes, at the rates of 10−10 per site per year during three billions of years, were not enough for destroying the observed patterns. Therefore, we conclude that most current prokaryotes may still contain relics of the primeval RNA World and that both extended RNA codes may well represent two plausible evolutionary paths between the RNA code and the current SGC. PMID:19183813

Fibromyalgia at an Educational Facility--Is There a Link to Indoor Air Quality?

ERIC Educational Resources Information Center

Wilson, Emily J.

1999-01-01

Discusses whether it is biologically plausible for an environmental laboratory contaminant to cause fibromyalgia. Presents a study of two populations which indicated that fibromyalgia was occurring at an elevated rate in a building where ventilation was deemed inadequate for laboratory activities. (Author/WRM)

Delta: a new web-based 3D genome visualization and analysis platform.

PubMed

Tang, Bixia; Li, Feifei; Li, Jing; Zhao, Wenming; Zhang, Zhihua

2018-04-15

Delta is an integrative visualization and analysis platform to facilitate visually annotating and exploring the 3D physical architecture of genomes. Delta takes Hi-C or ChIA-PET contact matrix as input and predicts the topologically associating domains and chromatin loops in the genome. It then generates a physical 3D model which represents the plausible consensus 3D structure of the genome. Delta features a highly interactive visualization tool which enhances the integration of genome topology/physical structure with extensive genome annotation by juxtaposing the 3D model with diverse genomic assay outputs. Finally, by visually comparing the 3D model of the β-globin gene locus and its annotation, we speculated a plausible transitory interaction pattern in the locus. Experimental evidence was found to support this speculation by literature survey. This served as an example of intuitive hypothesis testing with the help of Delta. Delta is freely accessible from http://delta.big.ac.cn, and the source code is available at https://github.com/zhangzhwlab/delta. zhangzhihua@big.ac.cn. Supplementary data are available at Bioinformatics online.

Reported Dietary Intake, Disparity between the Reported Consumption and the Level Needed for Adequacy and Food Sources of Calcium, Phosphorus, Magnesium and Vitamin D in the Spanish Population: Findings from the ANIBES Study.

PubMed

Olza, Josune; Aranceta-Bartrina, Javier; González-Gross, Marcela; Ortega, Rosa M; Serra-Majem, Lluis; Varela-Moreiras, Gregorio; Gil, Ángel

2017-02-21

Calcium, phosphorus, magnesium and vitamin D have important biological roles in the body, especially in bone metabolism. We aimed to study the reported intake, the disparity between the reported consumption and the level needed for adequacy and food sources of these four nutrients in the Spanish population. We assessed the reported intake for both, general population and plausible reporters. Results were extracted from the ANIBES survey, n = 2009. Three-day dietary reported intake data were obtained and misreporting was assessed according to the European Food Safety Authority (EFSA). Mean ± SEM (range) total reported consumption of calcium, phosphorus, magnesium, and vitamin D for the whole population were 698 ± 7 mg/day (71-2551 mg/day), 1176 ± 8 mg/day, (331-4429 mg/day), 222 ± 2 mg/day (73-782 mg/day), and 4.4 ± 0.1 µg/day (0.0-74.2 µg/day), respectively. In the whole group, 76% and 66%; 79% and 72%; and 94% and 93% of the population had reported intakes below 80% of the national and European recommended daily intakes for calcium, magnesium and vitamin D, respectively; these percentages were over 40% when the plausible reporters were analysed separately. The main food sources were milk and dairy products for calcium and phosphorus, cereals and grains for magnesium and fish for vitamin D. In conclusion, there is an important percentage of the Spanish ANIBES population not meeting the recommended intakes for calcium, magnesium and vitamin D.

Beyond terrestrial biology: charting the chemical universe of α-amino acid structures.

PubMed

Meringer, Markus; Cleaves, H James; Freeland, Stephen J

2013-11-25

α-Amino acids are fundamental to biochemistry as the monomeric building blocks with which cells construct proteins according to genetic instructions. However, the 20 amino acids of the standard genetic code represent a tiny fraction of the number of α-amino acid chemical structures that could plausibly play such a role, both from the perspective of natural processes by which life emerged and evolved, and from the perspective of human-engineered genetically coded proteins. Until now, efforts to describe the structures comprising this broader set, or even estimate their number, have been hampered by the complex combinatorial properties of organic molecules. Here, we use computer software based on graph theory and constructive combinatorics in order to conduct an efficient and exhaustive search of the chemical structures implied by two careful and precise definitions of the α-amino acids relevant to coded biological proteins. Our results include two virtual libraries of α-amino acid structures corresponding to these different approaches, comprising 121 044 and 3 846 structures, respectively, and suggest a simple approach to exploring much larger, as yet uncomputed, libraries of interest.

GeNN: a code generation framework for accelerated brain simulations

NASA Astrophysics Data System (ADS)

Yavuz, Esin; Turner, James; Nowotny, Thomas

2016-01-01

Large-scale numerical simulations of detailed brain circuit models are important for identifying hypotheses on brain functions and testing their consistency and plausibility. An ongoing challenge for simulating realistic models is, however, computational speed. In this paper, we present the GeNN (GPU-enhanced Neuronal Networks) framework, which aims to facilitate the use of graphics accelerators for computational models of large-scale neuronal networks to address this challenge. GeNN is an open source library that generates code to accelerate the execution of network simulations on NVIDIA GPUs, through a flexible and extensible interface, which does not require in-depth technical knowledge from the users. We present performance benchmarks showing that 200-fold speedup compared to a single core of a CPU can be achieved for a network of one million conductance based Hodgkin-Huxley neurons but that for other models the speedup can differ. GeNN is available for Linux, Mac OS X and Windows platforms. The source code, user manual, tutorials, Wiki, in-depth example projects and all other related information can be found on the project website http://genn-team.github.io/genn/.

GeNN: a code generation framework for accelerated brain simulations.

PubMed

Yavuz, Esin; Turner, James; Nowotny, Thomas

2016-01-07

Large-scale numerical simulations of detailed brain circuit models are important for identifying hypotheses on brain functions and testing their consistency and plausibility. An ongoing challenge for simulating realistic models is, however, computational speed. In this paper, we present the GeNN (GPU-enhanced Neuronal Networks) framework, which aims to facilitate the use of graphics accelerators for computational models of large-scale neuronal networks to address this challenge. GeNN is an open source library that generates code to accelerate the execution of network simulations on NVIDIA GPUs, through a flexible and extensible interface, which does not require in-depth technical knowledge from the users. We present performance benchmarks showing that 200-fold speedup compared to a single core of a CPU can be achieved for a network of one million conductance based Hodgkin-Huxley neurons but that for other models the speedup can differ. GeNN is available for Linux, Mac OS X and Windows platforms. The source code, user manual, tutorials, Wiki, in-depth example projects and all other related information can be found on the project website http://genn-team.github.io/genn/.

GeNN: a code generation framework for accelerated brain simulations

PubMed Central

Yavuz, Esin; Turner, James; Nowotny, Thomas

2016-01-01

Large-scale numerical simulations of detailed brain circuit models are important for identifying hypotheses on brain functions and testing their consistency and plausibility. An ongoing challenge for simulating realistic models is, however, computational speed. In this paper, we present the GeNN (GPU-enhanced Neuronal Networks) framework, which aims to facilitate the use of graphics accelerators for computational models of large-scale neuronal networks to address this challenge. GeNN is an open source library that generates code to accelerate the execution of network simulations on NVIDIA GPUs, through a flexible and extensible interface, which does not require in-depth technical knowledge from the users. We present performance benchmarks showing that 200-fold speedup compared to a single core of a CPU can be achieved for a network of one million conductance based Hodgkin-Huxley neurons but that for other models the speedup can differ. GeNN is available for Linux, Mac OS X and Windows platforms. The source code, user manual, tutorials, Wiki, in-depth example projects and all other related information can be found on the project website http://genn-team.github.io/genn/. PMID:26740369

The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins.

PubMed

Dehal, Paramvir; Satou, Yutaka; Campbell, Robert K; Chapman, Jarrod; Degnan, Bernard; De Tomaso, Anthony; Davidson, Brad; Di Gregorio, Anna; Gelpke, Maarten; Goodstein, David M; Harafuji, Naoe; Hastings, Kenneth E M; Ho, Isaac; Hotta, Kohji; Huang, Wayne; Kawashima, Takeshi; Lemaire, Patrick; Martinez, Diego; Meinertzhagen, Ian A; Necula, Simona; Nonaka, Masaru; Putnam, Nik; Rash, Sam; Saiga, Hidetoshi; Satake, Masanobu; Terry, Astrid; Yamada, Lixy; Wang, Hong-Gang; Awazu, Satoko; Azumi, Kaoru; Boore, Jeffrey; Branno, Margherita; Chin-Bow, Stephen; DeSantis, Rosaria; Doyle, Sharon; Francino, Pilar; Keys, David N; Haga, Shinobu; Hayashi, Hiroko; Hino, Kyosuke; Imai, Kaoru S; Inaba, Kazuo; Kano, Shungo; Kobayashi, Kenji; Kobayashi, Mari; Lee, Byung-In; Makabe, Kazuhiro W; Manohar, Chitra; Matassi, Giorgio; Medina, Monica; Mochizuki, Yasuaki; Mount, Steve; Morishita, Tomomi; Miura, Sachiko; Nakayama, Akie; Nishizaka, Satoko; Nomoto, Hisayo; Ohta, Fumiko; Oishi, Kazuko; Rigoutsos, Isidore; Sano, Masako; Sasaki, Akane; Sasakura, Yasunori; Shoguchi, Eiichi; Shin-i, Tadasu; Spagnuolo, Antoinetta; Stainier, Didier; Suzuki, Miho M; Tassy, Olivier; Takatori, Naohito; Tokuoka, Miki; Yagi, Kasumi; Yoshizaki, Fumiko; Wada, Shuichi; Zhang, Cindy; Hyatt, P Douglas; Larimer, Frank; Detter, Chris; Doggett, Norman; Glavina, Tijana; Hawkins, Trevor; Richardson, Paul; Lucas, Susan; Kohara, Yuji; Levine, Michael; Satoh, Nori; Rokhsar, Daniel S

2002-12-13

The first chordates appear in the fossil record at the time of the Cambrian explosion, nearly 550 million years ago. The modern ascidian tadpole represents a plausible approximation to these ancestral chordates. To illuminate the origins of chordate and vertebrates, we generated a draft of the protein-coding portion of the genome of the most studied ascidian, Ciona intestinalis. The Ciona genome contains approximately 16,000 protein-coding genes, similar to the number in other invertebrates, but only half that found in vertebrates. Vertebrate gene families are typically found in simplified form in Ciona, suggesting that ascidians contain the basic ancestral complement of genes involved in cell signaling and development. The ascidian genome has also acquired a number of lineage-specific innovations, including a group of genes engaged in cellulose metabolism that are related to those in bacteria and fungi.

Solar Ellerman Bombs in 1D Radiative Hydrodynamics

NASA Astrophysics Data System (ADS)

Reid, A.; Mathioudakis, M.; Kowalski, A.; Doyle, J. G.; Allred, J. C.

2017-02-01

Recent observations from the Interface Region Imaging Spectrograph appear to show impulsive brightenings in high temperature lines, which when combined with simultaneous ground-based observations in Hα, appear co-spatial to Ellerman Bombs (EBs). We use the RADYN one-dimensional radiative transfer code in an attempt to try and reproduce the observed line profiles and simulate the atmospheric conditions of these events. Combined with the MULTI/RH line synthesis codes, we compute the Hα, Ca II 8542 Å, and Mg II h and k lines for these simulated events and compare them to previous observations. Our findings hint that the presence of superheated regions in the photosphere (>10,000 K) is not a plausible explanation for the production of EB signatures. While we are able to recreate EB-like line profiles in Hα, Ca II 8542 Å, and Mg II h and k, we cannot achieve agreement with all of these simultaneously.

An active inference theory of allostasis and interoception in depression

PubMed Central

Quigley, Karen S.; Hamilton, Paul

2016-01-01

In this paper, we integrate recent theoretical and empirical developments in predictive coding and active inference accounts of interoception (including the Embodied Predictive Interoception Coding model) with working hypotheses from the theory of constructed emotion to propose a biologically plausible unified theory of the mind that places metabolism and energy regulation (i.e. allostasis), as well as the sensory consequences of that regulation (i.e. interoception), at its core. We then consider the implications of this approach for understanding depression. We speculate that depression is a disorder of allostasis, whose myriad symptoms result from a ‘locked in’ brain that is relatively insensitive to its sensory context. We conclude with a brief discussion of the ways our approach might reveal new insights for the treatment of depression. This article is part of the themed issue ‘Interoception beyond homeostasis: affect, cognition and mental health’. PMID:28080969

Predicting Plausible Impacts of Sets of Climate and Land Use Change Scenario on Water Resources

EPA Science Inventory

As the new decade ushers in, there will be new challenges. The world’s population is increasing and the land use patterns are changing. Inevitably with these global changes, there will be various environmental consequences. For example, our water resources, both in terms of qu...

Reporting Confidence Intervals and Effect Sizes: Collecting the Evidence

ERIC Educational Resources Information Center

Zientek, Linda Reichwein; Ozel, Z. Ebrar Yetkiner; Ozel, Serkan; Allen, Jeff

2012-01-01

Confidence intervals (CIs) and effect sizes are essential to encourage meta-analytic thinking and to accumulate research findings. CIs provide a range of plausible values for population parameters with a degree of confidence that the parameter is in that particular interval. CIs also give information about how precise the estimates are. Comparison…

Stochastic demographic forecasting.

PubMed

Lee, R D

1992-11-01

"This paper describes a particular approach to stochastic population forecasting, which is implemented for the U.S.A. through 2065. Statistical time series methods are combined with demographic models to produce plausible long run forecasts of vital rates, with probability distributions. The resulting mortality forecasts imply gains in future life expectancy that are roughly twice as large as those forecast by the Office of the Social Security Actuary.... Resulting stochastic forecasts of the elderly population, elderly dependency ratios, and payroll tax rates for health, education and pensions are presented." excerpt

Pedestrian evacuation modeling to reduce vehicle use for distant tsunami evacuations in Hawaiʻi

USGS Publications Warehouse

Wood, Nathan J.; Jones, Jamie; Peters, Jeff; Richards, Kevin

2018-01-01

Tsunami waves that arrive hours after generation elsewhere pose logistical challenges to emergency managers due to the perceived abundance of time and inclination of evacuees to use vehicles. We use coastal communities on the island of Oʻahu (Hawaiʻi, USA) to demonstrate regional evacuation modeling that can identify where successful pedestrian-based evacuations are plausible and where vehicle use could be discouraged. The island of Oʻahu has two tsunami-evacuation zones (standard and extreme), which provides the opportunity to examine if recommended travel modes vary based on zone. Geospatial path distance models are applied to estimate population exposure as a function of pedestrian travel time and speed out of evacuation zones. The use of the extreme zone triples the number of residents, employees, and facilities serving at-risk populations that would be encouraged to evacuate and slightly reduces the percentage of residents (98–76%) that could evacuate in less than 15 min at a plausible speed (with similar percentages for employees). Areas with lengthy evacuations are concentrated in the North Shore region for the standard zone but found all around the Oʻahu coastline for the extreme zone. The use of the extreme zone results in a 26% increase in the number of hotel visitors that would be encouraged to evacuate, and a 76% increase in the number of them that may require more than 15 min. Modeling can identify where pedestrian evacuations are plausible; however, there are logistical and behavioral issues that warrant attention before localized evacuation procedures may be realistic.

(I Can't Get No) Saturation: A simulation and guidelines for sample sizes in qualitative research.

PubMed

van Rijnsoever, Frank J

2017-01-01

I explore the sample size in qualitative research that is required to reach theoretical saturation. I conceptualize a population as consisting of sub-populations that contain different types of information sources that hold a number of codes. Theoretical saturation is reached after all the codes in the population have been observed once in the sample. I delineate three different scenarios to sample information sources: "random chance," which is based on probability sampling, "minimal information," which yields at least one new code per sampling step, and "maximum information," which yields the largest number of new codes per sampling step. Next, I use simulations to assess the minimum sample size for each scenario for systematically varying hypothetical populations. I show that theoretical saturation is more dependent on the mean probability of observing codes than on the number of codes in a population. Moreover, the minimal and maximal information scenarios are significantly more efficient than random chance, but yield fewer repetitions per code to validate the findings. I formulate guidelines for purposive sampling and recommend that researchers follow a minimum information scenario.

[Predicting Spectra of Accretion Disks Around Galactic Black Holes

NASA Technical Reports Server (NTRS)

Krolik, Julian H.

2004-01-01

The purpose of this grant was to construct detailed atmosphere solutions in order to predict the spectra of accretion disks around Galactic black holes. Our plan of action was to take an existing disk atmosphere code (TLUSTY, created by Ivan Hubeny) and introduce those additional physical processes necessary to make it applicable to disks of this variety. These modifications include: treating Comptonization; introducing continuous opacity due to heavy elements; incorporating line opacity due to heavy elements; adopting a disk structure that reflects readjustments due to radiation pressure effects; and injecting heat via a physically-plausible vertical distribution.

Community variations in population exposure to near-field tsunami hazards as a function of pedestrian travel time to safety

USGS Publications Warehouse

Wood, Nathan J.; Schmidtlein, Mathew C.

2013-01-01

Efforts to characterize population exposure to near-field tsunami threats typically focus on quantifying the number and type of people in tsunami-hazard zones. To develop and prioritize effective risk-reduction strategies, emergency managers also need information on the potential for successful evacuations and how this evacuation potential varies among communities. To improve efforts to properly characterize and differentiate near-field tsunami threats among multiple communities, we assess community variations in population exposure to tsunamis as a function of pedestrian travel time to safety. We focus our efforts on the multiple coastal communities in Grays Harbor and Pacific Counties (State of Washington, USA), where a substantial resident and visitor population is threatened by near-field tsunamis related to a potential Cascadia subduction zone earthquake. Anisotropic, path-distance modeling is conducted to estimate travel times to safety and results are merged with various population data, including residents, employees, public venues, and dependent-care facilities. Results suggest that there is substantial variability among communities in the number of people that may have insufficient time to evacuate. Successful evacuations may be possible in some communities assuming slow-walking speeds, are plausible in others if travel speeds are increased, and are unlikely in another set of communities given the large distances and short time horizon. Emergency managers can use these results to prioritize the location and determine the most appropriate type of tsunami risk-reduction strategies, such as education and training in areas where evacuations are plausible and vertical-evacuation structures in areas where they are not.

The "Wow! signal" of the terrestrial genetic code

NASA Astrophysics Data System (ADS)

shCherbak, Vladimir I.; Makukov, Maxim A.

2013-05-01

It has been repeatedly proposed to expand the scope for SETI, and one of the suggested alternatives to radio is the biological media. Genomic DNA is already used on Earth to store non-biological information. Though smaller in capacity, but stronger in noise immunity is the genetic code. The code is a flexible mapping between codons and amino acids, and this flexibility allows modifying the code artificially. But once fixed, the code might stay unchanged over cosmological timescales; in fact, it is the most durable construct known. Therefore it represents an exceptionally reliable storage for an intelligent signature, if that conforms to biological and thermodynamic requirements. As the actual scenario for the origin of terrestrial life is far from being settled, the proposal that it might have been seeded intentionally cannot be ruled out. A statistically strong intelligent-like "signal" in the genetic code is then a testable consequence of such scenario. Here we show that the terrestrial code displays a thorough precision-type orderliness matching the criteria to be considered an informational signal. Simple arrangements of the code reveal an ensemble of arithmetical and ideographical patterns of the same symbolic language. Accurate and systematic, these underlying patterns appear as a product of precision logic and nontrivial computing rather than of stochastic processes (the null hypothesis that they are due to chance coupled with presumable evolutionary pathways is rejected with P-value < 10-13). The patterns are profound to the extent that the code mapping itself is uniquely deduced from their algebraic representation. The signal displays readily recognizable hallmarks of artificiality, among which are the symbol of zero, the privileged decimal syntax and semantical symmetries. Besides, extraction of the signal involves logically straightforward but abstract operations, making the patterns essentially irreducible to any natural origin. Plausible ways of embedding the signal into the code and possible interpretation of its content are discussed. Overall, while the code is nearly optimized biologically, its limited capacity is used extremely efficiently to pass non-biological information.

PopCORN: Hunting down the differences between binary population synthesis codes

NASA Astrophysics Data System (ADS)

Toonen, S.; Claeys, J. S. W.; Mennekens, N.; Ruiter, A. J.

2014-02-01

Context. Binary population synthesis (BPS) modelling is a very effective tool to study the evolution and properties of various types of close binary systems. The uncertainty in the parameters of the model and their effect on a population can be tested in a statistical way, which then leads to a deeper understanding of the underlying (sometimes poorly understood) physical processes involved. Several BPS codes exist that have been developed with different philosophies and aims. Although BPS has been very successful for studies of many populations of binary stars, in the particular case of the study of the progenitors of supernovae Type Ia, the predicted rates and ZAMS progenitors vary substantially between different BPS codes. Aims: To understand the predictive power of BPS codes, we study the similarities and differences in the predictions of four different BPS codes for low- and intermediate-mass binaries. We investigate the differences in the characteristics of the predicted populations, and whether they are caused by different assumptions made in the BPS codes or by numerical effects, e.g. a lack of accuracy in BPS codes. Methods: We compare a large number of evolutionary sequences for binary stars, starting with the same initial conditions following the evolution until the first (and when applicable, the second) white dwarf (WD) is formed. To simplify the complex problem of comparing BPS codes that are based on many (often different) assumptions, we equalise the assumptions as much as possible to examine the inherent differences of the four BPS codes. Results: We find that the simulated populations are similar between the codes. Regarding the population of binaries with one WD, there is very good agreement between the physical characteristics, the evolutionary channels that lead to the birth of these systems, and their birthrates. Regarding the double WD population, there is a good agreement on which evolutionary channels exist to create double WDs and a rough agreement on the characteristics of the double WD population. Regarding which progenitor systems lead to a single and double WD system and which systems do not, the four codes agree well. Most importantly, we find that for these two populations, the differences in the predictions from the four codes are not due to numerical differences, but because of different inherent assumptions. We identify critical assumptions for BPS studies that need to be studied in more detail. Appendices are available in electronic form at http://www.aanda.org

Where is Population II?

NASA Astrophysics Data System (ADS)

Mould, J.; Bianchini, F.; Forbes, Duncan A.; Reichardt, C. L.

2018-03-01

The use of roman numerals for stellar populations represents a classification approach to galaxy formation which is now well behind us. Nevertheless, the concept of a pristine generation of stars, followed by a protogalactic era, and finally the mainstream stellar population is a plausible starting point for testing our physical understanding of early star formation. This will be observationally driven as never before in the coming decade. In this paper, we search out observational tests of an idealised coeval and homogeneous distribution of population II stars. We examine the spatial distribution of quasars, globular clusters, and the integrated free electron density of the intergalactic medium, in order to test the assumption of homogeneity. Any real inhomogeneity implies a population II that is not coeval.

Phylogeography and population structure of the Reevese's Butterfly Lizard (Leiolepis reevesii) inferred from mitochondrial DNA sequences.

PubMed

Lin, Long-Hui; Ji, Xiang; Diong, Cheong-Hoong; Du, Yu; Lin, Chi-Xian

2010-08-01

Butterfly lizards of the genus Leiolepis (Agamidae) are widely distributed in coastal regions of Southeast Asia and South China, with the Reevese's Butterfly Lizard Leiolepis reevesii having a most northerly distribution that ranges from Vietnam to South China. To assess the genetic diversity within L. reevesii, and its population structure and evolutionary history, we sequenced 1004 bp of cytochrome b for 448 individuals collected from 28 localities covering almost the whole range of the lizard. One hundred and forty variable sites were observed, and 93 haplotypes were defined. We identified three genetically distinct clades, of which Clade A includes haplotypes mainly from southeastern Hainan, Clade B from Guangdong and northern Hainan, and Clade C from Vietnam and the other localities of China. Clade A was well distinguished and divergent from the other two. The Wuzhishan and Yinggeling mountain ranges were important barriers limiting gene exchange between populations on the both sides of the mountain series, whereas the Gulf of Tonkin and the Qiongzhou Strait were not. One plausible scenario to explain our genetic data is a historical dispersion of L. reevesii as proceeding from Vietnam to Hainan, followed by a second wave of dispersal from Hainan to Guangdong and Guangxi. Another equally plausible scenario is a historically widespread population that has been structured by vicariant factors such as the mountains in Hainan and sea level fluctuations. Copyright 2010 Elsevier Inc. All rights reserved.

Detecting Directional Selection in the Presence of Recent Admixture in African-Americans

PubMed Central

Lohmueller, Kirk E.; Bustamante, Carlos D.; Clark, Andrew G.

2011-01-01

We investigate the performance of tests of neutrality in admixed populations using plausible demographic models for African-American history as well as resequencing data from African and African-American populations. The analysis of both simulated and human resequencing data suggests that recent admixture does not result in an excess of false-positive results for neutrality tests based on the frequency spectrum after accounting for the population growth in the parental African population. Furthermore, when simulating positive selection, Tajima's D, Fu and Li's D, and haplotype homozygosity have lower power to detect population-specific selection using individuals sampled from the admixed population than from the nonadmixed population. Fay and Wu's H test, however, has more power to detect selection using individuals from the admixed population than from the nonadmixed population, especially when the selective sweep ended long ago. Our results have implications for interpreting recent genome-wide scans for positive selection in human populations. PMID:21196524

Structures of Neural Correlation and How They Favor Coding

PubMed Central

Franke, Felix; Fiscella, Michele; Sevelev, Maksim; Roska, Botond; Hierlemann, Andreas; da Silveira, Rava Azeredo

2017-01-01

Summary The neural representation of information suffers from “noise”—the trial-to-trial variability in the response of neurons. The impact of correlated noise upon population coding has been debated, but a direct connection between theory and experiment remains tenuous. Here, we substantiate this connection and propose a refined theoretical picture. Using simultaneous recordings from a population of direction-selective retinal ganglion cells, we demonstrate that coding benefits from noise correlations. The effect is appreciable already in small populations, yet it is a collective phenomenon. Furthermore, the stimulus-dependent structure of correlation is key. We develop simple functional models that capture the stimulus-dependent statistics. We then use them to quantify the performance of population coding, which depends upon interplays of feature sensitivities and noise correlations in the population. Because favorable structures of correlation emerge robustly in circuits with noisy, nonlinear elements, they will arise and benefit coding beyond the confines of retina. PMID:26796692

Prevalence of Prescription Opioid Misuse/Abuse as Determined by International Classification of Diseases Codes: A Systematic Review.

PubMed

Roland, Carl L; Lake, Joanita; Oderda, Gary M

2016-12-01

We conducted a systematic review to evaluate worldwide human English published literature from 2009 to 2014 on prevalence of opioid misuse/abuse in retrospective databases where International Classification of Diseases (ICD) codes were used. Inclusion criteria for the studies were use of a retrospective database, measured abuse, dependence, and/or poisoning using ICD codes, stated prevalence or it could be derived, and documented time frame. A meta-analysis was not performed. A qualitative narrative synthesis was used, and 16 studies were included for data abstraction. ICD code use varies; 10 studies used ICD codes that encompassed all three terms: abuse, dependence, or poisoning. Eight studies limited determination of misuse/abuse to an opioid user population. Abuse prevalence among opioid users in commercial databases using all three terms of ICD codes varied depending on the opioid; 21 per 1000 persons (reformulated extended-release oxymorphone; 2011-2012) to 113 per 1000 persons (immediate-release opioids; 2010-2011). Abuse prevalence in general populations using all three ICD code terms ranged from 1.15 per 1000 persons (commercial; 6 months 2010) to 8.7 per 1000 persons (Medicaid; 2002-2003). Prevalence increased over time. When similar ICD codes are used, the highest prevalence is in US government-insured populations. Limiting population to continuous opioid users increases prevalence. Prevalence varies depending on ICD codes used, population, time frame, and years studied. Researchers using ICD codes to determine opioid abuse prevalence need to be aware of cautions and limitations.

Randomization-Based Inference about Latent Variables from Complex Samples: The Case of Two-Stage Sampling

ERIC Educational Resources Information Center

Li, Tiandong

2012-01-01

In large-scale assessments, such as the National Assessment of Educational Progress (NAEP), plausible values based on Multiple Imputations (MI) have been used to estimate population characteristics for latent constructs under complex sample designs. Mislevy (1991) derived a closed-form analytic solution for a fixed-effect model in creating…

Interval Estimation of Revision Effect on Scale Reliability via Covariance Structure Modeling

ERIC Educational Resources Information Center

Raykov, Tenko

2009-01-01

A didactic discussion of a procedure for interval estimation of change in scale reliability due to revision is provided, which is developed within the framework of covariance structure modeling. The method yields ranges of plausible values for the population gain or loss in reliability of unidimensional composites, which results from deletion or…

[Population density, age distribution and urbanisation as factors influencing the frequency of home visits--an analysis for Mecklenburg-West Pomerania].

PubMed

Heymann, R; Weitmann, K; Weiss, S; Thierfelder, D; Flessa, S; Hoffmann, W

2009-07-01

This study examines and compares the frequency of home visits by general practitioners in regions with a lower population density and regions with a higher population density. The discussion centres on the hypothesis whether the number of home visits in rural and remote areas with a low population density is, in fact, higher than in urbanised areas with a higher population density. The average age of the population has been considered in both cases. The communities of Mecklenburg West-Pomerania were aggregated into postal code regions. The analysis is based on these postal code regions. The average frequency of home visits per 100 inhabitants/km2 has been calculated via a bivariate, linear regression model with the population density and the average age for the postal code region as independent variables. The results are based on billing data of the year 2006 as provided by the Association of Statutory Health Insurance Physicians of Mecklenburg-Western Pomerania. In a second step a variable which clustered the postal codes of urbanised areas was added to a multivariate model. The hypothesis of a negative correlation between the frequency of home visits and the population density of the areas examined cannot be confirmed for Mecklenburg-Western Pomerania. Following the dichotomisation of the postal code regions into sparsely and densely populated areas, only the very sparsely populated postal code regions (less than 100 inhabitants/km2) show a tendency towards a higher frequency of home visits. Overall, the frequency of home visits in sparsely populated postal code regions is 28.9% higher than in the densely populated postal code regions (more than 100 inhabitants/km2), although the number of general practitioners is approximately the same in both groups. In part this association seems to be confirmed by a positive correlation between the average age in the individual postal code regions and the number of home visits carried out in the area. As calculated on the basis of the data at hand, only the very sparsely populated areas with a still gradually decreasing population show a tendency towards a higher frequency of home visits. According to the data of 2006, the number of home visits remains high in sparsely populated areas. It may increase in the near future as the number of general practitioners in these areas will gradually decrease while the number of immobile and older inhabitants will increase.

(I Can’t Get No) Saturation: A simulation and guidelines for sample sizes in qualitative research

PubMed Central

2017-01-01

I explore the sample size in qualitative research that is required to reach theoretical saturation. I conceptualize a population as consisting of sub-populations that contain different types of information sources that hold a number of codes. Theoretical saturation is reached after all the codes in the population have been observed once in the sample. I delineate three different scenarios to sample information sources: “random chance,” which is based on probability sampling, “minimal information,” which yields at least one new code per sampling step, and “maximum information,” which yields the largest number of new codes per sampling step. Next, I use simulations to assess the minimum sample size for each scenario for systematically varying hypothetical populations. I show that theoretical saturation is more dependent on the mean probability of observing codes than on the number of codes in a population. Moreover, the minimal and maximal information scenarios are significantly more efficient than random chance, but yield fewer repetitions per code to validate the findings. I formulate guidelines for purposive sampling and recommend that researchers follow a minimum information scenario. PMID:28746358

Hierarchical differences in population coding within auditory cortex.

PubMed

Downer, Joshua D; Niwa, Mamiko; Sutter, Mitchell L

2017-08-01

Most models of auditory cortical (AC) population coding have focused on primary auditory cortex (A1). Thus our understanding of how neural coding for sounds progresses along the cortical hierarchy remains obscure. To illuminate this, we recorded from two AC fields: A1 and middle lateral belt (ML) of rhesus macaques. We presented amplitude-modulated (AM) noise during both passive listening and while the animals performed an AM detection task ("active" condition). In both fields, neurons exhibit monotonic AM-depth tuning, with A1 neurons mostly exhibiting increasing rate-depth functions and ML neurons approximately evenly distributed between increasing and decreasing functions. We measured noise correlation ( r noise ) between simultaneously recorded neurons and found that whereas engagement decreased average r noise in A1, engagement increased average r noise in ML. This finding surprised us, because attentive states are commonly reported to decrease average r noise We analyzed the effect of r noise on AM coding in both A1 and ML and found that whereas engagement-related shifts in r noise in A1 enhance AM coding, r noise shifts in ML have little effect. These results imply that the effect of r noise differs between sensory areas, based on the distribution of tuning properties among the neurons within each population. A possible explanation of this is that higher areas need to encode nonsensory variables (e.g., attention, choice, and motor preparation), which impart common noise, thus increasing r noise Therefore, the hierarchical emergence of r noise -robust population coding (e.g., as we observed in ML) enhances the ability of sensory cortex to integrate cognitive and sensory information without a loss of sensory fidelity. NEW & NOTEWORTHY Prevailing models of population coding of sensory information are based on a limited subset of neural structures. An important and under-explored question in neuroscience is how distinct areas of sensory cortex differ in their population coding strategies. In this study, we compared population coding between primary and secondary auditory cortex. Our findings demonstrate striking differences between the two areas and highlight the importance of considering the diversity of neural structures as we develop models of population coding. Copyright © 2017 the American Physiological Society.

A hadronic origin for ultra-high-frequency-peaked BL Lac objects

NASA Astrophysics Data System (ADS)

Cerruti, M.; Zech, A.; Boisson, C.; Inoue, S.

2015-03-01

Current Cherenkov telescopes have identified a population of ultra-high-frequency peaked BL Lac objects (UHBLs), also known as extreme blazars, that exhibit exceptionally hard TeV spectra, including 1ES 0229+200, 1ES 0347-121, RGB J0710+591, 1ES 1101-232, and 1ES 1218+304. Although one-zone synchrotron-self-Compton (SSC) models have been generally successful in interpreting the high-energy emission observed in other BL Lac objects, they are problematic for UHBLs, necessitating very large Doppler factors and/or extremely high minimum Lorentz factors of the emitting leptonic population. In this context, we have investigated alternative scenarios where hadronic emission processes are important, using a newly developed (lepto-)hadronic numerical code to systematically explore the physical parameters of the emission region that reproduces the observed spectra while avoiding the extreme values encountered in pure SSC models. Assuming a fixed Doppler factor δ = 30, two principal parameter regimes are identified, where the high-energy emission is due to: (1) proton-synchrotron radiation, with magnetic fields B ˜ 1-100 G and maximum proton energies Ep; max ≲ 1019 eV; and (2) synchrotron emission from p-γ-induced cascades as well as SSC emission from primary leptons, with B ˜ 0.1-1 G and Ep; max ≲ 1017 eV. This can be realized with plausible, sub-Eddington values for the total (kinetic plus magnetic) power of the emitting plasma, in contrast to hadronic interpretations for other blazar classes that often warrant highly super-Eddington values.

Development of a surveillance case definition for heat-related illness using 911 medical dispatch data.

PubMed

Bassil, Kate L; Cole, Donald C; Moineddin, Rahim; Gournis, Effie; Schwartz, Brian; Craig, Alan M; Lou, W Y Wendy; Rea, Elizabeth

2008-01-01

The adverse effects of hot weather on public health are of increasing concern. A surveillance system using 911 medical dispatch data for the detection of heat-related illness (HRI) could provide new information on the impact of excessive heat on the population. This paper describes how we identified medical dispatch call codes, called "determinants", that could represent HRI events. Approximately 500 medical dispatch determinants were reviewed in focus groups composed of Emergency Medical Services (EMS) paramedics, dispatchers, physicians, and public health epidemiologists. Each group was asked to select those determinants that might adequately represent HRI. Selections were then assessed empirically using correlations with daily mean temperature over the study period (June 1-August 31,2005). The focus groups identified 12 determinant groupings and ranked them according to specificity for HRI. Of these, "Heat/cold exposure" was deemed the most specific. The call determinant groupings with the clearest positive associations with daily mean temperature empirically were "Heat/cold exposure" (Spearman's correlation coefficient (SCC) 0.71, p < 0.0001) and "Unknown problem (man down)" (SCC 0.21, p = 0.04). Within each grouping, the determinant "Unknown status (3rd party caller)" showed significant associations, SCC = 0.34 (p = 0.001) and SCC = 0.22 (p = 0.03) respectively. Clinically-informed expertise and empirical evidence both contributed to identification of a group of 911 medical dispatch call determinants that plausibly represent HRI events. Once evaluated prospectively, these may be used in public health surveillance to better understand environmental health impacts on human populations and inform targeted public health interventions.

Predictions of the spontaneous symmetry-breaking theory for visual code completeness and spatial scaling in single-cell learning rules.

PubMed

Webber, C J

2001-05-01

This article shows analytically that single-cell learning rules that give rise to oriented and localized receptive fields, when their synaptic weights are randomly and independently initialized according to a plausible assumption of zero prior information, will generate visual codes that are invariant under two-dimensional translations, rotations, and scale magnifications, provided that the statistics of their training images are sufficiently invariant under these transformations. Such codes span different image locations, orientations, and size scales with equal economy. Thus, single-cell rules could account for the spatial scaling property of the cortical simple-cell code. This prediction is tested computationally by training with natural scenes; it is demonstrated that a single-cell learning rule can give rise to simple-cell receptive fields spanning the full range of orientations, image locations, and spatial frequencies (except at the extreme high and low frequencies at which the scale invariance of the statistics of digitally sampled images must ultimately break down, because of the image boundary and the finite pixel resolution). Thus, no constraint on completeness, or any other coupling between cells, is necessary to induce the visual code to span wide ranges of locations, orientations, and size scales. This prediction is made using the theory of spontaneous symmetry breaking, which we have previously shown can also explain the data-driven self-organization of a wide variety of transformation invariances in neurons' responses, such as the translation invariance of complex cell response.

Computing travel time when the exact address is unknown: a comparison of point and polygon ZIP code approximation methods.

PubMed

Berke, Ethan M; Shi, Xun

2009-04-29

Travel time is an important metric of geographic access to health care. We compared strategies of estimating travel times when only subject ZIP code data were available. Using simulated data from New Hampshire and Arizona, we estimated travel times to nearest cancer centers by using: 1) geometric centroid of ZIP code polygons as origins, 2) population centroids as origin, 3) service area rings around each cancer center, assigning subjects to rings by assuming they are evenly distributed within their ZIP code, 4) service area rings around each center, assuming the subjects follow the population distribution within the ZIP code. We used travel times based on street addresses as true values to validate estimates. Population-based methods have smaller errors than geometry-based methods. Within categories (geometry or population), centroid and service area methods have similar errors. Errors are smaller in urban areas than in rural areas. Population-based methods are superior to the geometry-based methods, with the population centroid method appearing to be the best choice for estimating travel time. Estimates in rural areas are less reliable.

Diversity and Divergence of Dinoflagellate Histone Proteins

PubMed Central

Marinov, Georgi K.; Lynch, Michael

2015-01-01

Histone proteins and the nucleosomal organization of chromatin are near-universal eukaroytic features, with the exception of dinoflagellates. Previous studies have suggested that histones do not play a major role in the packaging of dinoflagellate genomes, although several genomic and transcriptomic surveys have detected a full set of core histone genes. Here, transcriptomic and genomic sequence data from multiple dinoflagellate lineages are analyzed, and the diversity of histone proteins and their variants characterized, with particular focus on their potential post-translational modifications and the conservation of the histone code. In addition, the set of putative epigenetic mark readers and writers, chromatin remodelers and histone chaperones are examined. Dinoflagellates clearly express the most derived set of histones among all autonomous eukaryote nuclei, consistent with a combination of relaxation of sequence constraints imposed by the histone code and the presence of numerous specialized histone variants. The histone code itself appears to have diverged significantly in some of its components, yet others are conserved, implying conservation of the associated biochemical processes. Specifically, and with major implications for the function of histones in dinoflagellates, the results presented here strongly suggest that transcription through nucleosomal arrays happens in dinoflagellates. Finally, the plausible roles of histones in dinoflagellate nuclei are discussed. PMID:26646152

Robust Nonlinear Neural Codes

NASA Astrophysics Data System (ADS)

Yang, Qianli; Pitkow, Xaq

2015-03-01

Most interesting natural sensory stimuli are encoded in the brain in a form that can only be decoded nonlinearly. But despite being a core function of the brain, nonlinear population codes are rarely studied and poorly understood. Interestingly, the few existing models of nonlinear codes are inconsistent with known architectural features of the brain. In particular, these codes have information content that scales with the size of the cortical population, even if that violates the data processing inequality by exceeding the amount of information entering the sensory system. Here we provide a valid theory of nonlinear population codes by generalizing recent work on information-limiting correlations in linear population codes. Although these generalized, nonlinear information-limiting correlations bound the performance of any decoder, they also make decoding more robust to suboptimal computation, allowing many suboptimal decoders to achieve nearly the same efficiency as an optimal decoder. Although these correlations are extremely difficult to measure directly, particularly for nonlinear codes, we provide a simple, practical test by which one can use choice-related activity in small populations of neurons to determine whether decoding is suboptimal or optimal and limited by correlated noise. We conclude by describing an example computation in the vestibular system where this theory applies. QY and XP was supported by a grant from the McNair foundation.

The Universal Plausibility Metric (UPM) & Principle (UPP).

PubMed

Abel, David L

2009-12-03

Mere possibility is not an adequate basis for asserting scientific plausibility. A precisely defined universal bound is needed beyond which the assertion of plausibility, particularly in life-origin models, can be considered operationally falsified. But can something so seemingly relative and subjective as plausibility ever be quantified? Amazingly, the answer is, "Yes." A method of objectively measuring the plausibility of any chance hypothesis (The Universal Plausibility Metric [UPM]) is presented. A numerical inequality is also provided whereby any chance hypothesis can be definitively falsified when its UPM metric of xi is < 1 (The Universal Plausibility Principle [UPP]). Both UPM and UPP pre-exist and are independent of any experimental design and data set. No low-probability hypothetical plausibility assertion should survive peer-review without subjection to the UPP inequality standard of formal falsification (xi < 1).

Cause-specific mortality time series analysis: a general method to detect and correct for abrupt data production changes

PubMed Central

2011-01-01

Background Monitoring the time course of mortality by cause is a key public health issue. However, several mortality data production changes may affect cause-specific time trends, thus altering the interpretation. This paper proposes a statistical method that detects abrupt changes ("jumps") and estimates correction factors that may be used for further analysis. Methods The method was applied to a subset of the AMIEHS (Avoidable Mortality in the European Union, toward better Indicators for the Effectiveness of Health Systems) project mortality database and considered for six European countries and 13 selected causes of deaths. For each country and cause of death, an automated jump detection method called Polydect was applied to the log mortality rate time series. The plausibility of a data production change associated with each detected jump was evaluated through literature search or feedback obtained from the national data producers. For each plausible jump position, the statistical significance of the between-age and between-gender jump amplitude heterogeneity was evaluated by means of a generalized additive regression model, and correction factors were deduced from the results. Results Forty-nine jumps were detected by the Polydect method from 1970 to 2005. Most of the detected jumps were found to be plausible. The age- and gender-specific amplitudes of the jumps were estimated when they were statistically heterogeneous, and they showed greater by-age heterogeneity than by-gender heterogeneity. Conclusion The method presented in this paper was successfully applied to a large set of causes of death and countries. The method appears to be an alternative to bridge coding methods when the latter are not systematically implemented because they are time- and resource-consuming. PMID:21929756

Phase synchronization motion and neural coding in dynamic transmission of neural information.

PubMed

Wang, Rubin; Zhang, Zhikang; Qu, Jingyi; Cao, Jianting

2011-07-01

In order to explore the dynamic characteristics of neural coding in the transmission of neural information in the brain, a model of neural network consisting of three neuronal populations is proposed in this paper using the theory of stochastic phase dynamics. Based on the model established, the neural phase synchronization motion and neural coding under spontaneous activity and stimulation are examined, for the case of varying network structure. Our analysis shows that, under the condition of spontaneous activity, the characteristics of phase neural coding are unrelated to the number of neurons participated in neural firing within the neuronal populations. The result of numerical simulation supports the existence of sparse coding within the brain, and verifies the crucial importance of the magnitudes of the coupling coefficients in neural information processing as well as the completely different information processing capability of neural information transmission in both serial and parallel couplings. The result also testifies that under external stimulation, the bigger the number of neurons in a neuronal population, the more the stimulation influences the phase synchronization motion and neural coding evolution in other neuronal populations. We verify numerically the experimental result in neurobiology that the reduction of the coupling coefficient between neuronal populations implies the enhancement of lateral inhibition function in neural networks, with the enhancement equivalent to depressing neuronal excitability threshold. Thus, the neuronal populations tend to have a stronger reaction under the same stimulation, and more neurons get excited, leading to more neurons participating in neural coding and phase synchronization motion.

Benchmark problems in computational aeroacoustics

NASA Technical Reports Server (NTRS)

Porter-Locklear, Freda

1994-01-01

A recent directive at NASA Langley is aimed at numerically predicting principal noise sources. During my summer stay, I worked with high-order ENO code, developed by Dr. Harold Atkins, for solving the unsteady compressible Navier-Stokes equations, as it applies to computational aeroacoustics (CAA). A CAA workshop, composed of six categories of benchmark problems, has been organized to test various numerical properties of code. My task was to determine the robustness of Atkins' code for these test problems. In one category, we tested the nonlinear wave propagation of the code for the one-dimensional Euler equations, with initial pressure, density, and velocity conditions. Using freestream boundary conditions, our results were plausible. In another category, we solved the linearized two-dimensional Euler equations to test the effectiveness of radiation boundary conditions. Here we utilized MAPLE to compute eigenvalues and eigenvectors of the Jacobian given variable and flux vectors. We experienced a minor problem with inflow and outflow boundary conditions. Next, we solved the quasi one dimensional unsteady flow equations with an incoming acoustic wave of amplitude 10(exp -6). The small amplitude sound wave was incident on a convergent-divergent nozzle. After finding a steady-state solution and then marching forward, our solution indicated that after 30 periods the acoustic wave had dissipated (a period is time required for sound wave to traverse one end of nozzle to other end).

The Universal Plausibility Metric (UPM) & Principle (UPP)

PubMed Central

2009-01-01

Background Mere possibility is not an adequate basis for asserting scientific plausibility. A precisely defined universal bound is needed beyond which the assertion of plausibility, particularly in life-origin models, can be considered operationally falsified. But can something so seemingly relative and subjective as plausibility ever be quantified? Amazingly, the answer is, "Yes." A method of objectively measuring the plausibility of any chance hypothesis (The Universal Plausibility Metric [UPM]) is presented. A numerical inequality is also provided whereby any chance hypothesis can be definitively falsified when its UPM metric of ξ is < 1 (The Universal Plausibility Principle [UPP]). Both UPM and UPP pre-exist and are independent of any experimental design and data set. Conclusion No low-probability hypothetical plausibility assertion should survive peer-review without subjection to the UPP inequality standard of formal falsification (ξ < 1). PMID:19958539

Climate Change Impacts on Agriculture and Food Security in 2050 under a Range of Plausible Socioeconomic and Emissions Scenarios

NASA Astrophysics Data System (ADS)

Wiebe, K.; Lotze-Campen, H.; Bodirsky, B.; Kavallari, A.; Mason-d'Croz, D.; van der Mensbrugghe, D.; Robinson, S.; Sands, R.; Tabeau, A.; Willenbockel, D.; Islam, S.; van Meijl, H.; Mueller, C.; Robertson, R.

2014-12-01

Previous studies have combined climate, crop and economic models to examine the impact of climate change on agricultural production and food security, but results have varied widely due to differences in models, scenarios and data. Recent work has examined (and narrowed) these differences through systematic model intercomparison using a high-emissions pathway to highlight the differences. New work extends that analysis to cover a range of plausible socioeconomic scenarios and emission pathways. Results from three general circulation models are combined with one crop model and five global economic models to examine the global and regional impacts of climate change on yields, area, production, prices and trade for coarse grains, rice, wheat, oilseeds and sugar to 2050. Results show that yield impacts vary with changes in population, income and technology as well as emissions, but are reduced in all cases by endogenous changes in prices and other variables.

Macroecological analyses support an overkill scenario for late Pleistocene extinctions.

PubMed

Diniz-Filho, J A F

2004-08-01

The extinction of megafauna at the end of Pleistocene has been traditionally explained by environmental changes or overexploitation by human hunting (overkill). Despite difficulties in choosing between these alternative (and not mutually exclusive) scenarios, the plausibility of the overkill hypothesis can be established by ecological models of predator-prey interactions. In this paper, I have developed a macroecological model for the overkill hypothesis, in which prey population dynamic parameters, including abundance, geographic extent, and food supply for hunters, were derived from empirical allometric relationships with body mass. The last output correctly predicts the final destiny (survival or extinction) for 73% of the species considered, a value only slightly smaller than those obtained by more complex models based on detailed archaeological and ecological data for each species. This illustrates the high selectivity of Pleistocene extinction in relation to body mass and confers more plausibility on the overkill scenario.

Detecting directional selection in the presence of recent admixture in African-Americans.

PubMed

Lohmueller, Kirk E; Bustamante, Carlos D; Clark, Andrew G

2011-03-01

We investigate the performance of tests of neutrality in admixed populations using plausible demographic models for African-American history as well as resequencing data from African and African-American populations. The analysis of both simulated and human resequencing data suggests that recent admixture does not result in an excess of false-positive results for neutrality tests based on the frequency spectrum after accounting for the population growth in the parental African population. Furthermore, when simulating positive selection, Tajima's D, Fu and Li's D, and haplotype homozygosity have lower power to detect population-specific selection using individuals sampled from the admixed population than from the nonadmixed population. Fay and Wu's H test, however, has more power to detect selection using individuals from the admixed population than from the nonadmixed population, especially when the selective sweep ended long ago. Our results have implications for interpreting recent genome-wide scans for positive selection in human populations. © 2011 by the Genetics Society of America

HYDICE data from Lake Tahoe: comparison to coincident AVIRIS and in-situ measurements

NASA Astrophysics Data System (ADS)

Kappus, Mary E.; Davis, Curtiss O.; Rhea, W. J.

1996-11-01

Coordinated flights of two calibrated airborne imaging spectrometers, HYDICE and AVIRIS, were conducted on June 22, 1995 over Lake Tahoe. As part of HYDICE's first operational mission, one objective was to test the system performance over the dark homogeneous target provided by the clear deep waters of the lake. The high altitude and clear atmosphere makes Lake Tahoe a simpler test target than near-shore marine environments, where large aerosols complicate atmospheric correction and sediment runoff and high chlorophyll levels make interpretation of he data difficult. Calibrated data from both runoff and high chlorophyll levels make interpretation of the data difficult. Calibrated data from both sensors was provided in physical units of radiance. The atmospheric radiative transfer code, MODTRAN was used to remove the path radiance between the ground and sensor and the skylight reflected from the water surface. The resulting water-leaving spectrometer, and with values calculated form in-water properties using the HYDROLIGHT radiative transfer code. The agreement of the water-leaving radiance for the HYDICE data, the ground-truth spectral measurements, and the results of the radiative transfer code are excellent for wavelengths greater than 0.45 micrometers . The AVIRIS flight took place more than an hour closer to noon, which makes the radiance measurements not directly comparable. Comparisons to radiative transfer output for this later time indicate that the AVIRIS data is strongly by sun glint. Because water-leaving radiance is dependent upon the characteristics of the water, it can be analyzed for some of those properties. Using the CZCS algorithm based on the water-leaving radiance at two wavelengths, the chlorophyll content of Lake Tahoe was computed from the HYDICE and ground-truth data. Resulting values are slightly higher than measurements made two weeks earlier from water samples, indicating a growth in the phytoplankton population which is very plausible given the intervening atmospheric conditions. The success in determining water-leaving radiance and interpreting it for pigment concentration are very positive results for this early HYDICE flight. The interpretations made so far do not make use of the full spectral content of the data, so much room for advancement remains.

Teachers' Prestige in Spain: Probing the Public's and the Teachers' Contrary Views

ERIC Educational Resources Information Center

Pérez-Díaz, Víctor; Rodríguez, Juan Carlos

2014-01-01

We use the results of a public opinion survey we carried out in 2012 on a sample of the Spanish adult population to offer a plausible explanation of one of the main conundrums of primary and secondary school teachers' prestige, not only in Spain, i.e. that, contrary to public discourse and to teachers' perceptions, this prestige has not fallen in…

Notes on the origin of the Trojan asteroids

NASA Technical Reports Server (NTRS)

Yoder, C. F.

1979-01-01

The dynamic plausibility of various ideas on the origin of the Trojans is briefly discussed. We take the point of view that the present, tightly bound population has secularly evolved through some mechanism from less to more tightly bound orbit configurations. The mechanisms considered are changes in the Jovian mass or semimajor axis during planetary formation, collisional interactions with external, asteroidal material, and cometary outgassing.

Role of the locus coeruleus in the emergence of power law wake bouts in a model of the brainstem sleep-wake system through early infancy.

PubMed

Patel, Mainak; Rangan, Aaditya

2017-08-07

Infant rats randomly cycle between the sleeping and waking states, which are tightly correlated with the activity of mutually inhibitory brainstem sleep and wake populations. Bouts of sleep and wakefulness are random; from P2-P10, sleep and wake bout lengths are exponentially distributed with increasing means, while during P10-P21, the sleep bout distribution remains exponential while the distribution of wake bouts gradually transforms to power law. The locus coeruleus (LC), via an undeciphered interaction with sleep and wake populations, has been shown experimentally to be responsible for the exponential to power law transition. Concurrently during P10-P21, the LC undergoes striking physiological changes - the LC exhibits strong global 0.3 Hz oscillations up to P10, but the oscillation frequency gradually rises and synchrony diminishes from P10-P21, with oscillations and synchrony vanishing at P21 and beyond. In this work, we construct a biologically plausible Wilson Cowan-style model consisting of the LC along with sleep and wake populations. We show that external noise and strong reciprocal inhibition can lead to switching between sleep and wake populations and exponentially distributed sleep and wake bout durations as during P2-P10, with the parameters of inhibition between the sleep and wake populations controlling mean bout lengths. Furthermore, we show that the changing physiology of the LC from P10-P21, coupled with reciprocal excitation between the LC and wake population, can explain the shift from exponential to power law of the wake bout distribution. To our knowledge, this is the first study that proposes a plausible biological mechanism, which incorporates the known changing physiology of the LC, for tying the developing sleep-wake circuit and its interaction with the LC to the transformation of sleep and wake bout dynamics from P2-P21. Copyright © 2017 Elsevier Ltd. All rights reserved.

Cardiovascular and Cerebrovascular Emergency Department Visits Associated With Wildfire Smoke Exposure in California in 2015.

PubMed

Wettstein, Zachary S; Hoshiko, Sumi; Fahimi, Jahan; Harrison, Robert J; Cascio, Wayne E; Rappold, Ana G

2018-04-11

Wildfire smoke is known to exacerbate respiratory conditions; however, evidence for cardiovascular and cerebrovascular events has been inconsistent, despite biological plausibility. A population-based epidemiologic analysis was conducted for daily cardiovascular and cerebrovascular emergency department (ED) visits and wildfire smoke exposure in 2015 among adults in 8 California air basins. A quasi-Poisson regression model was used for zip code-level counts of ED visits, adjusting for heat index, day of week, seasonality, and population. Satellite-imaged smoke plumes were classified as light, medium, or dense based on model-estimated concentrations of fine particulate matter. Relative risk was determined for smoky days for lag days 0 to 4. Rates of ED visits by age- and sex-stratified groups were also examined. Rates of all-cause cardiovascular ED visits were elevated across all lags, with the greatest increase on dense smoke days and among those aged ≥65 years at lag 0 (relative risk 1.15, 95% confidence interval [1.09, 1.22]). All-cause cerebrovascular visits were associated with smoke, especially among those 65 years and older, (1.22 [1.00, 1.49], dense smoke, lag 1). Respiratory conditions were also increased, as anticipated (1.18 [1.08, 1.28], adults >65 years, dense smoke, lag 1). No association was found for the control condition, acute appendicitis. Elevated risks for individual diagnoses included myocardial infarction, ischemic heart disease, heart failure, dysrhythmia, pulmonary embolism, ischemic stroke, and transient ischemic attack. Analysis of an extensive wildfire season found smoke exposure to be associated with cardiovascular and cerebrovascular ED visits for all adults, particularly for those over aged 65 years. © 2018 The Authors. Published on behalf of the American Heart Association, Inc., by Wiley.

Pesticides, chemical and industrial exposures in relation to systemic lupus erythematosus

PubMed Central

Parks, Christine G.; De Roos, Anneclaire J.

2013-01-01

Growing evidence suggests exposure to chemicals and industrial pollutants may increase risk of SLE. Here we review research on SLE associations with occupational and industrial exposures, primarily drawing on studies in human populations and summarizing epidemiologic research published in the past decade. The association of occupational silica exposure with SLE is well established, but key questions remain, including the required dose and susceptibility factors, and SLE risk due to other silicate exposures. Research on SLE and other exposures is less well developed, though several potential associations merit further consideration due to the consistency of preliminary human findings, experimental animal research, and biologic plausibility. These include pesticides and solvents, for which experimental findings also support investigation of specific agents, including organochlorines and trichloroethylene. Experimental findings and biologic plausibility suggest research on SLE and occupational exposure to hydrocarbons (i.e., mineral oils) is warranted, especially given the widespread exposures in the population. Experimental and limited human findings support further investigation of SLE related to mercury exposure, especially in dental occupations. Research on environmental risk factors in risk-enriched cohorts (family based) is recommended, as is further investigation of exposures in relation to intermediate markers of effect (e.g., antinuclear antibodies), clinical features (e.g., nephritis) and outcomes. PMID:24763537

Comparison of the Live Attenuated Yellow Fever Vaccine 17D-204 Strain to Its Virulent Parental Strain Asibi by Deep Sequencing

PubMed Central

Beck, Andrew; Tesh, Robert B.; Wood, Thomas G.; Widen, Steven G.; Ryman, Kate D.; Barrett, Alan D. T.

2014-01-01

Background. The first comparison of a live RNA viral vaccine strain to its wild-type parental strain by deep sequencing is presented using as a model the yellow fever virus (YFV) live vaccine strain 17D-204 and its wild-type parental strain, Asibi. Methods. The YFV 17D-204 vaccine genome was compared to that of the parental strain Asibi by massively parallel methods. Variability was compared on multiple scales of the viral genomes. A modeled exploration of small-frequency variants was performed to reconstruct plausible regions of mutational plasticity. Results. Overt quasispecies diversity is a feature of the parental strain, whereas the live vaccine strain lacks diversity according to multiple independent measurements. A lack of attenuating mutations in the Asibi population relative to that of 17D-204 was observed, demonstrating that the vaccine strain was derived by discrete mutation of Asibi and not by selection of genomes in the wild-type population. Conclusions. Relative quasispecies structure is a plausible correlate of attenuation for live viral vaccines. Analyses such as these of attenuated viruses improve our understanding of the molecular basis of vaccine attenuation and provide critical information on the stability of live vaccines and the risk of reversion to virulence. PMID:24141982

Comparison of the live attenuated yellow fever vaccine 17D-204 strain to its virulent parental strain Asibi by deep sequencing.

PubMed

Beck, Andrew; Tesh, Robert B; Wood, Thomas G; Widen, Steven G; Ryman, Kate D; Barrett, Alan D T

2014-02-01

The first comparison of a live RNA viral vaccine strain to its wild-type parental strain by deep sequencing is presented using as a model the yellow fever virus (YFV) live vaccine strain 17D-204 and its wild-type parental strain, Asibi. The YFV 17D-204 vaccine genome was compared to that of the parental strain Asibi by massively parallel methods. Variability was compared on multiple scales of the viral genomes. A modeled exploration of small-frequency variants was performed to reconstruct plausible regions of mutational plasticity. Overt quasispecies diversity is a feature of the parental strain, whereas the live vaccine strain lacks diversity according to multiple independent measurements. A lack of attenuating mutations in the Asibi population relative to that of 17D-204 was observed, demonstrating that the vaccine strain was derived by discrete mutation of Asibi and not by selection of genomes in the wild-type population. Relative quasispecies structure is a plausible correlate of attenuation for live viral vaccines. Analyses such as these of attenuated viruses improve our understanding of the molecular basis of vaccine attenuation and provide critical information on the stability of live vaccines and the risk of reversion to virulence.

Selfishness and altruism can coexist when help is subject to diminishing returns.

PubMed

Sibly, R M; Curnow, R N

2011-08-01

Altruism and selfishness are 30-50% heritable in man in both Western and non-Western populations. This genetically based variation in altruism and selfishness requires explanation. In non-human animals, altruism is generally directed towards relatives, and satisfies the condition known as Hamilton's rule. This nepotistic altruism evolves under natural selection only if the ratio of the benefit of receiving help to the cost of giving it exceeds a value that depends on the relatedness of the individuals involved. Standard analyses assume that the benefit provided by each individual is the same but it is plausible in some cases that as more individuals contribute, help is subject to diminishing returns. We analyse this situation using a single-locus two-allele model of selection in a diploid population with the altruistic allele dominant to the selfish allele. The analysis requires calculation of the relationship between the fitnesses of the genotypes and the frequencies of the genes. The fitnesses vary not only with the genotype of the individual but also with the distribution of phenotypes amongst the sibs of the individual and this depends on the genotypes of his parents. These calculations are not possible by direct fitness or ESS methods but are possible using population genetics. Our analysis shows that diminishing returns change the operation of natural selection and the outcome can now be a stable equilibrium between altruistic and selfish alleles rather than the elimination of one allele or the other. We thus provide a plausible genetic model of kin selection that leads to the stable coexistence in the same population of both altruistic and selfish individuals. This may explain reported genetic variation in altruism in man.

Optical signatures of high-redshift galaxy clusters

NASA Technical Reports Server (NTRS)

Evrard, August E.; Charlot, Stephane

1994-01-01

We combine an N-body and gasdynamic simulation of structure formation with an updated population synthesis code to explore the expected optical characteristics of a high-redshift cluster of galaxies. We examine a poor (2 keV) cluster formed in a biased, cold dark matter cosmology and employ simple, but plausible, threshold criteria to convert gas into stars. At z = 2, the forming cluster appears as a linear chain of very blue (g-r approximately equals 0) galaxies, with 15 objects brighter than r = 25 within a 1 square arcmin field of view. After 2 Gyr of evolution, the cluster viewed at z = 1 displays both freshly infalling blue galaxies and red galaxies robbed of recent accretion by interaction with the hot intracluster medium. The range in G-R colors is approximately 3 mag at z = 1, with the reddest objects lying at sites of highest galaxy density. We suggest that red, high-redshift galaxies lie in the cores of forming clusters and that their existence indicates the presence of a hot intracluster medium at redshifts z approximately equals 2. The simulated cluster viewed at z = 2 has several characteristics similar to the collection of faint, blue objects identified by Dressler et al. in a deep Hubble Space Telescope observation. The similarities provide some support for the interpretation of this collection as a high-redshift cluster of galaxies.

NORMAL TYPE Ia SUPERNOVAE FROM VIOLENT MERGERS OF WHITE DWARF BINARIES

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

Pakmor, R.; Kromer, M.; Taubenberger, S.

2012-03-15

One of the most important questions regarding the progenitor systems of Type Ia supernovae (SNe Ia) is whether mergers of two white dwarfs can lead to explosions that reproduce observations of normal events. Here we present a fully three-dimensional simulation of a violent merger of two carbon-oxygen white dwarfs with masses of 0.9 M{sub Sun} and 1.1 M{sub Sun} combining very high resolution and exact initial conditions. A well-tested combination of codes is used to study the system. We start with the dynamical inspiral phase and follow the subsequent thermonuclear explosion under the plausible assumption that a detonation forms inmore » the process of merging. We then perform detailed nucleosynthesis calculations and radiative transfer simulations to predict synthetic observables from the homologously expanding supernova ejecta. We find that synthetic color light curves of our merger, which produces about 0.62 M{sub Sun} of {sup 56}Ni, show good agreement with those observed for normal SNe Ia in all wave bands from U to K. Line velocities in synthetic spectra around maximum light also agree well with observations. We conclude that violent mergers of massive white dwarfs can closely resemble normal SNe Ia. Therefore, depending on the number of such massive systems available these mergers may contribute at least a small fraction to the observed population of normal SNe Ia.« less

Population coding in sparsely connected networks of noisy neurons.

PubMed

Tripp, Bryan P; Orchard, Jeff

2012-01-01

This study examines the relationship between population coding and spatial connection statistics in networks of noisy neurons. Encoding of sensory information in the neocortex is thought to require coordinated neural populations, because individual cortical neurons respond to a wide range of stimuli, and exhibit highly variable spiking in response to repeated stimuli. Population coding is rooted in network structure, because cortical neurons receive information only from other neurons, and because the information they encode must be decoded by other neurons, if it is to affect behavior. However, population coding theory has often ignored network structure, or assumed discrete, fully connected populations (in contrast with the sparsely connected, continuous sheet of the cortex). In this study, we modeled a sheet of cortical neurons with sparse, primarily local connections, and found that a network with this structure could encode multiple internal state variables with high signal-to-noise ratio. However, we were unable to create high-fidelity networks by instantiating connections at random according to spatial connection probabilities. In our models, high-fidelity networks required additional structure, with higher cluster factors and correlations between the inputs to nearby neurons.

Effects of urban sprawl on obesity.

PubMed

Zhao, Zhenxiang; Kaestner, Robert

2010-12-01

In this paper, we examine the effect of changes in population density-urban sprawl-between 1970 and 2000 on BMI and obesity of residents in metropolitan areas in the U.S. We address the possible endogeneity of population density by using a two-step instrumental variables approach. We exploit the plausibly exogenous variation in population density caused by the expansion of the U.S. Interstate Highway System, which largely followed the original 1947 plan for the Interstate Highway System. We find a negative association between population density and obesity, and estimates are robust across a wide range of specifications. Estimates indicate that if the average metropolitan area had not experienced the decline in the proportion of population living in dense areas over the last 30 years, the rate of obesity would have been reduced by approximately 13%. Copyright © 2010 Elsevier B.V. All rights reserved.

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

Vassilevska, Tanya

This is the first code, designed to run on a desktop, which models the intracellular replication and the cell-to-cell infection and demonstrates virus evolution at the molecular level. This code simulates the infection of a population of "idealized biological cells" (represented as objects that do not divide or have metabolism) with "virus" (represented by its genetic sequence), the replication and simultaneous mutation of the virus which leads to evolution of the population of genetically diverse viruses. The code is built to simulate single-stranded RNA viruses. The input for the code is 1. the number of biological cells in the culture,more » 2. the initial composition of the virus population, 3. the reference genome of the RNA virus, 4. the coordinates of the genome regions and their significance and, 5. parameters determining the dynamics of virus replication, such as the mutation rate. The simulation ends when all cells have been infected or when no more infections occurs after a given number of attempts. The code has the ability to simulate the evolution of the virus in serial passage of cell "cultures", i.e. after the end of a simulation, a new one is immediately scheduled with a new culture of infected cells. The code outputs characteristics of the resulting virus population dynamics and genetic composition of the virus population, such as the top dominant genomes, percentage of a genome with specific characteristics.« less

On the formation mechanisms of compact elliptical galaxies

NASA Astrophysics Data System (ADS)

Ferré-Mateu, Anna; Forbes, Duncan A.; Romanowsky, Aaron J.; Janz, Joachim; Dixon, Christopher

2018-01-01

In order to investigate the formation mechanisms of the rare compact elliptical (cE) galaxies, we have compiled a sample of 25 cEs with good SDSS spectra, covering a range of stellar masses, sizes and environments. They have been visually classified according to the interaction with their host, representing different evolutionary stages. We have included clearly disrupted galaxies, galaxies that despite not showing signs of interaction are located close to a massive neighbour (thus are good candidates for a stripping process), and cEs with no host nearby. For the latter, tidal stripping is less likely to have happened and instead they could simply represent the very low-mass, faint end of the ellipticals. We study a set of properties (structural parameters, stellar populations, star formation histories and mass ratios) that can be used to discriminate between an intrinsic or stripped origin. We find that one diagnostic tool alone is inconclusive for the majority of objects. However, if we combine all the tools a clear picture emerges. The most plausible origin, as well as the evolutionary stage and progenitor type, can be then determined. Our results favour the stripping mechanism for those galaxies in groups and clusters that have a plausible host nearby, but favours an intrinsic origin for those rare cEs without a plausible host and that are located in looser environments.

Why do you fear the bogeyman? An embodied predictive coding model of perceptual inference.

PubMed

Pezzulo, Giovanni

2014-09-01

Why are we scared by nonperceptual entities such as the bogeyman, and why does the bogeyman only visit us during the night? Why does hearing a window squeaking in the night suggest to us the unlikely idea of a thief or a killer? And why is this more likely to happen after watching a horror movie? To answer these and similar questions, we need to put mind and body together again and consider the embodied nature of perceptual and cognitive inference. Predictive coding provides a general framework for perceptual inference; I propose to extend it by including interoceptive and bodily information. The resulting embodied predictive coding inference permits one to compare alternative hypotheses (e.g., is the sound I hear generated by a thief or the wind?) using the same inferential scheme as in predictive coding, but using both sensory and interoceptive information as evidence, rather than just considering sensory events. If you hear a window squeaking in the night after watching a horror movie, you may consider plausible a very unlikely hypothesis (e.g., a thief, or even the bogeyman) because it explains both what you sense (e.g., the window squeaking in the night) and how you feel (e.g., your high heart rate). The good news is that the inference that I propose is fully rational and gives minds and bodies equal dignity. The bad news is that it also gives an embodiment to the bogeyman, and a reason to fear it.

Slow Feature Analysis on Retinal Waves Leads to V1 Complex Cells

PubMed Central

Dähne, Sven; Wilbert, Niko; Wiskott, Laurenz

2014-01-01

The developing visual system of many mammalian species is partially structured and organized even before the onset of vision. Spontaneous neural activity, which spreads in waves across the retina, has been suggested to play a major role in these prenatal structuring processes. Recently, it has been shown that when employing an efficient coding strategy, such as sparse coding, these retinal activity patterns lead to basis functions that resemble optimal stimuli of simple cells in primary visual cortex (V1). Here we present the results of applying a coding strategy that optimizes for temporal slowness, namely Slow Feature Analysis (SFA), to a biologically plausible model of retinal waves. Previously, SFA has been successfully applied to model parts of the visual system, most notably in reproducing a rich set of complex-cell features by training SFA with quasi-natural image sequences. In the present work, we obtain SFA units that share a number of properties with cortical complex-cells by training on simulated retinal waves. The emergence of two distinct properties of the SFA units (phase invariance and orientation tuning) is thoroughly investigated via control experiments and mathematical analysis of the input-output functions found by SFA. The results support the idea that retinal waves share relevant temporal and spatial properties with natural visual input. Hence, retinal waves seem suitable training stimuli to learn invariances and thereby shape the developing early visual system such that it is best prepared for coding input from the natural world. PMID:24810948

Resolving Conflicts Between Syntax and Plausibility in Sentence Comprehension

PubMed Central

Andrews, Glenda; Ogden, Jessica E.; Halford, Graeme S.

2017-01-01

Comprehension of plausible and implausible object- and subject-relative clause sentences with and without prepositional phrases was examined. Undergraduates read each sentence then evaluated a statement as consistent or inconsistent with the sentence. Higher acceptance of consistent than inconsistent statements indicated reliance on syntactic analysis. Higher acceptance of plausible than implausible statements reflected reliance on semantic plausibility. There was greater reliance on semantic plausibility and lesser reliance on syntactic analysis for more complex object-relatives and sentences with prepositional phrases than for less complex subject-relatives and sentences without prepositional phrases. Comprehension accuracy and confidence were lower when syntactic analysis and semantic plausibility yielded conflicting interpretations. The conflict effect on comprehension was significant for complex sentences but not for less complex sentences. Working memory capacity predicted resolution of the syntax-plausibility conflict in more and less complex items only when sentences and statements were presented sequentially. Fluid intelligence predicted resolution of the conflict in more and less complex items under sequential and simultaneous presentation. Domain-general processes appear to be involved in resolving syntax-plausibility conflicts in sentence comprehension. PMID:28458748

Direction-selective circuits shape noise to ensure a precise population code

PubMed Central

Zylberberg, Joel; Cafaro, Jon; Turner, Maxwell H

2016-01-01

Summary Neural responses are noisy, and circuit structure can correlate this noise across neurons. Theoretical studies show that noise correlations can have diverse effects on population coding, but these studies rarely explore stimulus dependence of noise correlations. Here, we show that noise correlations in responses of ON-OFF direction-selective retinal ganglion cells are strongly stimulus dependent and we uncover the circuit mechanisms producing this stimulus dependence. A population model based on these mechanistic studies shows that stimulus-dependent noise correlations improve the encoding of motion direction two-fold compared to independent noise. This work demonstrates a mechanism by which a neural circuit effectively shapes its signal and noise in concert, minimizing corruption of signal by noise. Finally, we generalize our findings beyond direction coding in the retina and show that stimulus-dependent correlations will generally enhance information coding in populations of diversely tuned neurons. PMID:26796691

Occupational self-coding and automatic recording (OSCAR): a novel web-based tool to collect and code lifetime job histories in large population-based studies.

PubMed

De Matteis, Sara; Jarvis, Deborah; Young, Heather; Young, Alan; Allen, Naomi; Potts, James; Darnton, Andrew; Rushton, Lesley; Cullinan, Paul

2017-03-01

Objectives The standard approach to the assessment of occupational exposures is through the manual collection and coding of job histories. This method is time-consuming and costly and makes it potentially unfeasible to perform high quality analyses on occupational exposures in large population-based studies. Our aim was to develop a novel, efficient web-based tool to collect and code lifetime job histories in the UK Biobank, a population-based cohort of over 500 000 participants. Methods We developed OSCAR (occupations self-coding automatic recording) based on the hierarchical structure of the UK Standard Occupational Classification (SOC) 2000, which allows individuals to collect and automatically code their lifetime job histories via a simple decision-tree model. Participants were asked to find each of their jobs by selecting appropriate job categories until they identified their job title, which was linked to a hidden 4-digit SOC code. For each occupation a job title in free text was also collected to estimate Cohen's kappa (κ) inter-rater agreement between SOC codes assigned by OSCAR and an expert manual coder. Results OSCAR was administered to 324 653 UK Biobank participants with an existing email address between June and September 2015. Complete 4-digit SOC-coded lifetime job histories were collected for 108 784 participants (response rate: 34%). Agreement between the 4-digit SOC codes assigned by OSCAR and the manual coder for a random sample of 400 job titles was moderately good [κ=0.45, 95% confidence interval (95% CI) 0.42-0.49], and improved when broader job categories were considered (κ=0.64, 95% CI 0.61-0.69 at a 1-digit SOC-code level). Conclusions OSCAR is a novel, efficient, and reasonably reliable web-based tool for collecting and automatically coding lifetime job histories in large population-based studies. Further application in other research projects for external validation purposes is warranted.

Counterfactual Plausibility and Comparative Similarity.

PubMed

Stanley, Matthew L; Stewart, Gregory W; Brigard, Felipe De

2017-05-01

Counterfactual thinking involves imagining hypothetical alternatives to reality. Philosopher David Lewis (1973, 1979) argued that people estimate the subjective plausibility that a counterfactual event might have occurred by comparing an imagined possible world in which the counterfactual statement is true against the current, actual world in which the counterfactual statement is false. Accordingly, counterfactuals considered to be true in possible worlds comparatively more similar to ours are judged as more plausible than counterfactuals deemed true in possible worlds comparatively less similar. Although Lewis did not originally develop his notion of comparative similarity to be investigated as a psychological construct, this study builds upon his idea to empirically investigate comparative similarity as a possible psychological strategy for evaluating the perceived plausibility of counterfactual events. More specifically, we evaluate judgments of comparative similarity between episodic memories and episodic counterfactual events as a factor influencing people's judgments of plausibility in counterfactual simulations, and we also compare it against other factors thought to influence judgments of counterfactual plausibility, such as ease of simulation and prior simulation. Our results suggest that the greater the perceived similarity between the original memory and the episodic counterfactual event, the greater the perceived plausibility that the counterfactual event might have occurred. While similarity between actual and counterfactual events, ease of imagining, and prior simulation of the counterfactual event were all significantly related to counterfactual plausibility, comparative similarity best captured the variance in ratings of counterfactual plausibility. Implications for existing theories on the determinants of counterfactual plausibility are discussed. Copyright © 2016 Cognitive Science Society, Inc.

Derivation of strontium-90 and cesium-137 residual radioactive material guidelines for the Laboratory for Energy-Related Health Research, University of California, Davis

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

Nimmagadda, M.; Yu, C.

1993-04-01

Residual radioactive material guidelines for strontium-90 and cesium-137 were derived for the Laboratory for Energy-Related Health Research (LEHR) site in Davis, California. The guideline derivation was based on a dose limit of 100 mrem/yr. The US Department of Energy (DOE) residual radioactive material guideline computer code, RESRAD, was used in this evaluation; this code implements the methodology described in the DOE manual for implementing residual radioactive material guidelines. Three potential site utilization scenarios were considered with the assumption that, for a period of 1,000 years following remedial action, the site will be utilized without radiological restrictions. The defined scenarios varymore » with regard to use of the site, time spent at the site, and sources of food consumed. The results of the evaluation indicate that the basic dose limit of 100 mrem/yr will not be exceeded within 1,000 years for either strontium-90 or cesium-137, provided that the soil concentrations of these radionuclides at the LEHR site do not exceed the following levels: 71,000 pCi/g for strontium-90 and 91 pCi/g for cesium-137 for Scenario A (researcher: the expected scenario); 160,000 pCi/g for strontium-90 and 220 pCi/g for cesium-137 for Scenario B (recreationist: a plausible scenario); and 37 pCi/g for strontium-90 and 32 pCi/g for cesium-137 for Scenario C (resident farmer ingesting food produced in the contaminated area: a plausible scenario). The derived guidelines are single-radionuclide guidelines and are linearly proportional to the dose limit used in the calculations. In setting the actual strontium-90 and cesium-137 guidelines for the LEHR site, DOE will apply the as low as reasonably achievable (ALARA) policy to the decision-making process, along with other factors such as whether a particular scenario is reasonable and appropriate.« less

Diagnosing the dangerous demography of manta rays using life history theory.

PubMed

Dulvy, Nicholas K; Pardo, Sebastián A; Simpfendorfer, Colin A; Carlson, John K

2014-01-01

Background. The directed harvest and global trade in the gill plates of mantas, and devil rays, has led to increased fishing pressure and steep population declines in some locations. The slow life history, particularly of the manta rays, is cited as a key reason why such species have little capacity to withstand directed fisheries. Here, we place their life history and demography within the context of other sharks and rays. Methods. Despite the limited availability of data, we use life history theory and comparative analysis to estimate the intrinsic risk of extinction (as indexed by the maximum intrinsic rate of population increase r max) for a typical generic manta ray using a variant of the classic Euler-Lotka demographic model. This model requires only three traits to calculate the maximum intrinsic population growth rate r max: von Bertalanffy growth rate, annual pup production and age at maturity. To account for the uncertainty in life history parameters, we created plausible parameter ranges and propagate these uncertainties through the model to calculate a distribution of the plausible range of r max values. Results. The maximum population growth rate r max of manta ray is most sensitive to the length of the reproductive cycle, and the median r max of 0.116 year(-1) 95th percentile [0.089-0.139] is one of the lowest known of the 106 sharks and rays for which we have comparable demographic information. Discussion. In common with other unprotected, unmanaged, high-value large-bodied sharks and rays the combination of very low population growth rates of manta rays, combined with the high value of their gill rakers and the international nature of trade, is highly likely to lead to rapid depletion and potential local extinction unless a rapid conservation management response occurs worldwide. Furthermore, we show that it is possible to derive important insights into the demography extinction risk of data-poor species using well-established life history theory.

Diagnosing the dangerous demography of manta rays using life history theory

PubMed Central

Pardo, Sebastián A.; Simpfendorfer, Colin A.; Carlson, John K.

2014-01-01

Background. The directed harvest and global trade in the gill plates of mantas, and devil rays, has led to increased fishing pressure and steep population declines in some locations. The slow life history, particularly of the manta rays, is cited as a key reason why such species have little capacity to withstand directed fisheries. Here, we place their life history and demography within the context of other sharks and rays. Methods. Despite the limited availability of data, we use life history theory and comparative analysis to estimate the intrinsic risk of extinction (as indexed by the maximum intrinsic rate of population increase rmax) for a typical generic manta ray using a variant of the classic Euler–Lotka demographic model. This model requires only three traits to calculate the maximum intrinsic population growth rate rmax: von Bertalanffy growth rate, annual pup production and age at maturity. To account for the uncertainty in life history parameters, we created plausible parameter ranges and propagate these uncertainties through the model to calculate a distribution of the plausible range of rmax values. Results. The maximum population growth rate rmax of manta ray is most sensitive to the length of the reproductive cycle, and the median rmax of 0.116 year−1 95th percentile [0.089–0.139] is one of the lowest known of the 106 sharks and rays for which we have comparable demographic information. Discussion. In common with other unprotected, unmanaged, high-value large-bodied sharks and rays the combination of very low population growth rates of manta rays, combined with the high value of their gill rakers and the international nature of trade, is highly likely to lead to rapid depletion and potential local extinction unless a rapid conservation management response occurs worldwide. Furthermore, we show that it is possible to derive important insights into the demography extinction risk of data-poor species using well-established life history theory. PMID:24918029

POPCORN: A comparison of binary population synthesis codes

NASA Astrophysics Data System (ADS)

Claeys, J. S. W.; Toonen, S.; Mennekens, N.

2013-01-01

We compare the results of three binary population synthesis codes to understand the differences in their results. As a first result we find that when equalizing the assumptions the results are similar. The main differences arise from deviating physical input.

Amygdaloid and non-amygdaloid fear both influence avoidance of risky foraging in hungry rats

PubMed Central

Kim, Earnest; Kim, Eun Joo; Yeh, Regina; Shin, Minkyung; Bobman, Jake; Krasne, Franklin B.; Kim, Jeansok J.

2014-01-01

Considerable evidence seems to show that emotional and reflex reactions to feared situations are mediated by the amygdala. It might therefore seem plausible to expect that amygdala-coded fear should also influence decisions when animals make choices about instrumental actions. However, there is not good evidence of this. In particular, it appears, though the literature is conflicted, that once learning is complete, the amygdala may often not be involved in instrumental avoidance behaviours. It is therefore of interest that we have found in rats living for extended periods in a semi-naturalistic ‘closed economy’, where they were given random shocks in regions that had to be entered to obtain food, choices about feeding behaviour were in fact influenced by amygdala-coded fear, in spite of the null effect of amygdalar lesions on fear of dangerous location per se. We suggest that avoidance of highly motivated voluntary behaviour does depend in part on fear signals originating in the amygdala. Such signalling may be one role of well-known projections from amygdala to cortico-striate circuitry. PMID:25056616

Rank Order Coding: a Retinal Information Decoding Strategy Revealed by Large-Scale Multielectrode Array Retinal Recordings.

PubMed

Portelli, Geoffrey; Barrett, John M; Hilgen, Gerrit; Masquelier, Timothée; Maccione, Alessandro; Di Marco, Stefano; Berdondini, Luca; Kornprobst, Pierre; Sernagor, Evelyne

2016-01-01

How a population of retinal ganglion cells (RGCs) encodes the visual scene remains an open question. Going beyond individual RGC coding strategies, results in salamander suggest that the relative latencies of a RGC pair encode spatial information. Thus, a population code based on this concerted spiking could be a powerful mechanism to transmit visual information rapidly and efficiently. Here, we tested this hypothesis in mouse by recording simultaneous light-evoked responses from hundreds of RGCs, at pan-retinal level, using a new generation of large-scale, high-density multielectrode array consisting of 4096 electrodes. Interestingly, we did not find any RGCs exhibiting a clear latency tuning to the stimuli, suggesting that in mouse, individual RGC pairs may not provide sufficient information. We show that a significant amount of information is encoded synergistically in the concerted spiking of large RGC populations. Thus, the RGC population response described with relative activities, or ranks, provides more relevant information than classical independent spike count- or latency- based codes. In particular, we report for the first time that when considering the relative activities across the whole population, the wave of first stimulus-evoked spikes is an accurate indicator of stimulus content. We show that this coding strategy coexists with classical neural codes, and that it is more efficient and faster. Overall, these novel observations suggest that already at the level of the retina, concerted spiking provides a reliable and fast strategy to rapidly transmit new visual scenes.

Scheduling Future Water Supply Investments Under Uncertainty

NASA Astrophysics Data System (ADS)

Huskova, I.; Matrosov, E. S.; Harou, J. J.; Kasprzyk, J. R.; Reed, P. M.

2014-12-01

Uncertain hydrological impacts of climate change, population growth and institutional changes pose a major challenge to planning of water supply systems. Planners seek optimal portfolios of supply and demand management schemes but also when to activate assets whilst considering many system goals and plausible futures. Incorporation of scheduling into the planning under uncertainty problem strongly increases its complexity. We investigate some approaches to scheduling with many-objective heuristic search. We apply a multi-scenario many-objective scheduling approach to the Thames River basin water supply system planning problem in the UK. Decisions include which new supply and demand schemes to implement, at what capacity and when. The impact of different system uncertainties on scheme implementation schedules are explored, i.e. how the choice of future scenarios affects the search process and its outcomes. The activation of schemes is influenced by the occurrence of extreme hydrological events in the ensemble of plausible scenarios and other factors. The approach and results are compared with a previous study where only the portfolio problem is addressed (without scheduling).

When plausibility manipulations work: an examination of their role in the development of false beliefs and memories.

PubMed

Bays, Rebecca B; Zabrucky, Karen M; Gagne, Phill

2012-01-01

In the current study we examined whether prevalence information and imagery encoding influence participants' general plausibility, personal plausibility, belief, and memory ratings for suggested childhood events. Results showed decreases in general and personal plausibility ratings for low prevalence events when encoding instructions were not elaborate; however, instructions to repeatedly imagine suggested events elicited personal plausibility increases for low-prevalence events, evidence that elaborate imagery negated the effect of our prevalence manipulation. We found no evidence of imagination inflation or false memory construction. We discuss critical differences in researchers' manipulations of plausibility and imagery that may influence results of false memory studies in the literature. In future research investigators should focus on the specific nature of encoding instructions when examining the development of false memories.

Auralization of concert hall acoustics using finite difference time domain methods and wave field synthesis

NASA Astrophysics Data System (ADS)

Hochgraf, Kelsey

Auralization methods have been used for a long time to simulate the acoustics of a concert hall for different seat positions. The goal of this thesis was to apply the concept of auralization to a larger audience area that the listener could walk through to compare differences in acoustics for a wide range of seat positions. For this purpose, the acoustics of Rensselaer's Experimental Media and Performing Arts Center (EMPAC) Concert Hall were simulated to create signals for a 136 channel wave field synthesis (WFS) system located at Rensselaer's Collaborative Research Augmented Immersive Virtual Environment (CRAIVE) Laboratory. By allowing multiple people to dynamically experience the concert hall's acoustics at the same time, this research gained perspective on what is important for achieving objective accuracy and subjective plausibility in an auralization. A finite difference time domain (FDTD) simulation on a three-dimensional face-centered cubic grid, combined at a crossover frequency of 800 Hz with a CATT-Acoustic(TM) simulation, was found to have a reverberation time, direct to reverberant sound energy ratio, and early reflection pattern that more closely matched measured data from the hall compared to a CATT-Acoustic(TM) simulation and other hybrid simulations. In the CRAIVE lab, nine experienced listeners found all hybrid auralizations (with varying source location, grid resolution, crossover frequency, and number of loudspeakers) to be more perceptually plausible than the CATT-Acoustic(TM) auralization. The FDTD simulation required two days to compute, while the CATT-Acoustic(TM) simulation required three separate TUCT(TM) computations, each taking four hours, to accommodate the large number of receivers. Given the perceptual advantages realized with WFS for auralization of a large, inhomogeneous sound field, it is recommended that hybrid simulations be used in the future to achieve more accurate and plausible auralizations. Predictions are made for a parallelized version of the simulation code that could achieve such auralizations in less than one hour, making the tool practical for everyday application.

Local variations in the timing of RSV epidemics.

PubMed

Noveroske, Douglas B; Warren, Joshua L; Pitzer, Virginia E; Weinberger, Daniel M

2016-11-11

Respiratory syncytial virus (RSV) is a primary cause of hospitalizations in children worldwide. The timing of seasonal RSV epidemics needs to be known in order to administer prophylaxis to high-risk infants at the appropriate time. We used data from the Connecticut State Inpatient Database to identify RSV hospitalizations based on ICD-9 diagnostic codes. Harmonic regression analyses were used to evaluate RSV epidemic timing at the county level and ZIP code levels. Linear regression was used to investigate associations between the socioeconomic status of a locality and RSV epidemic timing. 9,740 hospitalizations coded as RSV occurred among children less than 2 years old between July 1, 1997 and June 30, 2013. The earliest ZIP code had a seasonal RSV epidemic that peaked, on average, 4.64 weeks earlier than the latest ZIP code. Earlier epidemic timing was significantly associated with demographic characteristics (higher population density and larger fraction of the population that was black). Seasonal RSV epidemics in Connecticut occurred earlier in areas that were more urban (higher population density and larger fraction of the population that was). These findings could be used to better time the administration of prophylaxis to high-risk infants.

Evolution of a predator-induced, nonlinear reaction norm.

PubMed

Carter, Mauricio J; Lind, Martin I; Dennis, Stuart R; Hentley, William; Beckerman, Andrew P

2017-08-30

Inducible, anti-predator traits are a classic example of phenotypic plasticity. Their evolutionary dynamics depend on their genetic basis, the historical pattern of predation risk that populations have experienced and current selection gradients. When populations experience predators with contrasting hunting strategies and size preferences, theory suggests contrasting micro-evolutionary responses to selection. Daphnia pulex is an ideal species to explore the micro-evolutionary response of anti-predator traits because they face heterogeneous predation regimes, sometimes experiencing only invertebrate midge predators and other times experiencing vertebrate fish and invertebrate midge predators. We explored plausible patterns of adaptive evolution of a predator-induced morphological reaction norm. We combined estimates of selection gradients that characterize the various habitats that D. pulex experiences with detail on the quantitative genetic architecture of inducible morphological defences. Our data reveal a fine scale description of daphnid defensive reaction norms, and a strong covariance between the sensitivity to cues and the maximum response to cues. By analysing the response of the reaction norm to plausible, predator-specific selection gradients, we show how in the context of this covariance, micro-evolution may be more uniform than predicted from size-selective predation theory. Our results show how covariance between the sensitivity to cues and the maximum response to cues for morphological defence can shape the evolutionary trajectory of predator-induced defences in D. pulex . © 2017 The Authors.

Sensory Afferents Use Different Coding Strategies for Heat and Cold.

PubMed

Wang, Feng; Bélanger, Erik; Côté, Sylvain L; Desrosiers, Patrick; Prescott, Steven A; Côté, Daniel C; De Koninck, Yves

2018-05-15

Primary afferents transduce environmental stimuli into electrical activity that is transmitted centrally to be decoded into corresponding sensations. However, it remains unknown how afferent populations encode different somatosensory inputs. To address this, we performed two-photon Ca 2+ imaging from thousands of dorsal root ganglion (DRG) neurons in anesthetized mice while applying mechanical and thermal stimuli to hind paws. We found that approximately half of all neurons are polymodal and that heat and cold are encoded very differently. As temperature increases, more heating-sensitive neurons are activated, and most individual neurons respond more strongly, consistent with graded coding at population and single-neuron levels, respectively. In contrast, most cooling-sensitive neurons respond in an ungraded fashion, inconsistent with graded coding and suggesting combinatorial coding, based on which neurons are co-activated. Although individual neurons may respond to multiple stimuli, our results show that different stimuli activate distinct combinations of diversely tuned neurons, enabling rich population-level coding. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

Modelling Trial-by-Trial Changes in the Mismatch Negativity

PubMed Central

Lieder, Falk; Daunizeau, Jean; Garrido, Marta I.; Friston, Karl J.; Stephan, Klaas E.

2013-01-01

The mismatch negativity (MMN) is a differential brain response to violations of learned regularities. It has been used to demonstrate that the brain learns the statistical structure of its environment and predicts future sensory inputs. However, the algorithmic nature of these computations and the underlying neurobiological implementation remain controversial. This article introduces a mathematical framework with which competing ideas about the computational quantities indexed by MMN responses can be formalized and tested against single-trial EEG data. This framework was applied to five major theories of the MMN, comparing their ability to explain trial-by-trial changes in MMN amplitude. Three of these theories (predictive coding, model adjustment, and novelty detection) were formalized by linking the MMN to different manifestations of the same computational mechanism: approximate Bayesian inference according to the free-energy principle. We thereby propose a unifying view on three distinct theories of the MMN. The relative plausibility of each theory was assessed against empirical single-trial MMN amplitudes acquired from eight healthy volunteers in a roving oddball experiment. Models based on the free-energy principle provided more plausible explanations of trial-by-trial changes in MMN amplitude than models representing the two more traditional theories (change detection and adaptation). Our results suggest that the MMN reflects approximate Bayesian learning of sensory regularities, and that the MMN-generating process adjusts a probabilistic model of the environment according to prediction errors. PMID:23436989

Validation of a Novel Molecular Host Response Assay to Diagnose Infection in Hospitalized Patients Admitted to the ICU With Acute Respiratory Failure.

PubMed

Koster-Brouwer, Maria E; Verboom, Diana M; Scicluna, Brendon P; van de Groep, Kirsten; Frencken, Jos F; Janssen, Davy; Schuurman, Rob; Schultz, Marcus J; van der Poll, Tom; Bonten, Marc J M; Cremer, Olaf L

2018-03-01

Discrimination between infectious and noninfectious causes of acute respiratory failure is difficult in patients admitted to the ICU after a period of hospitalization. Using a novel biomarker test (SeptiCyte LAB), we aimed to distinguish between infection and inflammation in this population. Nested cohort study. Two tertiary mixed ICUs in the Netherlands. Hospitalized patients with acute respiratory failure requiring mechanical ventilation upon ICU admission from 2011 to 2013. Patients having an established infection diagnosis or an evidently noninfectious reason for intubation were excluded. None. Blood samples were collected upon ICU admission. Test results were categorized into four probability bands (higher bands indicating higher infection probability) and compared with the infection plausibility as rated by post hoc assessment using strict definitions. Of 467 included patients, 373 (80%) were treated for a suspected infection at admission. Infection plausibility was classified as ruled out, undetermined, or confirmed in 135 (29%), 135 (29%), and 197 (42%) patients, respectively. Test results correlated with infection plausibility (Spearman's rho 0.332; p < 0.001). After exclusion of undetermined cases, positive predictive values were 29%, 54%, and 76% for probability bands 2, 3, and 4, respectively, whereas the negative predictive value for band 1 was 76%. Diagnostic discrimination of SeptiCyte LAB and C-reactive protein was similar (p = 0.919). Among hospitalized patients admitted to the ICU with clinical uncertainty regarding the etiology of acute respiratory failure, the diagnostic value of SeptiCyte LAB was limited.

Robust information propagation through noisy neural circuits

PubMed Central

Pouget, Alexandre

2017-01-01

Sensory neurons give highly variable responses to stimulation, which can limit the amount of stimulus information available to downstream circuits. Much work has investigated the factors that affect the amount of information encoded in these population responses, leading to insights about the role of covariability among neurons, tuning curve shape, etc. However, the informativeness of neural responses is not the only relevant feature of population codes; of potentially equal importance is how robustly that information propagates to downstream structures. For instance, to quantify the retina’s performance, one must consider not only the informativeness of the optic nerve responses, but also the amount of information that survives the spike-generating nonlinearity and noise corruption in the next stage of processing, the lateral geniculate nucleus. Our study identifies the set of covariance structures for the upstream cells that optimize the ability of information to propagate through noisy, nonlinear circuits. Within this optimal family are covariances with “differential correlations”, which are known to reduce the information encoded in neural population activities. Thus, covariance structures that maximize information in neural population codes, and those that maximize the ability of this information to propagate, can be very different. Moreover, redundancy is neither necessary nor sufficient to make population codes robust against corruption by noise: redundant codes can be very fragile, and synergistic codes can—in some cases—optimize robustness against noise. PMID:28419098

Decoding and optimized implementation of SECDED codes over GF(q)

DOEpatents

Ward, H. Lee; Ganti, Anand; Resnick, David R

2013-10-22

A plurality of columns for a check matrix that implements a distance d linear error correcting code are populated by providing a set of vectors from which to populate the columns, and applying to the set of vectors a filter operation that reduces the set by eliminating therefrom all vectors that would, if used to populate the columns, prevent the check matrix from satisfying a column-wise linear independence requirement associated with check matrices of distance d linear codes. One of the vectors from the reduced set may then be selected to populate one of the columns. The filtering and selecting repeats iteratively until either all of the columns are populated or the number of currently unpopulated columns exceeds the number of vectors in the reduced set. Columns for the check matrix may be processed to reduce the amount of logic needed to implement the check matrix in circuit logic.

Design, decoding and optimized implementation of SECDED codes over GF(q)

DOEpatents

Ward, H Lee; Ganti, Anand; Resnick, David R

2014-06-17

A plurality of columns for a check matrix that implements a distance d linear error correcting code are populated by providing a set of vectors from which to populate the columns, and applying to the set of vectors a filter operation that reduces the set by eliminating therefrom all vectors that would, if used to populate the columns, prevent the check matrix from satisfying a column-wise linear independence requirement associated with check matrices of distance d linear codes. One of the vectors from the reduced set may then be selected to populate one of the columns. The filtering and selecting repeats iteratively until either all of the columns are populated or the number of currently unpopulated columns exceeds the number of vectors in the reduced set. Columns for the check matrix may be processed to reduce the amount of logic needed to implement the check matrix in circuit logic.

Decoding and optimized implementation of SECDED codes over GF(q)

DOEpatents

Ward, H Lee; Ganti, Anand; Resnick, David R

2014-11-18

A plurality of columns for a check matrix that implements a distance d linear error correcting code are populated by providing a set of vectors from which to populate the columns, and applying to the set of vectors a filter operation that reduces the set by eliminating therefrom all vectors that would, if used to populate the columns, prevent the check matrix from satisfying a column-wise linear independence requirement associated with check matrices of distance d linear codes. One of the vectors from the reduced set may then be selected to populate one of the columns. The filtering and selecting repeats iteratively until either all of the columns are populated or the number of currently unpopulated columns exceeds the number of vectors in the reduced set. Columns for the check matrix may be processed to reduce the amount of logic needed to implement the check matrix in circuit logic.

Food Self-Sufficiency across scales: How local can we go?

NASA Astrophysics Data System (ADS)

Pradhan, Prajal; Lüdeke, Matthias K. B.; Reusser, Dominik E.; Kropp, Jürgen P.

2013-04-01

"Think global, act local" is a phrase often used in sustainability debates. Here, we explore the potential of regions to go for local supply in context of sustainable food consumption considering both the present state and the plausible future scenarios. We analyze data on the gridded crop calories production, the gridded livestock calories production, the gridded feed calories use and the gridded food calories consumption in 5' resolution. We derived these gridded data from various sources: Global Agro-ecological Zone (GAEZ v3.0), Gridded Livestock of the World (GLW), FAOSTAT, and Global Rural-Urban Mapping Project (GRUMP). For scenarios analysis, we considered changes in population, dietary patterns and possibility of obtaining the maximum potential yield. We investigate the food self-sufficiency multiple spatial scales. We start from the 5' resolution (i.e. around 10 km x 10 km in the equator) and look at 8 levels of aggregation ranging from the plausible lowest administrative level to the continental level. Results for the different spatial scales show that about 1.9 billion people live in the area of 5' resolution where enough calories can be produced to sustain their food consumption and the feed used. On the country level, about 4.4 billion population can be sustained without international food trade. For about 1 billion population from Asia and Africa, there is a need for cross-continental food trade. However, if we were able to achieve the maximum potential crop yield, about 2.6 billion population can be sustained within their living area of 5' resolution. Furthermore, Africa and Asia could be food self-sufficient by achieving their maximum potential crop yield and only round 630 million populations would be dependent on the international food trade. However, the food self-sufficiency status might differ under consideration of the future change in population, dietary patterns and climatic conditions. We provide an initial approach for investigating the regional and the local potential to address food security across multiple spatial scales. We identify the areas where one can depend more on local/regional products as a transition path towards sustainable consumption and production.

Insights Gained from Forensic Analysis with MELCOR of the Fukushima-Daiichi Accidents.

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

Andrews, Nathan C.; Gauntt, Randall O.

Since the accidents at Fukushima-Daiichi, Sandia National Laboratories has been modeling these accident scenarios using the severe accident analysis code, MELCOR. MELCOR is a widely used computer code developed at Sandia National Laboratories since ~1982 for the U.S. Nuclear Regulatory Commission. Insights from the modeling of these accidents is being used to better inform future code development and potentially improved accident management. To date, our necessity to better capture in-vessel thermal-hydraulic and ex-vessel melt coolability and concrete interactions has led to the implementation of new models. The most recent analyses, presented in this paper, have been in support of themore » of the Organization for Economic Cooperation and Development Nuclear Energy Agency’s (OECD/NEA) Benchmark Study of the Accident at the Fukushima Daiichi Nuclear Power Station (BSAF) Project. The goal of this project is to accurately capture the source term from all three releases and then model the atmospheric dispersion. In order to do this, a forensic approach is being used in which available plant data and release timings is being used to inform the modeled MELCOR accident scenario. For example, containment failures, core slumping events and lower head failure timings are all enforced parameters in these analyses. This approach is fundamentally different from a blind code assessment analysis often used in standard problem exercises. The timings of these events are informed by representative spikes or decreases in plant data. The combination of improvements to the MELCOR source code resulting from analysis previous accident analysis and this forensic approach has allowed Sandia to generate representative and plausible source terms for all three accidents at Fukushima Daiichi out to three weeks after the accident to capture both early and late releases. In particular, using the source terms developed by MELCOR, the MACCS software code, which models atmospheric dispersion and deposition, we are able to reasonably capture the deposition of radionuclides to the northwest of the reactor site.« less

The artificial zinc finger coding gene 'Jazz' binds the utrophin promoter and activates transcription.

PubMed

Corbi, N; Libri, V; Fanciulli, M; Tinsley, J M; Davies, K E; Passananti, C

2000-06-01

Up-regulation of utrophin gene expression is recognized as a plausible therapeutic approach in the treatment of Duchenne muscular dystrophy (DMD). We have designed and engineered new zinc finger-based transcription factors capable of binding and activating transcription from the promoter of the dystrophin-related gene, utrophin. Using the recognition 'code' that proposes specific rules between zinc finger primary structure and potential DNA binding sites, we engineered a new gene named 'Jazz' that encodes for a three-zinc finger peptide. Jazz belongs to the Cys2-His2 zinc finger type and was engineered to target the nine base pair DNA sequence: 5'-GCT-GCT-GCG-3', present in the promoter region of both the human and mouse utrophin gene. The entire zinc finger alpha-helix region, containing the amino acid positions that are crucial for DNA binding, was specifically chosen on the basis of the contacts more frequently represented in the available list of the 'code'. Here we demonstrate that Jazz protein binds specifically to the double-stranded DNA target, with a dissociation constant of about 32 nM. Band shift and super-shift experiments confirmed the high affinity and specificity of Jazz protein for its DNA target. Moreover, we show that chimeric proteins, named Gal4-Jazz and Sp1-Jazz, are able to drive the transcription of a test gene from the human utrophin promoter.

Galaxy formation and physical bias

NASA Technical Reports Server (NTRS)

Cen, Renyue; Ostriker, Jeremiah P.

1992-01-01

We have supplemented our code, which computes the evolution of the physical state of a representative piece of the universe to include, not only the dynamics of dark matter (with a standard PM code), and the hydrodynamics of the gaseous component (including detailed collisional and radiative processes), but also galaxy formation on a heuristic but plausible basis. If, within a cell the gas is Jeans' unstable, collapsing, and cooling rapidly, it is transformed to galaxy subunits, which are then followed with a collisionless code. After grouping them into galaxies, we estimate the relative distributions of galaxies and dark matter and the relative velocities of galaxies and dark matter. In a large scale CDM run of 80/h Mpc size with 8 x 10 exp 6 cells and dark matter particles, we find that physical bias b is on the 8/h Mpc scale is about 1.6 and increases towards smaller scales, and that velocity bias is about 0.8 on the same scale. The comparable HDM simulation is highly biased with b = 2.7 on the 8/h Mpc scale. Implications of these results are discussed in the light of the COBE observations which provide an accurate normalization for the initial power spectrum. CDM can be ruled out on the basis of too large a predicted small scale velocity dispersion at greater than 95 percent confidence level.

Modelling multiple threats to water security in the Peruvian Amazon using the WaterWorld policy support system

NASA Astrophysics Data System (ADS)

van Soesbergen, A. J. J.; Mulligan, M.

2014-01-01

This paper describes the application of WaterWorld (www.policysupport.org/waterworld) to the Peruvian Amazon, an area that is increasingly under pressure from deforestation and water pollution as a result of population growth, rural-to-urban migration and oil and gas extraction, potentially impacting both water quantity and water quality. By applying single and combined plausible scenarios of climate change, deforestation around existing and planned roads, population growth and rural-urban migration, mining and oil and gas exploitation, we explore the potential combined impacts of these multiple changes on water resources in the Peruvian Amazon.

Mapping Impact of Urbanization in the Continental U.S. from 2001-2020

NASA Technical Reports Server (NTRS)

Bounoua, Lahouari; Nigro, Joseph; Zhang, Ping; Thome, Kurtis

2016-01-01

Data fusion, from Landsat and MODIS, was used to characterize US buildup and to derive a plausible 2020 impervious surface area (ISA) projection based on observed rates of ISA change as a function of population from 2006 to 2011. The analysis shows that urbanization in the U.S. implicitly includes a cultural character whereby depending on the region, cities are either built horizontally with large ISA per capita or vertically with a minimal spatial footprint. This cultural character can also be forced by land availability, topography and inland water. In other regions, cities seem to have adapted to their population growth and adjusted their ISA use per capita.

Accuracy of external cause-of-injury coding in VA polytrauma patient discharge records.

PubMed

Carlson, Kathleen F; Nugent, Sean M; Grill, Joseph; Sayer, Nina A

2010-01-01

Valid and efficient methods of identifying the etiology of treated injuries are critical for characterizing patient populations and developing prevention and rehabilitation strategies. We examined the accuracy of external cause-of-injury codes (E-codes) in Veterans Health Administration (VHA) administrative data for a population of injured patients. Chart notes and E-codes were extracted for 566 patients treated at any one of four VHA Polytrauma Rehabilitation Center sites between 2001 and 2006. Two expert coders, blinded to VHA E-codes, used chart notes to assign "gold standard" E-codes to injured patients. The accuracy of VHA E-coding was examined based on these gold standard E-codes. Only 382 of 517 (74%) injured patients were assigned E-codes in VHA records. Sensitivity of VHA E-codes varied significantly by site (range: 59%-91%, p < 0.001). Sensitivity was highest for combat-related injuries (81%) and lowest for fall-related injuries (60%). Overall specificity of E-codes was high (92%). E-coding accuracy was markedly higher when we restricted analyses to records that had been assigned VHA E-codes. E-codes may not be valid for ascertaining source-of-injury data for all injuries among VHA rehabilitation inpatients at this time. Enhanced training and policies may ensure more widespread, standardized use and accuracy of E-codes for injured veterans treated in the VHA.

Galactic civilizations - Population dynamics and interstellar diffusion

NASA Technical Reports Server (NTRS)

Newman, W. I.; Sagan, C.

1981-01-01

A model is developed of the interstellar diffusion of galactic civilizations which takes into account the population dynamics of such civilizations. The problem is formulated in terms of potential theory, with a family of nonlinear partial differential and difference equations specifying population growth and diffusion for an organism with advantageous genes that undergoes random dispersal while increasing in population locally, and a population at zero population growth. In the case of nonlinear diffusion with growth and saturation, it is found that the colonization wavefront from the nearest independently arisen galactic civilization can have reached the earth only if its lifetime exceeds 2.6 million years, or 20 million years if discretization can be neglected. For zero population growth, the corresponding lifetime is 13 billion years. It is concluded that the earth is uncolonized not because interstellar spacefaring civilizations are rare, but because there are too many worlds to be colonized in the plausible colonization lifetime of nearby civilizations, and that there exist no very old galactic civilizations with a consistent policy of the conquest of inhabited worlds.

Coding completeness and quality of relative survival-related variables in the National Program of Cancer Registries Cancer Surveillance System, 1995-2008.

PubMed

Wilson, Reda J; O'Neil, M E; Ntekop, E; Zhang, Kevin; Ren, Y

2014-01-01

Calculating accurate estimates of cancer survival is important for various analyses of cancer patient care and prognosis. Current US survival rates are estimated based on data from the National Cancer Institute's (NCI's) Surveillance, Epidemiology, and End RESULTS (SEER) program, covering approximately 28 percent of the US population. The National Program of Cancer Registries (NPCR) covers about 96 percent of the US population. Using a population-based database with greater US population coverage to calculate survival rates at the national, state, and regional levels can further enhance the effective monitoring of cancer patient care and prognosis in the United States. The first step is to establish the coding completeness and coding quality of the NPCR data needed for calculating survival rates and conducting related validation analyses. Using data from the NPCR-Cancer Surveillance System (CSS) from 1995 through 2008, we assessed coding completeness and quality on 26 data elements that are needed to calculate cancer relative survival estimates and conduct related analyses. Data elements evaluated consisted of demographic, follow-up, prognostic, and cancer identification variables. Analyses were performed showing trends of these variables by diagnostic year, state of residence at diagnosis, and cancer site. Mean overall percent coding completeness by each NPCR central cancer registry averaged across all data elements and diagnosis years ranged from 92.3 percent to 100 percent. RESULTS showing the mean percent coding completeness for the relative survival-related variables in NPCR data are presented. All data elements but 1 have a mean coding completeness greater than 90 percent as was the mean completeness by data item group type. Statistically significant differences in coding completeness were found in the ICD revision number, cause of death, vital status, and date of last contact variables when comparing diagnosis years. The majority of data items had a coding quality greater than 90 percent, with exceptions found in cause of death, follow-up source, and the SEER Summary Stage 1977, and SEER Summary Stage 2000. Percent coding completeness and quality are very high for variables in the NPCR-CSS that are covariates to calculating relative survival. NPCR provides the opportunity to calculate relative survival that may be more generalizable to the US population.

Pilgrims sailing the Titanic: plausibility effects on memory for misinformation.

PubMed

Hinze, Scott R; Slaten, Daniel G; Horton, William S; Jenkins, Ryan; Rapp, David N

2014-02-01

People rely on information they read even when it is inaccurate (Marsh, Meade, & Roediger, Journal of Memory and Language 49:519-536, 2003), but how ubiquitous is this phenomenon? In two experiments, we investigated whether this tendency to encode and rely on inaccuracies from text might be influenced by the plausibility of misinformation. In Experiment 1, we presented stories containing inaccurate plausible statements (e.g., "The Pilgrims' ship was the Godspeed"), inaccurate implausible statements (e.g., . . . the Titanic), or accurate statements (e.g., . . . the Mayflower). On a subsequent test of general knowledge, participants relied significantly less on implausible than on plausible inaccuracies from the texts but continued to rely on accurate information. In Experiment 2, we replicated these results with the addition of a think-aloud procedure to elicit information about readers' noticing and evaluative processes for plausible and implausible misinformation. Participants indicated more skepticism and less acceptance of implausible than of plausible inaccuracies. In contrast, they often failed to notice, completely ignored, and at times even explicitly accepted the misinformation provided by plausible lures. These results offer insight into the conditions under which reliance on inaccurate information occurs and suggest potential mechanisms that may underlie reported misinformation effects.

The Utility of Cognitive Plausibility in Language Acquisition Modeling: Evidence From Word Segmentation.

PubMed

Phillips, Lawrence; Pearl, Lisa

2015-11-01

The informativity of a computational model of language acquisition is directly related to how closely it approximates the actual acquisition task, sometimes referred to as the model's cognitive plausibility. We suggest that though every computational model necessarily idealizes the modeled task, an informative language acquisition model can aim to be cognitively plausible in multiple ways. We discuss these cognitive plausibility checkpoints generally and then apply them to a case study in word segmentation, investigating a promising Bayesian segmentation strategy. We incorporate cognitive plausibility by using an age-appropriate unit of perceptual representation, evaluating the model output in terms of its utility, and incorporating cognitive constraints into the inference process. Our more cognitively plausible model shows a beneficial effect of cognitive constraints on segmentation performance. One interpretation of this effect is as a synergy between the naive theories of language structure that infants may have and the cognitive constraints that limit the fidelity of their inference processes, where less accurate inference approximations are better when the underlying assumptions about how words are generated are less accurate. More generally, these results highlight the utility of incorporating cognitive plausibility more fully into computational models of language acquisition. Copyright © 2015 Cognitive Science Society, Inc.

Biofertilizers and sustainable agriculture: exploring arbuscular mycorrhizal fungi.

PubMed

Igiehon, Nicholas O; Babalola, Olubukola O

2017-06-01

Worldwide agricultural food production has to double in 2050 so as to feed the global increasing population while reducing dependency on conventional chemical fertilizers plus pesticides. To accomplish this objective, there is the need to explore the several mutualistic interactions between plant roots and rhizosphere microbiome. Biofertilization is the process of boosting the abundance of microorganisms such as arbuscular mycorrhizal fungi (AMF) in the natural plant rhizosphere which depicts a beneficial alternative to chemical fertilization practices. Mineral nutrients uptake by AMF are plausible by means of transporters coded for by different genes and example include phosphate transporter. These fungi can be produced industrially using plant host and these, including the possibility of AMF contamination by other microorganism, are factors militating against large scale production of AMF. AMF isolates can be inoculated in the greenhouse or field, and it has been shown that AMF survival and colonization level were enhanced in soybeans grown on land that was previously cultivated with the same plant. Next generation sequencing (NGS) is now used to gain insight into how AMF interact with indigenous AMF and screen for beneficial microbial candidates. Besides application as biofertilizers, novel findings on AMF that could contribute to maintenance of agricultural development include AMF roles in controlling soil erosion, enhancing phytoremediation, and elimination of other organisms that may be harmful to crops through common mycelia network. The combination of these potentials when fully harnessed under agricultural scenario will help to sustain agriculture and boost food security globally.

IsoWeb: A Bayesian Isotope Mixing Model for Diet Analysis of the Whole Food Web

PubMed Central

Kadoya, Taku; Osada, Yutaka; Takimoto, Gaku

2012-01-01

Quantitative description of food webs provides fundamental information for the understanding of population, community, and ecosystem dynamics. Recently, stable isotope mixing models have been widely used to quantify dietary proportions of different food resources to a focal consumer. Here we propose a novel mixing model (IsoWeb) that estimates diet proportions of all consumers in a food web based on stable isotope information. IsoWeb requires a topological description of a food web, and stable isotope signatures of all consumers and resources in the web. A merit of IsoWeb is that it takes into account variation in trophic enrichment factors among different consumer-resource links. Sensitivity analysis using realistic hypothetical food webs suggests that IsoWeb is applicable to a wide variety of food webs differing in the number of species, connectance, sample size, and data variability. Sensitivity analysis based on real topological webs showed that IsoWeb can allow for a certain level of topological uncertainty in target food webs, including erroneously assuming false links, omission of existent links and species, and trophic aggregation into trophospecies. Moreover, using an illustrative application to a real food web, we demonstrated that IsoWeb can compare the plausibility of different candidate topologies for a focal web. These results suggest that IsoWeb provides a powerful tool to analyze food-web structure from stable isotope data. We provide R and BUGS codes to aid efficient applications of IsoWeb. PMID:22848427

Constitutional CHEK2 mutations are infrequent in early-onset and familial breast/ovarian cancer patients from Pakistan.

PubMed

Rashid, Muhammad U; Muhammad, Noor; Faisal, Saima; Amin, Asim; Hamann, Ute

2013-06-27

Less than 20% of Pakistani women with early-onset or familial breast/ovarian cancer harbor germ line mutations in the high-penetrance genes BRCA1, BRCA2 and TP53. Thus, mutations in other genes confer genetic susceptibility to breast cancer, of which CHEK2 is a plausible candidate. CHEK2 encodes a checkpoint kinase, involved in response to DNA damage. In the present study we assessed the prevalence of CHEK2 germ line mutations in 145 BRCA1/2-negative early-onset and familial breast/ovarian cancer patients from Pakistan (Group 1). Mutation analysis of the complete CHEK2 coding region was performed using denaturing high-performance liquid chromatography analysis, followed by DNA sequencing of variant fragments. Two potentially deleterious missense mutations, c.275C>G (p.P92R) and c.1216C>T, (p.R406C), were identified (1.4%). The c.275C>G mutation is novel and has not been described in other populations. It was detected in a 30-year-old breast cancer patient with a family history of breast and multiple other cancers. The c.1216C>T mutation was found in a 34-year-old ovarian cancer patient from a family with two breast cancer cases. Both mutations were not detected in 229 recently recruited BRCA1/2-negative high risk patients (Group 2). Our findings suggest that CHEK2 mutations may not contribute significantly to breast/ovarian cancer risk in Pakistani women.

[Anthropogenic sources of radiation hazard in the near-Earth space].

PubMed

Fedoseev, G A

2004-01-01

All plausible artificial radioactive sources entering the near-Earth space (NES) were systematized and consequences of various large radiation accidents and catastrophes to Earth and NES were analyzed. Aggressive "population" of near-Earth orbits by space stations with rotating crews, unmanned research platforms and observatories extends "borderlines" of the noosphere raising at the same time concerns about the noosphere radiation safety and global radioecology. Specifically, consideration is given to the facts of negative effects of space power reactor facilities on results of orbital astrophysical investigations.

Isotopic Dichotomy among Meteorites and Its Bearing on the Protoplanetary Disk

NASA Astrophysics Data System (ADS)

Scott, Edward R. D.; Krot, Alexander N.; Sanders, Ian S.

2018-02-01

Whole rock Δ17O and nucleosynthetic isotopic variations for chromium, titanium, nickel, and molybdenum in meteorites define two isotopically distinct populations: carbonaceous chondrites (CCs) and some achondrites, pallasites, and irons in one and all other chondrites and differentiated meteorites in the other. Since differentiated bodies accreted 1–3 Myr before the chondrites, the isotopic dichotomy cannot be attributed to temporal variations in the disk. Instead, the two populations were most likely separated in space, plausibly by proto-Jupiter. Formation of CCs outside Jupiter could account for their characteristic chemical and isotopic composition. The abundance of refractory inclusions in CCs can be explained if they were ejected by disk winds from near the Sun to the disk periphery where they spiraled inward due to gas drag. Once proto-Jupiter reached 10–20 M ⊕, its external pressure bump could have prevented millimeter- and centimeter-sized particles from reaching the inner disk. This scenario would account for the enrichment in CCs of refractory inclusions, refractory elements, and water. Chondrules in CCs show wide ranges in Δ17O as they formed in the presence of abundant 16O-rich refractory grains and 16O-poor ice particles. Chondrules in other chondrites (ordinary, E, R, and K groups) show relatively uniform, near-zero Δ17O values as refractory inclusions and ice were much less abundant in the inner solar system. The two populations were plausibly mixed together by the Grand Tack when Jupiter and Saturn migrated inward emptying and then repopulating the asteroid belt with roughly equal masses of planetesimals from inside and outside Jupiter’s orbit (S- and C-type asteroids).

Efficient transformation of an auditory population code in a small sensory system.

PubMed

Clemens, Jan; Kutzki, Olaf; Ronacher, Bernhard; Schreiber, Susanne; Wohlgemuth, Sandra

2011-08-16

Optimal coding principles are implemented in many large sensory systems. They include the systematic transformation of external stimuli into a sparse and decorrelated neuronal representation, enabling a flexible readout of stimulus properties. Are these principles also applicable to size-constrained systems, which have to rely on a limited number of neurons and may only have to fulfill specific and restricted tasks? We studied this question in an insect system--the early auditory pathway of grasshoppers. Grasshoppers use genetically fixed songs to recognize mates. The first steps of neural processing of songs take place in a small three-layer feed-forward network comprising only a few dozen neurons. We analyzed the transformation of the neural code within this network. Indeed, grasshoppers create a decorrelated and sparse representation, in accordance with optimal coding theory. Whereas the neuronal input layer is best read out as a summed population, a labeled-line population code for temporal features of the song is established after only two processing steps. At this stage, information about song identity is maximal for a population decoder that preserves neuronal identity. We conclude that optimal coding principles do apply to the early auditory system of the grasshopper, despite its size constraints. The inputs, however, are not encoded in a systematic, map-like fashion as in many larger sensory systems. Already at its periphery, part of the grasshopper auditory system seems to focus on behaviorally relevant features, and is in this property more reminiscent of higher sensory areas in vertebrates.

GPU accelerated population annealing algorithm

NASA Astrophysics Data System (ADS)

Barash, Lev Yu.; Weigel, Martin; Borovský, Michal; Janke, Wolfhard; Shchur, Lev N.

2017-11-01

Population annealing is a promising recent approach for Monte Carlo simulations in statistical physics, in particular for the simulation of systems with complex free-energy landscapes. It is a hybrid method, combining importance sampling through Markov chains with elements of sequential Monte Carlo in the form of population control. While it appears to provide algorithmic capabilities for the simulation of such systems that are roughly comparable to those of more established approaches such as parallel tempering, it is intrinsically much more suitable for massively parallel computing. Here, we tap into this structural advantage and present a highly optimized implementation of the population annealing algorithm on GPUs that promises speed-ups of several orders of magnitude as compared to a serial implementation on CPUs. While the sample code is for simulations of the 2D ferromagnetic Ising model, it should be easily adapted for simulations of other spin models, including disordered systems. Our code includes implementations of some advanced algorithmic features that have only recently been suggested, namely the automatic adaptation of temperature steps and a multi-histogram analysis of the data at different temperatures. Program Files doi:http://dx.doi.org/10.17632/sgzt4b7b3m.1 Licensing provisions: Creative Commons Attribution license (CC BY 4.0) Programming language: C, CUDA External routines/libraries: NVIDIA CUDA Toolkit 6.5 or newer Nature of problem: The program calculates the internal energy, specific heat, several magnetization moments, entropy and free energy of the 2D Ising model on square lattices of edge length L with periodic boundary conditions as a function of inverse temperature β. Solution method: The code uses population annealing, a hybrid method combining Markov chain updates with population control. The code is implemented for NVIDIA GPUs using the CUDA language and employs advanced techniques such as multi-spin coding, adaptive temperature steps and multi-histogram reweighting. Additional comments: Code repository at https://github.com/LevBarash/PAising. The system size and size of the population of replicas are limited depending on the memory of the GPU device used. For the default parameter values used in the sample programs, L = 64, θ = 100, β0 = 0, βf = 1, Δβ = 0 . 005, R = 20 000, a typical run time on an NVIDIA Tesla K80 GPU is 151 seconds for the single spin coded (SSC) and 17 seconds for the multi-spin coded (MSC) program (see Section 2 for a description of these parameters).

A neural coding scheme reproducing foraging trajectories

NASA Astrophysics Data System (ADS)

Gutiérrez, Esther D.; Cabrera, Juan Luis

2015-12-01

The movement of many animals may follow Lévy patterns. The underlying generating neuronal dynamics of such a behavior is unknown. In this paper we show that a novel discovery of multifractality in winnerless competition (WLC) systems reveals a potential encoding mechanism that is translatable into two dimensional superdiffusive Lévy movements. The validity of our approach is tested on a conductance based neuronal model showing WLC and through the extraction of Lévy flights inducing fractals from recordings of rat hippocampus during open field foraging. Further insights are gained analyzing mice motor cortex neurons and non motor cell signals. The proposed mechanism provides a plausible explanation for the neuro-dynamical fundamentals of spatial searching patterns observed in animals (including humans) and illustrates an until now unknown way to encode information in neuronal temporal series.

Dietary assessment of British police force employees: a description of diet record coding procedures and cross-sectional evaluation of dietary energy intake reporting (The Airwave Health Monitoring Study)

PubMed Central

Gibson, Rachel; Eriksen, Rebeca; Lamb, Kathryn; McMeel, Yvonne; Vergnaud, Anne-Claire; Spear, Jeanette; Aresu, Maria; Chan, Queenie; Elliott, Paul; Frost, Gary

2017-01-01

Objectives Dietary intake is a key aspect of occupational health. To capture the characteristics of dietary behaviour that is affected by occupational environment that may affect disease risk, a collection of prospective multiday dietary records is required. The aims of this paper are to: (1) collect multiday dietary data in the Airwave Health Monitoring Study, (2) describe the dietary coding procedures applied and (3) investigate the plausibility of dietary reporting in this occupational cohort. Design A dietary coding protocol for this large-scale study was developed to minimise coding error rate. Participants (n 4412) who completed 7-day food records were included for cross-sectional analyses. Energy intake (EI) misreporting was estimated using the Goldberg method. Multivariate logistic regression models were applied to determine participant characteristics associated with EI misreporting. Setting British police force employees enrolled (2007–2012) into the Airwave Health Monitoring Study. Results The mean code error rate per food diary was 3.7% (SD 3.2%). The strongest predictors of EI under-reporting were body mass index (BMI) and physical activity. Compared with participants with BMI<25 kg/m2, those with BMI>30 kg/m2 had increased odds of being classified as under-reporting EI (men OR 5.20 95% CI 3.92 to 6.89; women OR 2.66 95% CI 1.85 to 3.83). Men and women in the highest physical activity category compared with the lowest were also more likely to be classified as under-reporting (men OR 3.33 95% CI 2.46 to 4.50; women OR 4.34 95% CI 2.91 to 6.55). Conclusions A reproducible dietary record coding procedure has been developed to minimise coding error in complex 7-day diet diaries. The prevalence of EI under-reporting is comparable with existing national UK cohorts and, in agreement with previous studies, classification of under-reporting was biased towards specific subgroups of participants. PMID:28377391

Plausibility Judgments in Conceptual Change and Epistemic Cognition

ERIC Educational Resources Information Center

Lombardi, Doug; Nussbaum, E. Michael; Sinatra, Gale M.

2016-01-01

Plausibility judgments rarely have been addressed empirically in conceptual change research. Recent research, however, suggests that these judgments may be pivotal to conceptual change about certain topics where a gap exists between what scientists and laypersons find plausible. Based on a philosophical and empirical foundation, this article…

Dynamic state estimation based on Poisson spike trains—towards a theory of optimal encoding

NASA Astrophysics Data System (ADS)

Susemihl, Alex; Meir, Ron; Opper, Manfred

2013-03-01

Neurons in the nervous system convey information to higher brain regions by the generation of spike trains. An important question in the field of computational neuroscience is how these sensory neurons encode environmental information in a way which may be simply analyzed by subsequent systems. Many aspects of the form and function of the nervous system have been understood using the concepts of optimal population coding. Most studies, however, have neglected the aspect of temporal coding. Here we address this shortcoming through a filtering theory of inhomogeneous Poisson processes. We derive exact relations for the minimal mean squared error of the optimal Bayesian filter and, by optimizing the encoder, obtain optimal codes for populations of neurons. We also show that a class of non-Markovian, smooth stimuli are amenable to the same treatment, and provide results for the filtering and prediction error which hold for a general class of stochastic processes. This sets a sound mathematical framework for a population coding theory that takes temporal aspects into account. It also formalizes a number of studies which discussed temporal aspects of coding using time-window paradigms, by stating them in terms of correlation times and firing rates. We propose that this kind of analysis allows for a systematic study of temporal coding and will bring further insights into the nature of the neural code.

The Decennial Census: Potential Risks to Data Quality Resulting from Budget Reductions and Cost Increases

DTIC Science & Technology

1990-03-27

coding of certain population characteristic data and thus delay the publication of these data. This is similar to what happened in the 1980 census...when, because of budget shortfalls, the Bureau reduced the number of staff who coded population characteristic 5 data from questionnaires, contributing...Decennial Census: An Update, (GAO/T-GGD-89-15, Mar. 23, 1989). 6 missing population characteristic data would have been resolved either by telephone or a

[Prevalence of Cardiovascular Risk Factors at The Population Level: A Comparison of Ambulatory Physician-Coded Claims Data With Clinical Data From A Population-Based Study].

PubMed

Angelow, Aniela; Reber, Katrin Christiane; Schmidt, Carsten Oliver; Baumeister, Sebastian Edgar; Chenot, Jean-Francois

2018-06-04

The study assesses the validity of ICD-10 coded cardiovascular risk factors in claims data using gold-standard measurements from a population-based study for arterial hypertension, diabetes, dyslipidemia, smoking and obesity as a reference. Data of 1941 participants (46 % male, mean age 58±13 years) of the Study of Health in Pomerania (SHIP) were linked to electronic medical records from the regional association of statutory health insurance physicians from 2008 to 2012 used for billing purposes. Clinical data from SHIP was used as a gold standard to assess the agreement with claims data for ICD-10 codes I10.- (arterial hypertension), E10.- to E14.- (diabetes mellitus), E78.- (dyslipidemia), F17.- (smoking) and E65.- to E68.- (obesity). A higher agreement between ICD-coded and clinical diagnosis was found for diabetes (sensitivity (sens) 84%, specificity (spec) 95%, positive predictive value (ppv) 80%) and hypertension (sens 72%, spec 93%, ppv 97%) and a low level of agreement for smoking (sens 18%, spec 99%, ppv 89%), obesity (sens 22%, spec 99%, ppv 99%) and dyslipidemia (sens 40%, spec 60%, ppv 70%). Depending on the investigated cardiovascular risk factor, medication, documented additional cardiovascular co-morbidities, age, sex and clinical severity were associated with the ICD-coded cardiovascular risk factor. The quality of ICD-coding in ambulatory care is highly variable for different cardiovascular risk factors and outcomes. Diagnoses were generally undercoded, but those relevant for billing were coded more frequently. Our results can be used to quantify errors in population-based estimates of prevalence based on claims data for the investigated cardiovascular risk factors. © Georg Thieme Verlag KG Stuttgart · New York.

MRI Proton Density Fat Fraction Is Robust Across the Biologically Plausible Range of Triglyceride Spectra in Adults With Nonalcoholic Steatohepatitis

PubMed Central

Hong, Cheng William; Mamidipalli, Adrija; Hooker, Jonathan C.; Hamilton, Gavin; Wolfson, Tanya; Chen, Dennis H.; Dehkordy, Soudabeh Fazeli; Middleton, Michael S.; Reeder, Scott B.; Loomba, Rohit; Sirlin, Claude B.

2017-01-01

Background Proton density fat fraction (PDFF) estimation requires spectral modeling of the hepatic triglyceride (TG) signal. Deviations in the TG spectrum may occur, leading to bias in PDFF quantification. Purpose To investigate the effects of varying six-peak TG spectral models on PDFF estimation bias. Study Type Retrospective secondary analysis of prospectively acquired clinical research data. Population Forty-four adults with biopsy-confirmed nonalcoholic steatohepatitis. Field Strength/Sequence Confounder-corrected chemical-shift-encoded 3T MRI (using a 2D multiecho gradient-recalled echo technique with magnitude reconstruction) and MR spectroscopy. Assessment In each patient, 61 pairs of colocalized MRI-PDFF and MRS-PDFF values were estimated: one pair used the standard six-peak spectral model, the other 60 were six-peak variants calculated by adjusting spectral model parameters over their biologically plausible ranges. MRI-PDFF values calculated using each variant model and the standard model were compared, and the agreement between MRI-PDFF and MRS-PDFF was assessed. Statistical Tests MRS-PDFF and MRI-PDFF were summarized descriptively. Bland–Altman (BA) analyses were performed between PDFF values calculated using each variant model and the standard model. Linear regressions were performed between BA biases and mean PDFF values for each variant model, and between MRI-PDFF and MRS-PDFF. Results Using the standard model, mean MRS-PDFF of the study population was 17.9±8.0% (range: 4.1–34.3%). The difference between the highest and lowest mean variant MRI-PDFF values was 1.5%. Relative to the standard model, the model with the greatest absolute BA bias overestimated PDFF by 1.2%. Bias increased with increasing PDFF (P < 0.0001 for 59 of the 60 variant models). MRI-PDFF and MRS-PDFF agreed closely for all variant models (R2=0.980, P < 0.0001). Data Conclusion Over a wide range of hepatic fat content, PDFF estimation is robust across the biologically plausible range of TG spectra. Although absolute estimation bias increased with higher PDFF, its magnitude was small and unlikely to be clinically meaningful. Level of Evidence 3 Technical Efficacy Stage 2 PMID:28851124

Constructing Precisely Computing Networks with Biophysical Spiking Neurons.

PubMed

Schwemmer, Michael A; Fairhall, Adrienne L; Denéve, Sophie; Shea-Brown, Eric T

2015-07-15

While spike timing has been shown to carry detailed stimulus information at the sensory periphery, its possible role in network computation is less clear. Most models of computation by neural networks are based on population firing rates. In equivalent spiking implementations, firing is assumed to be random such that averaging across populations of neurons recovers the rate-based approach. Recently, however, Denéve and colleagues have suggested that the spiking behavior of neurons may be fundamental to how neuronal networks compute, with precise spike timing determined by each neuron's contribution to producing the desired output (Boerlin and Denéve, 2011; Boerlin et al., 2013). By postulating that each neuron fires to reduce the error in the network's output, it was demonstrated that linear computations can be performed by networks of integrate-and-fire neurons that communicate through instantaneous synapses. This left open, however, the possibility that realistic networks, with conductance-based neurons with subthreshold nonlinearity and the slower timescales of biophysical synapses, may not fit into this framework. Here, we show how the spike-based approach can be extended to biophysically plausible networks. We then show that our network reproduces a number of key features of cortical networks including irregular and Poisson-like spike times and a tight balance between excitation and inhibition. Lastly, we discuss how the behavior of our model scales with network size or with the number of neurons "recorded" from a larger computing network. These results significantly increase the biological plausibility of the spike-based approach to network computation. We derive a network of neurons with standard spike-generating currents and synapses with realistic timescales that computes based upon the principle that the precise timing of each spike is important for the computation. We then show that our network reproduces a number of key features of cortical networks including irregular, Poisson-like spike times, and a tight balance between excitation and inhibition. These results significantly increase the biological plausibility of the spike-based approach to network computation, and uncover how several components of biological networks may work together to efficiently carry out computation. Copyright © 2015 the authors 0270-6474/15/3510112-23$15.00/0.

Methods for Ensuring High Quality of Coding of Cause of Death. The Mortality Register to Follow Southern Urals Populations Exposed to Radiation.

PubMed

Startsev, N; Dimov, P; Grosche, B; Tretyakov, F; Schüz, J; Akleyev, A

2015-01-01

To follow up populations exposed to several radiation accidents in the Southern Urals, a cause-of-death registry was established at the Urals Center capturing deaths in the Chelyabinsk, Kurgan and Sverdlovsk region since 1950. When registering deaths over such a long time period, quality measures need to be in place to maintain quality and reduce the impact of individual coders as well as quality changes in death certificates. To ensure the uniformity of coding, a method for semi-automatic coding was developed, which is described here. Briefly, the method is based on a dynamic thesaurus, database-supported coding and parallel coding by two different individuals. A comparison of the proposed method for organizing the coding process with the common procedure of coding showed good agreement, with, at the end of the coding process, 70  - 90% agreement for the three-digit ICD -9 rubrics. The semi-automatic method ensures a sufficiently high quality of coding by at the same time providing an opportunity to reduce the labor intensity inherent in the creation of large-volume cause-of-death registries.

Breastfeeding and breast cancer risk: an evaluation based on a systematic review of epidemiologic evidence among the Japanese population.

PubMed

Nagata, Chisato; Mizoue, Tetsuya; Tanaka, Keitaro; Tsuji, Ichiro; Tamakoshi, Akiko; Wakai, Kenji; Matsuo, Keitaro; Ito, Hidemi; Sasazuki, Shizuka; Inoue, Manami; Tsugane, Shoichiro

2012-02-01

We reviewed epidemiological studies on breastfeeding and breast cancer among Japanese women. This report is part of a series of articles written by our research group, whose aim was to evaluate the existing evidence concerning the association between health-related lifestyles and cancer. Original data were obtained from MEDLINE searches using PubMed or from searches of the Ichushi database, complemented by manual searches. Evaluation of associations was based on the strength of evidence and the magnitude of association, together with biological plausibility. Three cohort studies and five case-control studies were identified. Cohort studies failed to find a significant inverse association between breastfeeding and the risk of breast cancer. Most of the case-control studies observed a statistically significant or non-significant risk reduction for women who ever had breastfed or for women with a longer duration of breastfeeding. Experimental studies have supported the biological plausibility of a protective effect of breastfeeding on breast cancer risk. We conclude that breastfeeding possibly decreases the risk of breast cancer among Japanese women.

The missing link between sleep disorders and age-related dementia: recent evidence and plausible mechanisms.

PubMed

Zhang, Feng; Zhong, Rujia; Li, Song; Chang, Raymond Chuen-Chung; Le, Weidong

2017-05-01

Sleep disorders are among the most common clinical problems and possess a significant concern for the geriatric population. More importantly, while around 40% of elderly adults have sleep-related complaints, sleep disorders are more frequently associated with co-morbidities including age-related neurodegenerative diseases and mild cognitive impairment. Recently, increasing evidence has indicated that disturbed sleep may not only serve as the consequence of brain atrophy, but also contribute to the pathogenesis of dementia and, therefore, significantly increase dementia risk. Since the current therapeutic interventions lack efficacies to prevent, delay or reverse the pathological progress of dementia, a better understanding of underlying mechanisms by which sleep disorders interact with the pathogenesis of dementia will provide possible targets for the prevention and treatment of dementia. In this review, we briefly describe the physiological roles of sleep in learning/memory, and specifically update the recent research evidence demonstrating the association between sleep disorders and dementia. Plausible mechanisms are further discussed. Moreover, we also evaluate the possibility of sleep therapy as a potential intervention for dementia.

Large-scale two-photon imaging revealed super-sparse population codes in the V1 superficial layer of awake monkeys.

PubMed

Tang, Shiming; Zhang, Yimeng; Li, Zhihao; Li, Ming; Liu, Fang; Jiang, Hongfei; Lee, Tai Sing

2018-04-26

One general principle of sensory information processing is that the brain must optimize efficiency by reducing the number of neurons that process the same information. The sparseness of the sensory representations in a population of neurons reflects the efficiency of the neural code. Here, we employ large-scale two-photon calcium imaging to examine the responses of a large population of neurons within the superficial layers of area V1 with single-cell resolution, while simultaneously presenting a large set of natural visual stimuli, to provide the first direct measure of the population sparseness in awake primates. The results show that only 0.5% of neurons respond strongly to any given natural image - indicating a ten-fold increase in the inferred sparseness over previous measurements. These population activities are nevertheless necessary and sufficient to discriminate visual stimuli with high accuracy, suggesting that the neural code in the primary visual cortex is both super-sparse and highly efficient. © 2018, Tang et al.

The world population explosion: causes, backgrounds and projections for the future

PubMed Central

Van Bavel, J.

2013-01-01

At the beginning of the nineteenth century, the total world population crossed the threshold of 1 billion people for the first time in the history of the homo sapiens sapiens. Since then, growth rates have been increasing exponentially, reaching staggeringly high peaks in the 20th century and slowing down a bit thereafter. Total world population reached 7 billion just after 2010 and is expected to count 9 billion by 2045. This paper first charts the differences in population growth between the world regions. Next, the mechanisms behind unprecedented population growth are explained and plausible scenarios for future developments are discussed. Crucial for the long term trend will be the rate of decline of the number of births per woman, called total fertility. Improvements in education, reproductive health and child survival will be needed to speed up the decline of total fertility, particularly in Africa. But in all scenarios, world population will continue to grow for some time due to population momentum. Finally, the paper outlines the debate about the consequences of the population explosion, involving poverty and food security, the impact on the natural environment, and migration flows. Key words: Fertility, family planning, world population, population growth, demographic transition, urbanization, population momentum, population projections. PMID:24753956

Source Effects and Plausibility Judgments When Reading about Climate Change

ERIC Educational Resources Information Center

Lombardi, Doug; Seyranian, Viviane; Sinatra, Gale M.

2014-01-01

Gaps between what scientists and laypeople find plausible may act as a barrier to learning complex and/or controversial socioscientific concepts. For example, individuals may consider scientific explanations that human activities are causing current climate change as implausible. This plausibility judgment may be due-in part-to individuals'…

Plausibility and Perspective Influence the Processing of Counterfactual Narratives

ERIC Educational Resources Information Center

Ferguson, Heather J.; Jayes, Lewis T.

2018-01-01

Previous research has established that readers' eye movements are sensitive to the difficulty with which a word is processed. One important factor that influences processing is the fit of a word within the wider context, including its plausibility. Here we explore the influence of plausibility in counterfactual language processing. Counterfactuals…

Conversion of Phase Information into a Spike-Count Code by Bursting Neurons

PubMed Central

Samengo, Inés; Montemurro, Marcelo A.

2010-01-01

Single neurons in the cerebral cortex are immersed in a fluctuating electric field, the local field potential (LFP), which mainly originates from synchronous synaptic input into the local neural neighborhood. As shown by recent studies in visual and auditory cortices, the angular phase of the LFP at the time of spike generation adds significant extra information about the external world, beyond the one contained in the firing rate alone. However, no biologically plausible mechanism has yet been suggested that allows downstream neurons to infer the phase of the LFP at the soma of their pre-synaptic afferents. Therefore, so far there is no evidence that the nervous system can process phase information. Here we study a model of a bursting pyramidal neuron, driven by a time-dependent stimulus. We show that the number of spikes per burst varies systematically with the phase of the fluctuating input at the time of burst onset. The mapping between input phase and number of spikes per burst is a robust response feature for a broad range of stimulus statistics. Our results suggest that cortical bursting neurons could play a crucial role in translating LFP phase information into an easily decodable spike count code. PMID:20300632

A border-ownership model based on computational electromagnetism.

PubMed

Zainal, Zaem Arif; Satoh, Shunji

2018-03-01

The mathematical relation between a vector electric field and its corresponding scalar potential field is useful to formulate computational problems of lower/middle-order visual processing, specifically related to the assignment of borders to the side of the object: so-called border ownership (BO). BO coding is a key process for extracting the objects from the background, allowing one to organize a cluttered scene. We propose that the problem is solvable simultaneously by application of a theorem of electromagnetism, i.e., "conservative vector fields have zero rotation, or "curl." We hypothesize that (i) the BO signal is definable as a vector electric field with arrowheads pointing to the inner side of perceived objects, and (ii) its corresponding scalar field carries information related to perceived order in depth of occluding/occluded objects. A simple model was developed based on this computational theory. Model results qualitatively agree with object-side selectivity of BO-coding neurons, and with perceptions of object order. The model update rule can be reproduced as a plausible neural network that presents new interpretations of existing physiological results. Results of this study also suggest that T-junction detectors are unnecessary to calculate depth order. Copyright © 2017 Elsevier Ltd. All rights reserved.

Amygdaloid and non-amygdaloid fear both influence avoidance of risky foraging in hungry rats.

PubMed

Kim, Earnest; Kim, Eun Joo; Yeh, Regina; Shin, Minkyung; Bobman, Jake; Krasne, Franklin B; Kim, Jeansok J

2014-09-07

Considerable evidence seems to show that emotional and reflex reactions to feared situations are mediated by the amygdala. It might therefore seem plausible to expect that amygdala-coded fear should also influence decisions when animals make choices about instrumental actions. However, there is not good evidence of this. In particular, it appears, though the literature is conflicted, that once learning is complete, the amygdala may often not be involved in instrumental avoidance behaviours. It is therefore of interest that we have found in rats living for extended periods in a semi-naturalistic 'closed economy', where they were given random shocks in regions that had to be entered to obtain food, choices about feeding behaviour were in fact influenced by amygdala-coded fear, in spite of the null effect of amygdalar lesions on fear of dangerous location per se. We suggest that avoidance of highly motivated voluntary behaviour does depend in part on fear signals originating in the amygdala. Such signalling may be one role of well-known projections from amygdala to cortico-striate circuitry. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Toward Petascale Biologically Plausible Neural Networks

NASA Astrophysics Data System (ADS)

Long, Lyle

This talk will describe an approach to achieving petascale neural networks. Artificial intelligence has been oversold for many decades. Computers in the beginning could only do about 16,000 operations per second. Computer processing power, however, has been doubling every two years thanks to Moore's law, and growing even faster due to massively parallel architectures. Finally, 60 years after the first AI conference we have computers on the order of the performance of the human brain (1016 operations per second). The main issues now are algorithms, software, and learning. We have excellent models of neurons, such as the Hodgkin-Huxley model, but we do not know how the human neurons are wired together. With careful attention to efficient parallel computing, event-driven programming, table lookups, and memory minimization massive scale simulations can be performed. The code that will be described was written in C + + and uses the Message Passing Interface (MPI). It uses the full Hodgkin-Huxley neuron model, not a simplified model. It also allows arbitrary network structures (deep, recurrent, convolutional, all-to-all, etc.). The code is scalable, and has, so far, been tested on up to 2,048 processor cores using 107 neurons and 109 synapses.

Action understanding and active inference

PubMed Central

Mattout, Jérémie; Kilner, James

2012-01-01

We have suggested that the mirror-neuron system might be usefully understood as implementing Bayes-optimal perception of actions emitted by oneself or others. To substantiate this claim, we present neuronal simulations that show the same representations can prescribe motor behavior and encode motor intentions during action–observation. These simulations are based on the free-energy formulation of active inference, which is formally related to predictive coding. In this scheme, (generalised) states of the world are represented as trajectories. When these states include motor trajectories they implicitly entail intentions (future motor states). Optimizing the representation of these intentions enables predictive coding in a prospective sense. Crucially, the same generative models used to make predictions can be deployed to predict the actions of self or others by simply changing the bias or precision (i.e. attention) afforded to proprioceptive signals. We illustrate these points using simulations of handwriting to illustrate neuronally plausible generation and recognition of itinerant (wandering) motor trajectories. We then use the same simulations to produce synthetic electrophysiological responses to violations of intentional expectations. Our results affirm that a Bayes-optimal approach provides a principled framework, which accommodates current thinking about the mirror-neuron system. Furthermore, it endorses the general formulation of action as active inference. PMID:21327826

OGLE14-073 - a promising pair-instability supernova candidate

NASA Astrophysics Data System (ADS)

Kozyreva, Alexandra; Kromer, Markus; Noebauer, Ulrich M.; Hirschi, Raphael

2018-05-01

The recently discovered bright type II supernova OGLE14-073 evolved very slowly. The light curve rose to maximum for 90 days from discovery and then declined at a rate compatible with the radioactive decay of 56Co. In this study, we show that a pair-instability supernova is a plausible mechanism for this event. We calculate explosion models and light curves with the radiation hydrodynamics code STELLA starting from two MZAMS = 150 M⊙, Z=0.001 progenitors. We obtain satisfactory fits to OGLE14-073 broadband light curves by including additional 56Ni in the centre of the models and mixing hydrogen down into the inner layers of the ejecta to a radial mass coordinate of 10 M⊙. The extra 56Ni required points to a slightly more massive progenitor star. The mixing of hydrogen could be due to large scale mixing during the explosion. We also present synthetic spectra for our models simulated with the Monte Carlo radiative transfer code ARTIS. The synthetic spectra reproduce the main features of the observed spectra of OGLE14-073. We conclude that OGLE14-073 is one of the most promising candidates for a pair-instability explosion.

A quantitative dynamic systems model of health-related quality of life among older adults

PubMed Central

Roppolo, Mattia; Kunnen, E Saskia; van Geert, Paul L; Mulasso, Anna; Rabaglietti, Emanuela

2015-01-01

Health-related quality of life (HRQOL) is a person-centered concept. The analysis of HRQOL is highly relevant in the aged population, which is generally suffering from health decline. Starting from a conceptual dynamic systems model that describes the development of HRQOL in individuals over time, this study aims to develop and test a quantitative dynamic systems model, in order to reveal the possible dynamic trends of HRQOL among older adults. The model is tested in different ways: first, with a calibration procedure to test whether the model produces theoretically plausible results, and second, with a preliminary validation procedure using empirical data of 194 older adults. This first validation tested the prediction that given a particular starting point (first empirical data point), the model will generate dynamic trajectories that lead to the observed endpoint (second empirical data point). The analyses reveal that the quantitative model produces theoretically plausible trajectories, thus providing support for the calibration procedure. Furthermore, the analyses of validation show a good fit between empirical and simulated data. In fact, no differences were found in the comparison between empirical and simulated final data for the same subgroup of participants, whereas the comparison between different subgroups of people resulted in significant differences. These data provide an initial basis of evidence for the dynamic nature of HRQOL during the aging process. Therefore, these data may give new theoretical and applied insights into the study of HRQOL and its development with time in the aging population. PMID:26604722

Application of Johnson et al.'s speciation threshold model to apparent colonization times of island biotas.

PubMed

Ricklefs, Robert E; Bermingham, Eldredge

2004-08-01

Understanding patterns of diversity can be furthered by analysis of the dynamics of colonization, speciation, and extinction on islands using historical information provided by molecular phylogeography. The land birds of the Lesser Antilles are one of the most thoroughly described regional faunas in this context. In an analysis of colonization times, Ricklefs and Bermingham (2001) found that the cumulative distribution of lineages with respect to increasing time since colonization exhibits a striking change in slope at a genetic distance of about 2% mitochondrial DNA sequence divergence (about one million years). They further showed how this heterogeneity could be explained by either an abrupt increase in colonization rates or a mass extinction event. Cherry et al. (2002), referring to a model developed by Johnson et al. (2000), argued instead that the pattern resulted from a speciation threshold for reproductive isolation of island populations from their continental source populations. Prior to this threshold, genetic divergence is slowed by migration from the source, and species of varying age accumulate at a low genetic distance. After the threshold is reached, source and island populations diverge more rapidly, creating heterogeneity in the distribution of apparent ages of island taxa. We simulated of Johnson et al.'s speciation-threshold model, incorporating genetic divergence at rate k and fixation at rate M of genes that have migrated between the source and the island population. Fixation resets the divergence clock to zero. The speciation-threshold model fits the distribution of divergence times of Lesser Antillean birds well with biologically plausible parameter estimates. Application of the model to the Hawaiian avifauna, which does not exhibit marked heterogeneity of genetic divergence, and the West Indian herpetofauna, which does, required unreasonably high migration-fixation rates, several orders of magnitude greater than the colonization rate. However, the plausibility of the speciation-divergence model for Lesser Antillean birds emphasizes the importance of further investigation of historical biogeography on a regional scale for whole biotas, as well as the migration of genes between populations on long time scales and the achievement of reproductive isolation.

Social Gradients in the Health of Indigenous Australians

PubMed Central

Li, Jianghong; Zubrick, Stephen R.

2012-01-01

The pattern of association between socioeconomic factors and health outcomes has primarily depicted better health for those who are higher in the social hierarchy. Although this is a ubiquitous finding in the health literature, little is known about the interplay between these factors among indigenous populations. We begin to bridge this knowledge gap by assessing evidence on social gradients in indigenous health in Australia. We reveal a less universal and less consistent socioeconomic status patterning in health among Indigenous Australians, and discuss the plausibility of unique historical circumstances and social and cultural characteristics in explaining these patterns. A more robust evidence base in this field is fundamental to processes that aim to reduce the pervasive disparities between indigenous and nonindigenous population health. PMID:22095336

Where Do Freestanding Emergency Departments Choose to Locate? A National Inventory and Geographic Analysis in Three States.

PubMed

Schuur, Jeremiah D; Baker, Olesya; Freshman, Jaclyn; Wilson, Michael; Cutler, David M

2017-04-01

We determine the number and location of freestanding emergency departments (EDs) across the United States and determine the population characteristics of areas where freestanding EDs are located. We conducted a systematic inventory of US freestanding EDs. For the 3 states with the highest number of freestanding EDs, we linked demographic, insurance, and health services data, using the 5-digit ZIP code corresponding to the freestanding ED's location. To create a comparison nonfreestanding ED group, we matched 187 freestanding EDs to 1,048 nonfreestanding ED ZIP codes on land and population within state. We compared differences in demographic, insurance, and health services factors between matched ZIP codes with and without freestanding EDs, using univariate regressions with weights. We identified 360 freestanding EDs located in 30 states; 54.2% of freestanding EDs were hospital satellites, 36.6% were independent, and 9.2% were not classifiable. The 3 states with the highest number of freestanding EDs accounted for 66% of all freestanding EDs: Texas (181), Ohio (34), and Colorado (24). Across all 3 states, freestanding EDs were located in ZIP codes that had higher incomes and a lower proportion of the population with Medicaid. In Texas and Ohio, freestanding EDs were located in ZIP codes with a higher proportion of the population with private insurance. In Texas, freestanding EDs were located in ZIP codes that had fewer Hispanics, had a greater number of hospital-based EDs and physician offices, and had more physician visits and medical spending per year than ZIP codes without a freestanding ED. In Ohio, freestanding EDs were located in ZIP codes with fewer hospital-based EDs. In Texas, Ohio, and Colorado, freestanding EDs were located in areas with a better payer mix. The location of freestanding EDs in relation to other health care facilities and use and spending on health care varied between states. Copyright © 2016 American College of Emergency Physicians. Published by Elsevier Inc. All rights reserved.

Semantic and Plausibility Preview Benefit Effects in English: Evidence from Eye Movements

PubMed Central

Schotter, Elizabeth R.; Jia, Annie

2016-01-01

Theories of preview benefit in reading hinge on integration across saccades and the idea that preview benefit is greater the more similar the preview and target are. Schotter (2013) reported preview benefit from a synonymous preview, but it is unclear whether this effect occurs because of similarity between the preview and target (integration), or because of contextual fit of the preview—synonyms satisfy both accounts. Studies in Chinese have found evidence for preview benefit for words that are unrelated to the target, but are contextually plausible (Yang, Li, Wang, Slattery, & Rayner, 2014; Yang, Wang, Tong, & Rayner, 2012), which is incompatible with an integration account but supports a contextual fit account. Here, we used plausible and implausible unrelated previews in addition to plausible synonym, antonym, and identical previews to further investigate these accounts for readers of English. Early reading measures were shorter for all plausible preview conditions compared to the implausible preview condition. In later reading measures, a benefit for the plausible unrelated preview condition was not observed. In a second experiment, we asked questions that probed whether the reader encoded the preview or target. Readers were more likely to report the preview when they had skipped the word and not regressed to it, and when the preview was plausible. Thus, under certain circumstances, the preview word is processed to a high level of representation (i.e., semantic plausibility) regardless of its relationship to the target, but its influence on reading is relatively short-lived, being replaced by the target word, when fixated. PMID:27123754

Understanding Karma Police: The Perceived Plausibility of Noun Compounds as Predicted by Distributional Models of Semantic Representation

PubMed Central

Günther, Fritz; Marelli, Marco

2016-01-01

Noun compounds, consisting of two nouns (the head and the modifier) that are combined into a single concept, differ in terms of their plausibility: school bus is a more plausible compound than saddle olive. The present study investigates which factors influence the plausibility of attested and novel noun compounds. Distributional Semantic Models (DSMs) are used to obtain formal (vector) representations of word meanings, and compositional methods in DSMs are employed to obtain such representations for noun compounds. From these representations, different plausibility measures are computed. Three of those measures contribute in predicting the plausibility of noun compounds: The relatedness between the meaning of the head noun and the compound (Head Proximity), the relatedness between the meaning of modifier noun and the compound (Modifier Proximity), and the similarity between the head noun and the modifier noun (Constituent Similarity). We find non-linear interactions between Head Proximity and Modifier Proximity, as well as between Modifier Proximity and Constituent Similarity. Furthermore, Constituent Similarity interacts non-linearly with the familiarity with the compound. These results suggest that a compound is perceived as more plausible if it can be categorized as an instance of the category denoted by the head noun, if the contribution of the modifier to the compound meaning is clear but not redundant, and if the constituents are sufficiently similar in cases where this contribution is not clear. Furthermore, compounds are perceived to be more plausible if they are more familiar, but mostly for cases where the relation between the constituents is less clear. PMID:27732599

Selective population rate coding: a possible computational role of gamma oscillations in selective attention.

PubMed

Masuda, Naoki

2009-12-01

Selective attention is often accompanied by gamma oscillations in local field potentials and spike field coherence in brain areas related to visual, motor, and cognitive information processing. Gamma oscillations are implicated to play an important role in, for example, visual tasks including object search, shape perception, and speed detection. However, the mechanism by which gamma oscillations enhance cognitive and behavioral performance of attentive subjects is still elusive. Using feedforward fan-in networks composed of spiking neurons, we examine a possible role for gamma oscillations in selective attention and population rate coding of external stimuli. We implement the concept proposed by Fries ( 2005 ) that under dynamic stimuli, neural populations effectively communicate with each other only when there is a good phase relationship among associated gamma oscillations. We show that the downstream neural population selects a specific dynamic stimulus received by an upstream population and represents it by population rate coding. The encoded stimulus is the one for which gamma rhythm in the corresponding upstream population is resonant with the downstream gamma rhythm. The proposed role for gamma oscillations in stimulus selection is to enable top-down control, a neural version of time division multiple access used in communication engineering.

Parameter as a Switch Between Dynamical States of a Network in Population Decoding.

PubMed

Yu, Jiali; Mao, Hua; Yi, Zhang

2017-04-01

Population coding is a method to represent stimuli using the collective activities of a number of neurons. Nevertheless, it is difficult to extract information from these population codes with the noise inherent in neuronal responses. Moreover, it is a challenge to identify the right parameter of the decoding model, which plays a key role for convergence. To address the problem, a population decoding model is proposed for parameter selection. Our method successfully identified the key conditions for a nonzero continuous attractor. Both the theoretical analysis and the application studies demonstrate the correctness and effectiveness of this strategy.

Making More Plausible What is Hard To Believe: Historical Justifications and Illustrations of Newton's Third Law.

ERIC Educational Resources Information Center

Gauld, Colin

1998-01-01

Reports that many students do not believe Newton's law of action and reaction and suggests ways in which its plausibility might be enhanced. Reviews how this law has been made more plausible over time by Newton and those who succeeded him. Contains 25 references. (DDR)

Plausibility Reappraisals and Shifts in Middle School Students' Climate Change Conceptions

ERIC Educational Resources Information Center

Lombardi, Doug; Sinatra, Gale M.; Nussbaum, E. Michael

2013-01-01

Plausibility is a central but under-examined topic in conceptual change research. Climate change is an important socio-scientific topic; however, many view human-induced climate change as implausible. When learning about climate change, students need to make plausibility judgments but they may not be sufficiently critical or reflective. The…

Wealth Transmission and Inequality Among Hunter-Gatherers

PubMed Central

Hill, Kim; Marlowe, Frank; Nolin, David; Wiessner, Polly; Gurven, Michael; Bowles, Samuel; Mulder, Monique Borgerhoff; Hertz, Tom; Bell, Adrian

2010-01-01

We report quantitative estimates of intergenerational transmission and population-wide inequality for wealth measures in a set of hunter-gatherer populations. Wealth is defined broadly as factors that contribute to individual or household well-being, ranging from embodied forms such as weight and hunting success to material forms such household goods, as well as relational wealth in exchange partners. Intergenerational wealth transmission is low to moderate in these populations, but is still expected to have measurable influence on an individual’s life chances. Wealth inequality (measured with Gini coefficients) is moderate for most wealth types, matching what qualitative ethnographic research has generally indicated (if not the stereotype of hunter-gatherers as extreme egalitarians). We discuss some plausible mechanisms for these patterns, and suggest ways in which future research could resolve questions about the role of wealth in hunter-gatherer social and economic life. PMID:21151711

MAISTAS: a tool for automatic structural evaluation of alternative splicing products.

PubMed

Floris, Matteo; Raimondo, Domenico; Leoni, Guido; Orsini, Massimiliano; Marcatili, Paolo; Tramontano, Anna

2011-06-15

Analysis of the human genome revealed that the amount of transcribed sequence is an order of magnitude greater than the number of predicted and well-characterized genes. A sizeable fraction of these transcripts is related to alternatively spliced forms of known protein coding genes. Inspection of the alternatively spliced transcripts identified in the pilot phase of the ENCODE project has clearly shown that often their structure might substantially differ from that of other isoforms of the same gene, and therefore that they might perform unrelated functions, or that they might even not correspond to a functional protein. Identifying these cases is obviously relevant for the functional assignment of gene products and for the interpretation of the effect of variations in the corresponding proteins. Here we describe a publicly available tool that, given a gene or a protein, retrieves and analyses all its annotated isoforms, provides users with three-dimensional models of the isoform(s) of his/her interest whenever possible and automatically assesses whether homology derived structural models correspond to plausible structures. This information is clearly relevant. When the homology model of some isoforms of a gene does not seem structurally plausible, the implications are that either they assume a structure unrelated to that of the other isoforms of the same gene with presumably significant functional differences, or do not correspond to functional products. We provide indications that the second hypothesis is likely to be true for a substantial fraction of the cases. http://maistas.bioinformatica.crs4.it/.

Inference generation and story comprehension among children with ADHD.

PubMed

Van Neste, Jessica; Hayden, Angela; Lorch, Elizabeth P; Milich, Richard

2015-02-01

Academic difficulties are well-documented among children with ADHD. Exploring these difficulties through story comprehension research has revealed deficits among children with ADHD in making causal connections between events and in using causal structure and thematic importance to guide recall of stories. Important to theories of story comprehension and implied in these deficits is the ability to make inferences. Often, characters' goals are implicit and explanations of events must be inferred. The purpose of the present study was to compare the inferences generated during story comprehension by 23 7- to 11-year-old children with ADHD (16 males) and 35 comparison peers (19 males). Children watched two televised stories, each paused at five points. In the experimental condition, at each pause children told what they were thinking about the story, whereas in the control condition no responses were made during pauses. After viewing, children recalled the story. Several types of inferences and inference plausibility were coded. Children with ADHD generated fewer of the most essential inferences, plausible explanatory inferences, than did comparison children, both during story processing and during story recall. The groups did not differ on production of other types of inferences. Group differences in generating inferences during the think-aloud task significantly mediated group differences in patterns of recall. Both groups recalled more of the most important story information after completing the think-aloud task. Generating fewer explanatory inferences has important implications for story comprehension deficits in children with ADHD.

A thesaurus for a neural population code

PubMed Central

Ganmor, Elad; Segev, Ronen; Schneidman, Elad

2015-01-01

Information is carried in the brain by the joint spiking patterns of large groups of noisy, unreliable neurons. This noise limits the capacity of the neural code and determines how information can be transmitted and read-out. To accurately decode, the brain must overcome this noise and identify which patterns are semantically similar. We use models of network encoding noise to learn a thesaurus for populations of neurons in the vertebrate retina responding to artificial and natural videos, measuring the similarity between population responses to visual stimuli based on the information they carry. This thesaurus reveals that the code is organized in clusters of synonymous activity patterns that are similar in meaning but may differ considerably in their structure. This organization is highly reminiscent of the design of engineered codes. We suggest that the brain may use this structure and show how it allows accurate decoding of novel stimuli from novel spiking patterns. DOI: http://dx.doi.org/10.7554/eLife.06134.001 PMID:26347983

Super-linear Precision in Simple Neural Population Codes

NASA Astrophysics Data System (ADS)

Schwab, David; Fiete, Ila

2015-03-01

A widely used tool for quantifying the precision with which a population of noisy sensory neurons encodes the value of an external stimulus is the Fisher Information (FI). Maximizing the FI is also a commonly used objective for constructing optimal neural codes. The primary utility and importance of the FI arises because it gives, through the Cramer-Rao bound, the smallest mean-squared error achievable by any unbiased stimulus estimator. However, it is well-known that when neural firing is sparse, optimizing the FI can result in codes that perform very poorly when considering the resulting mean-squared error, a measure with direct biological relevance. Here we construct optimal population codes by minimizing mean-squared error directly and study the scaling properties of the resulting network, focusing on the optimal tuning curve width. We then extend our results to continuous attractor networks that maintain short-term memory of external stimuli in their dynamics. Here we find similar scaling properties in the structure of the interactions that minimize diffusive information loss.

Decoding a Decision Process in the Neuronal Population of Dorsal Premotor Cortex.

PubMed

Rossi-Pool, Román; Zainos, Antonio; Alvarez, Manuel; Zizumbo, Jerónimo; Vergara, José; Romo, Ranulfo

2017-12-20

When trained monkeys discriminate the temporal structure of two sequential vibrotactile stimuli, dorsal premotor cortex (DPC) showed high heterogeneity among its neuronal responses. Notably, DPC neurons coded stimulus patterns as broader categories and signaled them during working memory, comparison, and postponed decision periods. Here, we show that such population activity can be condensed into two major coding components: one that persistently represented in working memory both the first stimulus identity and the postponed informed choice and another that transiently coded the initial sensory information and the result of the comparison between the two stimuli. Additionally, we identified relevant signals that coded the timing of task events. These temporal and task-parameter readouts were shown to be strongly linked to the monkeys' behavior when contrasted to those obtained in a non-demanding cognitive control task and during error trials. These signals, hidden in the heterogeneity, were prominently represented by the DPC population response. Copyright © 2017 Elsevier Inc. All rights reserved.

Floaters may buffer the extinction risk of small populations: an empirical assessment

PubMed Central

2017-01-01

The high extinction risk of small populations is commonly explained by reductions in fecundity and breeder survival associated with demographic and environmental stochasticity. However, ecological theory suggests that population extinctions may also arise from reductions in the number of floaters able to replace the lost breeders. This can be particularly plausible under harsh fragmentation scenarios, where species must survive as small populations subjected to severe effects of stochasticity. Using a woodpecker study in fragmented habitats (2004–2016), we provide here empirical support for the largely neglected hypothesis that floaters buffer population extirpation risks. After controlling for population size, patch size and the intrinsic quality of habitat, populations in patches with floaters had a lower extinction probability than populations in patches without floaters (0.013 versus 0.131). Floaters, which often replace the lost breeders, were less likely to occur in small and low-quality patches, showing that population extirpations may arise from unnoticed reductions in floater numbers in poor-quality habitats. We argue that adequate pools of the typically overlooked floaters may buffer extirpation risks by reducing the detrimental impacts of demographic and environmental stochasticity. However, unravelling the influence of floaters in buffering stochastic effects and promoting population stability require additional studies in an ample array of species and stochastic scenarios. PMID:28424345

Floaters may buffer the extinction risk of small populations: an empirical assessment.

PubMed

Robles, Hugo; Ciudad, Carlos

2017-04-26

The high extinction risk of small populations is commonly explained by reductions in fecundity and breeder survival associated with demographic and environmental stochasticity. However, ecological theory suggests that population extinctions may also arise from reductions in the number of floaters able to replace the lost breeders. This can be particularly plausible under harsh fragmentation scenarios, where species must survive as small populations subjected to severe effects of stochasticity. Using a woodpecker study in fragmented habitats (2004-2016), we provide here empirical support for the largely neglected hypothesis that floaters buffer population extirpation risks. After controlling for population size, patch size and the intrinsic quality of habitat, populations in patches with floaters had a lower extinction probability than populations in patches without floaters (0.013 versus 0.131). Floaters, which often replace the lost breeders, were less likely to occur in small and low-quality patches, showing that population extirpations may arise from unnoticed reductions in floater numbers in poor-quality habitats. We argue that adequate pools of the typically overlooked floaters may buffer extirpation risks by reducing the detrimental impacts of demographic and environmental stochasticity. However, unravelling the influence of floaters in buffering stochastic effects and promoting population stability require additional studies in an ample array of species and stochastic scenarios. © 2017 The Author(s).

Quasi-extinction risk and population targets for the Eastern, migratory population of monarch butterflies (Danaus plexippus)

USGS Publications Warehouse

Semmens, Brice X.; Semmens, Darius J.; Thogmartin, Wayne E.; Wiederholt, Ruscena; Lopez-Hoffman, Laura; Diffendorfer, James E.; Pleasants, John M.; Oberhauser, Karen S.; Taylor, Orley R.

2016-01-01

The Eastern, migratory population of monarch butterflies (Danaus plexippus), an iconic North American insect, has declined by ~80% over the last decade. The monarch’s multi-generational migration between overwintering grounds in central Mexico and the summer breeding grounds in the northern U.S. and southern Canada is celebrated in all three countries and creates shared management responsibilities across North America. Here we present a novel Bayesian multivariate auto-regressive state-space model to assess quasi-extinction risk and aid in the establishment of a target population size for monarch conservation planning. We find that, given a range of plausible quasi-extinction thresholds, the population has a substantial probability of quasi-extinction, from 11–57% over 20 years, although uncertainty in these estimates is large. Exceptionally high population stochasticity, declining numbers, and a small current population size act in concert to drive this risk. An approximately 5-fold increase of the monarch population size (relative to the winter of 2014–15) is necessary to halve the current risk of quasi-extinction across all thresholds considered. Conserving the monarch migration thus requires active management to reverse population declines, and the establishment of an ambitious target population size goal to buffer against future environmentally driven variability.

How a modified approach to dental coding can benefit personal and professional development with improved clinical outcomes.

PubMed

Lam, Raymond; Kruger, Estie; Tennant, Marc

2014-12-01

One disadvantage of the remarkable achievements in dentistry is that treatment options have never been more varied or confusing. This has made the concept of Evidenced Based Dentistry more applicable to modern dental practice. Despite merit in the concept whereby clinical decisions are guided by scientific evidence, there are problems with establishing a scientific base. This is no more challenging than in modern dentistry where the gap between rapidly developing products/procedures and its evidence base are widening. Furthermore, the burden of oral disease continues to remain high at the population level. These problems have prompted new approaches to enhancing research. The aim of this paper is to outline how a modified approach to dental coding may benefit clinical and population level research. Using publically assessable data obtained from the Australian Chronic Disease Dental Scheme and item codes contained within the Australian Schedule of Dental Services and Glossary, a suggested approach to dental informatics is illustrated. A selection of item codes have been selected and expanded with the addition of suffixes. These suffixes provided circumstantial information that will assist in assessing clinical outcomes such as success rates and prognosis. The use of item codes in administering the CDDS yielded a large database of item codes. These codes are amenable to dental informatics which has been shown to enhance research at both the clinical and population level. This is a cost effective method to supplement existing research methods. Copyright © 2014 Elsevier Inc. All rights reserved.

Decoding the encoding of functional brain networks: An fMRI classification comparison of non-negative matrix factorization (NMF), independent component analysis (ICA), and sparse coding algorithms.

PubMed

Xie, Jianwen; Douglas, Pamela K; Wu, Ying Nian; Brody, Arthur L; Anderson, Ariana E

2017-04-15

Brain networks in fMRI are typically identified using spatial independent component analysis (ICA), yet other mathematical constraints provide alternate biologically-plausible frameworks for generating brain networks. Non-negative matrix factorization (NMF) would suppress negative BOLD signal by enforcing positivity. Spatial sparse coding algorithms (L1 Regularized Learning and K-SVD) would impose local specialization and a discouragement of multitasking, where the total observed activity in a single voxel originates from a restricted number of possible brain networks. The assumptions of independence, positivity, and sparsity to encode task-related brain networks are compared; the resulting brain networks within scan for different constraints are used as basis functions to encode observed functional activity. These encodings are then decoded using machine learning, by using the time series weights to predict within scan whether a subject is viewing a video, listening to an audio cue, or at rest, in 304 fMRI scans from 51 subjects. The sparse coding algorithm of L1 Regularized Learning outperformed 4 variations of ICA (p<0.001) for predicting the task being performed within each scan using artifact-cleaned components. The NMF algorithms, which suppressed negative BOLD signal, had the poorest accuracy compared to the ICA and sparse coding algorithms. Holding constant the effect of the extraction algorithm, encodings using sparser spatial networks (containing more zero-valued voxels) had higher classification accuracy (p<0.001). Lower classification accuracy occurred when the extracted spatial maps contained more CSF regions (p<0.001). The success of sparse coding algorithms suggests that algorithms which enforce sparsity, discourage multitasking, and promote local specialization may capture better the underlying source processes than those which allow inexhaustible local processes such as ICA. Negative BOLD signal may capture task-related activations. Copyright © 2017 Elsevier B.V. All rights reserved.

Auditory spatial processing in the human cortex.

PubMed

Salminen, Nelli H; Tiitinen, Hannu; May, Patrick J C

2012-12-01

The auditory system codes spatial locations in a way that deviates from the spatial representations found in other modalities. This difference is especially striking in the cortex, where neurons form topographical maps of visual and tactile space but where auditory space is represented through a population rate code. In this hemifield code, sound source location is represented in the activity of two widely tuned opponent populations, one tuned to the right and the other to the left side of auditory space. Scientists are only beginning to uncover how this coding strategy adapts to various spatial processing demands. This review presents the current understanding of auditory spatial processing in the cortex. To this end, the authors consider how various implementations of the hemifield code may exist within the auditory cortex and how these may be modulated by the stimulation and task context. As a result, a coherent set of neural strategies for auditory spatial processing emerges.

Using critical evaluation to reappraise plausibility judgments: A critical cognitive component of conceptual change

NASA Astrophysics Data System (ADS)

Lombardi, D.

2011-12-01

Plausibility judgments-although well represented in conceptual change theories (see, for example, Chi, 2005; diSessa, 1993; Dole & Sinatra, 1998; Posner et al., 1982)-have received little empirical attention until our recent work investigating teachers' and students' understanding of and perceptions about human-induced climate change (Lombardi & Sinatra, 2010, 2011). In our first study with undergraduate students, we found that greater plausibility perceptions of human-induced climate accounted for significantly greater understanding of weather and climate distinctions after instruction, even after accounting for students' prior knowledge (Lombardi & Sinatra, 2010). In a follow-up study with inservice science and preservice elementary teachers, we showed that anger about the topic of climate change and teaching about climate change was significantly related to implausible perceptions about human-induced climate change (Lombardi & Sinatra, 2011). Results from our recent studies helped to inform our development of a model of the role of plausibility judgments in conceptual change situations. The model applies to situations involving cognitive dissonance, where background knowledge conflicts with an incoming message. In such situations, we define plausibility as a judgment on the relative potential truthfulness of incoming information compared to one's existing mental representations (Rescher, 1976). Students may not consciously think when making plausibility judgments, expending only minimal mental effort in what is referred to as an automatic cognitive process (Stanovich, 2009). However, well-designed instruction could facilitate students' reappraisal of plausibility judgments in more effortful and conscious cognitive processing. Critical evaluation specifically may be one effective method to promote plausibility reappraisal in a classroom setting (Lombardi & Sinatra, in progress). In science education, critical evaluation involves the analysis of how evidentiary data support a hypothesis and its alternatives. The presentation will focus on how instruction promoting critical evaluation can encourage individuals to reappraise their plausibility judgments and initiate knowledge reconstruction. In a recent pilot study, teachers experienced an instructional scaffold promoting critical evaluation of two competing climate change theories (i.e., human-induced and increasing solar irradiance) and significantly changed both their plausibility judgments and perceptions of correctness toward the scientifically-accepted model of human-induced climate change. A comparison group of teachers who did not experience the critical evaluation activity showed no significant change. The implications of these studies for future research and instruction will be discussed in the presentation, including effective ways to increase students' and teachers' ability to be critically evaluative and reappraise their plausibility judgments. With controversial science issues, such as climate change, such abilities may be necessary to facilitate conceptual change.

Accounting for misreporting when comparing energy intake across time in Canada.

PubMed

Garriguet, Didier

2018-05-16

Estimates of energy intake are lower in 2015 compared with 2004. The difference observed is too large to be explained by a change in energy requirements or physical activity at the population level. Self-reported dietary intake is subject to misreporting and may explain part of this difference. The objectives of this study are to assess how misreporting has changed from 2004 to 2015 and to demonstrate how these changes may affect the interpretation of the national intake data of Canadians. Data from the 2004 Canadian Community Health Survey - Nutrition (CCHS - Nutrition) and the 2015 CCHS - Nutrition were used to estimate energy intake and requirements for all participants aged 2 or older. The ratio of energy intake to total energy expenditure requirements (EI:TEE) was used to categorize respondents as under-reporters (EI:TEE ⟨ 0.70), over-reporters (EI:TEE ⟩ 1.42) or plausible reporters (EI:TEE = 0.70 to 1.42). Descriptive analyses by category of respondent were conducted for respondents aged 2 or older who participated in the measured height and weight component. The main caloric sources that contributed to the difference in estimated energy requirements were used to show the impact of misreporting on the analysis. The prevalence of under-reporters was 7.5% higher in 2015 compared with 2004, while the prevalence of over-reporters was 7.4% lower. There was no change in the prevalence of plausible reporters. Estimated energy intake from participants categorized as plausible reporters showed a difference of 84 kcal from 2004 to 2015, compared with a difference of 250 kcal for the entire sample. Estimated energy intake was lower in 2015 compared with 2004 across all categories of respondents for many foods, including sugar-sweetened beverages and milk, and was higher for only pastries and nuts. Misreporting changes will affect analysis and should, at a minimum, be acknowledged when comparing 2015 with 2004. Using a comparable category of plausible reporters or adjusting for reporting status are options that will allow a better comparison of these two datasets.

Population Projections

Science.gov Websites

United States Census Bureau Topics Population Latest Information Age and Sex Ancestry Children Mobility Population Estimates Population Projections Race Veterans Economy Latest Information Portal Other Economic Programs Business Latest Information Business Characteristics Classification Codes

Conceptualizing socio‐hydrological drought processes: The case of the Maya collapse

PubMed Central

Carr, Gemma; Viglione, Alberto; Prskawetz, Alexia; Blöschl, Günter

2016-01-01

Abstract With population growth, increasing water demands and climate change the need to understand the current and future pathways to water security is becoming more pressing. To contribute to addressing this challenge, we examine the link between water stress and society through socio‐hydrological modeling. We conceptualize the interactions between an agricultural society with its environment in a stylized way. We apply the model to the case of the ancient Maya, a population that experienced a peak during the Classic Period (AD 600–830) and then declined during the ninth century. The hypothesis that modest drought periods played a major role in the society's collapse is explored. Simulating plausible feedbacks between water and society we show that a modest reduction in rainfall may lead to an 80% population collapse. Population density and crop sensitivity to droughts, however, may play an equally important role. The simulations indicate that construction of reservoirs results in less frequent drought impacts, but if the reservoirs run dry, drought impact may be more severe and the population drop may be larger. PMID:27840455

Conceptualizing socio-hydrological drought processes: The case of the Maya collapse.

PubMed

Kuil, Linda; Carr, Gemma; Viglione, Alberto; Prskawetz, Alexia; Blöschl, Günter

2016-08-01

With population growth, increasing water demands and climate change the need to understand the current and future pathways to water security is becoming more pressing. To contribute to addressing this challenge, we examine the link between water stress and society through socio-hydrological modeling. We conceptualize the interactions between an agricultural society with its environment in a stylized way. We apply the model to the case of the ancient Maya, a population that experienced a peak during the Classic Period (AD 600-830) and then declined during the ninth century. The hypothesis that modest drought periods played a major role in the society's collapse is explored. Simulating plausible feedbacks between water and society we show that a modest reduction in rainfall may lead to an 80% population collapse. Population density and crop sensitivity to droughts, however, may play an equally important role. The simulations indicate that construction of reservoirs results in less frequent drought impacts, but if the reservoirs run dry, drought impact may be more severe and the population drop may be larger.

Conceptualizing socio-hydrological drought processes: The case of the Maya collapse

NASA Astrophysics Data System (ADS)

Kuil, Linda; Carr, Gemma; Viglione, Alberto; Prskawetz, Alexia; Blöschl, Günter

2016-08-01

With population growth, increasing water demands and climate change the need to understand the current and future pathways to water security is becoming more pressing. To contribute to addressing this challenge, we examine the link between water stress and society through socio-hydrological modeling. We conceptualize the interactions between an agricultural society with its environment in a stylized way. We apply the model to the case of the ancient Maya, a population that experienced a peak during the Classic Period (AD 600-830) and then declined during the ninth century. The hypothesis that modest drought periods played a major role in the society's collapse is explored. Simulating plausible feedbacks between water and society we show that a modest reduction in rainfall may lead to an 80% population collapse. Population density and crop sensitivity to droughts, however, may play an equally important role. The simulations indicate that construction of reservoirs results in less frequent drought impacts, but if the reservoirs run dry, drought impact may be more severe and the population drop may be larger.

Strong Support for the Millisecond Pulsar Origin of the Galactic Center GeV Excess.

PubMed

Bartels, Richard; Krishnamurthy, Suraj; Weniger, Christoph

2016-02-05

Using γ-ray data from the Fermi Large Area Telescope, various groups have identified a clear excess emission in the Inner Galaxy, at energies around a few GeV. This excess resembles remarkably well a signal from dark-matter annihilation. One of the most compelling astrophysical interpretations is that the excess is caused by the combined effect of a previously undetected population of dim γ-ray sources. Because of their spectral similarity, the best candidates are millisecond pulsars. Here, we search for this hypothetical source population, using a novel approach based on wavelet decomposition of the γ-ray sky and the statistics of Gaussian random fields. Using almost seven years of Fermi-LAT data, we detect a clustering of photons as predicted for the hypothetical population of millisecond pulsar, with a statistical significance of 10.0σ. For plausible values of the luminosity function, this population explains 100% of the observed excess emission. We argue that other extragalactic or Galactic sources, a mismodeling of Galactic diffuse emission, or the thick-disk population of pulsars are unlikely to account for this observation.

Religious groups as adaptive units.

PubMed

Wilson, D S

2001-01-01

This essay provides a sketch of religion as a set of biologically and culturally evolved adaptations that enable human groups to function as adaptive units. Recent developments in evolutionary biology make such a group-level interpretation of religion more plausible than in the past. A brief survey of relevant concepts is followed by a relatively detailed interpretation of Calvinism as a religious system in which explicit behavioral prescriptions, beliefs about God and his relationship with people, and numerous social control mechanisms combined to change the city of Geneva from a collection of warring factions to a unified population.

Quality of coding diagnoses in emergency departments: effects on mapping the public's health.

PubMed

Aharonson-Daniel, Limor; Schwartz, Dagan; Hornik-Lurie, Tzipi; Halpern, Pinchas

2014-01-01

Emergency department (ED) attendees reflect the health of the population served by that hospital and the availability of health care services in the community. To examine the quality and accuracy of diagnoses recorded in the ED to appraise its potential utility as a guage of the population's medical needs. Using the Delphi process, a preliminary list of health indicators generated by an expert focus group was converted to a query to the Ministry of Health's database. In parallel, medical charts were reviewed in four hospitals to compare the handwritten diagnosis in the medical record with that recorded on the standard diagnosis "pick list" coding sheet. Quantity and quality of coding were assessed using explicit criteria. During 2010 a total of 17,761 charts were reviewed; diagnoses were not coded in 42%. The accuracy of existing coding was excellent (mismatch 1%-5%). Database query (2,670,300 visits to 28 hospitals in 2009) demonstrated potential benefits of these data as indicators of regional health needs. The findings suggest that an increase in the provision of community care may reduce ED attendance. Information on ED visits can be used to support health care planning. A "pick list" form with common diagnoses can facilitate quality recording of diagnoses in a busy ED, profiling the population's health needs in order to optimize care. Better compliance with the directive to code diagnosis is desired.

Assessment of the effects and limitations of the 1998 to 2008 Abbreviated Injury Scale map using a large population-based dataset.

PubMed

Palmer, Cameron S; Franklyn, Melanie

2011-01-07

Trauma systems should consistently monitor a given trauma population over a period of time. The Abbreviated Injury Scale (AIS) and derived scores such as the Injury Severity Score (ISS) are commonly used to quantify injury severities in trauma registries. To reflect contemporary trauma management and treatment, the most recent version of the AIS (AIS08) contains many codes which differ in severity from their equivalents in the earlier 1998 version (AIS98). Consequently, the adoption of AIS08 may impede comparisons between data coded using different AIS versions. It may also affect the number of patients classified as major trauma. The entire AIS98-coded injury dataset of a large population based trauma registry was retrieved and mapped to AIS08 using the currently available AIS98-AIS08 dictionary map. The percentage of codes which had increased or decreased in severity, or could not be mapped, was examined in conjunction with the effect of these changes to the calculated ISS. The potential for free text information accompanying AIS coding to improve the quality of AIS mapping was explored. A total of 128280 AIS98-coded injuries were evaluated in 32134 patients, 15471 patients of whom were classified as major trauma. Although only 4.5% of dictionary codes decreased in severity from AIS98 to AIS08, this represented almost 13% of injuries in the registry. In 4.9% of patients, no injuries could be mapped. ISS was potentially unreliable in one-third of patients, as they had at least one AIS98 code which could not be mapped. Using AIS08, the number of patients classified as major trauma decreased by between 17.3% and 30.3%. Evaluation of free text descriptions for some injuries demonstrated the potential to improve mapping between AIS versions. Converting AIS98-coded data to AIS08 results in a significant decrease in the number of patients classified as major trauma. Many AIS98 codes are missing from the existing AIS map, and across a trauma population the AIS08 dataset estimates which it produces are of insufficient quality to be used in practice. However, it may be possible to improve AIS98 to AIS08 mapping to the point where it is useful to established registries.

Assessment of the effects and limitations of the 1998 to 2008 Abbreviated Injury Scale map using a large population-based dataset

PubMed Central

2011-01-01

Background Trauma systems should consistently monitor a given trauma population over a period of time. The Abbreviated Injury Scale (AIS) and derived scores such as the Injury Severity Score (ISS) are commonly used to quantify injury severities in trauma registries. To reflect contemporary trauma management and treatment, the most recent version of the AIS (AIS08) contains many codes which differ in severity from their equivalents in the earlier 1998 version (AIS98). Consequently, the adoption of AIS08 may impede comparisons between data coded using different AIS versions. It may also affect the number of patients classified as major trauma. Methods The entire AIS98-coded injury dataset of a large population based trauma registry was retrieved and mapped to AIS08 using the currently available AIS98-AIS08 dictionary map. The percentage of codes which had increased or decreased in severity, or could not be mapped, was examined in conjunction with the effect of these changes to the calculated ISS. The potential for free text information accompanying AIS coding to improve the quality of AIS mapping was explored. Results A total of 128280 AIS98-coded injuries were evaluated in 32134 patients, 15471 patients of whom were classified as major trauma. Although only 4.5% of dictionary codes decreased in severity from AIS98 to AIS08, this represented almost 13% of injuries in the registry. In 4.9% of patients, no injuries could be mapped. ISS was potentially unreliable in one-third of patients, as they had at least one AIS98 code which could not be mapped. Using AIS08, the number of patients classified as major trauma decreased by between 17.3% and 30.3%. Evaluation of free text descriptions for some injuries demonstrated the potential to improve mapping between AIS versions. Conclusions Converting AIS98-coded data to AIS08 results in a significant decrease in the number of patients classified as major trauma. Many AIS98 codes are missing from the existing AIS map, and across a trauma population the AIS08 dataset estimates which it produces are of insufficient quality to be used in practice. However, it may be possible to improve AIS98 to AIS08 mapping to the point where it is useful to established registries. PMID:21214906

A neural coding scheme reproducing foraging trajectories

PubMed Central

Gutiérrez, Esther D.; Cabrera, Juan Luis

2015-01-01

The movement of many animals may follow Lévy patterns. The underlying generating neuronal dynamics of such a behavior is unknown. In this paper we show that a novel discovery of multifractality in winnerless competition (WLC) systems reveals a potential encoding mechanism that is translatable into two dimensional superdiffusive Lévy movements. The validity of our approach is tested on a conductance based neuronal model showing WLC and through the extraction of Lévy flights inducing fractals from recordings of rat hippocampus during open field foraging. Further insights are gained analyzing mice motor cortex neurons and non motor cell signals. The proposed mechanism provides a plausible explanation for the neuro-dynamical fundamentals of spatial searching patterns observed in animals (including humans) and illustrates an until now unknown way to encode information in neuronal temporal series. PMID:26648311

Shock and Static Compression of Nitrobenzene

NASA Astrophysics Data System (ADS)

Kozu, Naoshi; Arai, Mitsuru; Tamura, Masamitsu; Fujihisa, Hiroshi; Aoki, Katsutoshi; Yoshida, Masatake

2000-08-01

The Hugoniot and static compression curve (isotherm) were investigated using explosive plane wave generators and diamond anvil cells, respectively. The obtained Hugoniot from the shock experiments is represented by two linear lines: Us=2.52+1.23 up (0.8

Synthetic constructs in/for the environment: Managing the interplay between natural and engineered Biology

PubMed Central

Schmidt, Markus; de Lorenzo, Víctor

2012-01-01

The plausible release of deeply engineered or even entirely synthetic/artificial microorganisms raises the issue of their intentional (e.g. bioremediation) or accidental interaction with the Environment. Containment systems designed in the 1980s–1990s for limiting the spread of genetically engineered bacteria and their recombinant traits are still applicable to contemporary Synthetic Biology constructs. Yet, the ease of DNA synthesis and the uncertainty on how non-natural properties and strains could interplay with the existing biological word poses yet again the challenge of designing safe and efficacious firewalls to curtail possible interactions. Such barriers may include xeno-nucleic acids (XNAs) instead of DNA as information-bearing molecules, rewriting the genetic code to make it non-understandable by the existing gene expression machineries, and/or making growth dependent on xenobiotic chemicals. PMID:22710182

45 CFR 309.10 - Who is eligible to apply for and receive Federal funding to operate a Tribal IV-D program?

Code of Federal Regulations, 2010 CFR

2010-10-01

... Tribal law or code, in the population subject to the jurisdiction of the Tribal court or administrative... defined by Tribal laws or codes, in the population of the Tribes subject to the jurisdiction of the Tribal... and provide justification for operating a program with less than the minimum number of children may be...

45 CFR 309.10 - Who is eligible to apply for and receive Federal funding to operate a Tribal IV-D program?

Code of Federal Regulations, 2011 CFR

2011-10-01

... Tribal law or code, in the population subject to the jurisdiction of the Tribal court or administrative... defined by Tribal laws or codes, in the population of the Tribes subject to the jurisdiction of the Tribal... and provide justification for operating a program with less than the minimum number of children may be...

45 CFR 309.10 - Who is eligible to apply for and receive Federal funding to operate a Tribal IV-D program?

Code of Federal Regulations, 2012 CFR

2012-10-01

... Tribal law or code, in the population subject to the jurisdiction of the Tribal court or administrative... defined by Tribal laws or codes, in the population of the Tribes subject to the jurisdiction of the Tribal... and provide justification for operating a program with less than the minimum number of children may be...

45 CFR 309.10 - Who is eligible to apply for and receive Federal funding to operate a Tribal IV-D program?

Code of Federal Regulations, 2013 CFR

2013-10-01

... Tribal law or code, in the population subject to the jurisdiction of the Tribal court or administrative... defined by Tribal laws or codes, in the population of the Tribes subject to the jurisdiction of the Tribal... and provide justification for operating a program with less than the minimum number of children may be...

45 CFR 309.10 - Who is eligible to apply for and receive Federal funding to operate a Tribal IV-D program?

Code of Federal Regulations, 2014 CFR

2014-10-01

... Tribal law or code, in the population subject to the jurisdiction of the Tribal court or administrative... defined by Tribal laws or codes, in the population of the Tribes subject to the jurisdiction of the Tribal... and provide justification for operating a program with less than the minimum number of children may be...

Exome sequencing in an admixed isolated population indicates NFXL1 variants confer a risk for specific language impairment.

PubMed

Villanueva, Pía; Nudel, Ron; Hoischen, Alexander; Fernández, María Angélica; Simpson, Nuala H; Gilissen, Christian; Reader, Rose H; Jara, Lillian; Echeverry, María Magdalena; Echeverry, Maria Magdalena; Francks, Clyde; Baird, Gillian; Conti-Ramsden, Gina; O'Hare, Anne; Bolton, Patrick F; Hennessy, Elizabeth R; Palomino, Hernán; Carvajal-Carmona, Luis; Veltman, Joris A; Cazier, Jean-Baptiste; De Barbieri, Zulema; Fisher, Simon E; Newbury, Dianne F

2015-03-01

Children affected by Specific Language Impairment (SLI) fail to acquire age appropriate language skills despite adequate intelligence and opportunity. SLI is highly heritable, but the understanding of underlying genetic mechanisms has proved challenging. In this study, we use molecular genetic techniques to investigate an admixed isolated founder population from the Robinson Crusoe Island (Chile), who are affected by a high incidence of SLI, increasing the power to discover contributory genetic factors. We utilize exome sequencing in selected individuals from this population to identify eight coding variants that are of putative significance. We then apply association analyses across the wider population to highlight a single rare coding variant (rs144169475, Minor Allele Frequency of 4.1% in admixed South American populations) in the NFXL1 gene that confers a nonsynonymous change (N150K) and is significantly associated with language impairment in the Robinson Crusoe population (p = 2.04 × 10-4, 8 variants tested). Subsequent sequencing of NFXL1 in 117 UK SLI cases identified four individuals with heterozygous variants predicted to be of functional consequence. We conclude that coding variants within NFXL1 confer an increased risk of SLI within a complex genetic model.

Negotiating plausibility: intervening in the future of nanotechnology.

PubMed

Selin, Cynthia

2011-12-01

The national-level scenarios project NanoFutures focuses on the social, political, economic, and ethical implications of nanotechnology, and is initiated by the Center for Nanotechnology in Society at Arizona State University (CNS-ASU). The project involves novel methods for the development of plausible visions of nanotechnology-enabled futures, elucidates public preferences for various alternatives, and, using such preferences, helps refine future visions for research and outreach. In doing so, the NanoFutures project aims to address a central question: how to deliberate the social implications of an emergent technology whose outcomes are not known. The solution pursued by the NanoFutures project is twofold. First, NanoFutures limits speculation about the technology to plausible visions. This ambition introduces a host of concerns about the limits of prediction, the nature of plausibility, and how to establish plausibility. Second, it subjects these visions to democratic assessment by a range of stakeholders, thus raising methodological questions as to who are relevant stakeholders and how to activate different communities so as to engage the far future. This article makes the dilemmas posed by decisions about such methodological issues transparent and therefore articulates the role of plausibility in anticipatory governance.

Population and Housing Unit Estimates

Science.gov Websites

United States Census Bureau Topics Population Latest Information Age and Sex Ancestry Children Mobility Population Estimates Population Projections Race Veterans Economy Latest Information Portal Other Economic Programs Business Latest Information Business Characteristics Classification Codes

Validity of Administrative Data in Identifying Cancer-related Events in Adolescents and Young Adults: A Population-based Study Using the IMPACT Cohort.

PubMed

Gupta, Sumit; Nathan, Paul C; Baxter, Nancy N; Lau, Cindy; Daly, Corinne; Pole, Jason D

2018-06-01

Despite the importance of estimating population level cancer outcomes, most registries do not collect critical events such as relapse. Attempts to use health administrative data to identify these events have focused on older adults and have been mostly unsuccessful. We developed and tested administrative data-based algorithms in a population-based cohort of adolescents and young adults with cancer. We identified all Ontario adolescents and young adults 15-21 years old diagnosed with leukemia, lymphoma, sarcoma, or testicular cancer between 1992-2012. Chart abstraction determined the end of initial treatment (EOIT) date and subsequent cancer-related events (progression, relapse, second cancer). Linkage to population-based administrative databases identified fee and procedure codes indicating cancer treatment or palliative care. Algorithms determining EOIT based on a time interval free of treatment-associated codes, and new cancer-related events based on billing codes, were compared with chart-abstracted data. The cohort comprised 1404 patients. Time periods free of treatment-associated codes did not validly identify EOIT dates; using subsequent codes to identify new cancer events was thus associated with low sensitivity (56.2%). However, using administrative data codes that occurred after the EOIT date based on chart abstraction, the first cancer-related event was identified with excellent validity (sensitivity, 87.0%; specificity, 93.3%; positive predictive value, 81.5%; negative predictive value, 95.5%). Although administrative data alone did not validly identify cancer-related events, administrative data in combination with chart collected EOIT dates was associated with excellent validity. The collection of EOIT dates by cancer registries would significantly expand the potential of administrative data linkage to assess cancer outcomes.

Implications of Supermarket Access, Neighborhood Walkability, and Poverty Rates for Diabetes Risk in an Employee Population

PubMed Central

Herrick, Cynthia J.; Yount, Byron W.; Eyler, Amy A.

2016-01-01

Objective Diabetes is a growing public health problem, and the environment in which people live and work may affect diabetes risk. The goal of this study was to examine the association between multiple aspects of environment and diabetes risk in an employee population. Design This was a retrospective cross-sectional analysis. Home environment variables were derived using employee zip code. Descriptive statistics were run on all individual and zip code level variables, stratified by diabetes risk and worksite. A multivariable logistic regression analysis was then conducted to determine the strongest associations with diabetes risk. Setting Data was collected from employee health fairs in a Midwestern health system 2009–2012. Subjects The dataset contains 25,227 unique individuals across four years of data. From this group, using an individual’s first entry into the database, 15,522 individuals had complete data for analysis. Results The prevalence of high diabetes risk in this population was 2.3%. There was significant variability in individual and zip code level variables across worksites. From the multivariable analysis, living in a zip code with higher percent poverty and higher walk score was positively associated with high diabetes risk, while living in a zip code with higher supermarket density was associated with a reduction in high diabetes risk. Conclusions Our study underscores the important relationship between poverty, home neighborhood environment, and diabetes risk, even in a relatively healthy employed population, and suggests a role for the employer in promoting health. PMID:26638995

Implications of supermarket access, neighbourhood walkability and poverty rates for diabetes risk in an employee population.

PubMed

Herrick, Cynthia J; Yount, Byron W; Eyler, Amy A

2016-08-01

Diabetes is a growing public health problem, and the environment in which people live and work may affect diabetes risk. The goal of the present study was to examine the association between multiple aspects of environment and diabetes risk in an employee population. This was a retrospective cross-sectional analysis. Home environment variables were derived using employees' zip code. Descriptive statistics were run on all individual- and zip-code-level variables, stratified by diabetes risk and worksite. A multivariable logistic regression analysis was then conducted to determine the strongest associations with diabetes risk. Data were collected from employee health fairs in a Midwestern health system, 2009-2012. The data set contains 25 227 unique individuals across four years of data. From this group, using an individual's first entry into the database, 15 522 individuals had complete data for analysis. The prevalence of high diabetes risk in this population was 2·3 %. There was significant variability in individual- and zip-code-level variables across worksites. From the multivariable analysis, living in a zip code with higher percentage of poverty and higher walk score was positively associated with high diabetes risk, while living in a zip code with higher supermarket density was associated with a reduction in high diabetes risk. Our study underscores the important relationship between poverty, home neighbourhood environment and diabetes risk, even in a relatively healthy employed population, and suggests a role for the employer in promoting health.

PSRPOPPy: an open-source package for pulsar population simulations

NASA Astrophysics Data System (ADS)

Bates, S. D.; Lorimer, D. R.; Rane, A.; Swiggum, J.

2014-04-01

We have produced a new software package for the simulation of pulsar populations, PSRPOPPY, based on the PSRPOP package. The codebase has been re-written in Python (save for some external libraries, which remain in their native Fortran), utilizing the object-oriented features of the language, and improving the modularity of the code. Pre-written scripts are provided for running the simulations in `standard' modes of operation, but the code is flexible enough to support the writing of personalised scripts. The modular structure also makes the addition of experimental features (such as new models for period or luminosity distributions) more straightforward than with the previous code. We also discuss potential additions to the modelling capabilities of the software. Finally, we demonstrate some potential applications of the code; first, using results of surveys at different observing frequencies, we find pulsar spectral indices are best fitted by a normal distribution with mean -1.4 and standard deviation 1.0. Secondly, we model pulsar spin evolution to calculate the best fit for a relationship between a pulsar's luminosity and spin parameters. We used the code to replicate the analysis of Faucher-Giguère & Kaspi, and have subsequently optimized their power-law dependence of radio luminosity, L, with period, P, and period derivative, Ṗ. We find that the underlying population is best described by L ∝ P-1.39±0.09 Ṗ0.48±0.04 and is very similar to that found for γ-ray pulsars by Perera et al. Using this relationship, we generate a model population and examine the age-luminosity relation for the entire pulsar population, which may be measurable after future large-scale surveys with the Square Kilometre Array.

Inference in the brain: Statistics flowing in redundant population codes

PubMed Central

Pitkow, Xaq; Angelaki, Dora E

2017-01-01

It is widely believed that the brain performs approximate probabilistic inference to estimate causal variables in the world from ambiguous sensory data. To understand these computations, we need to analyze how information is represented and transformed by the actions of nonlinear recurrent neural networks. We propose that these probabilistic computations function by a message-passing algorithm operating at the level of redundant neural populations. To explain this framework, we review its underlying concepts, including graphical models, sufficient statistics, and message-passing, and then describe how these concepts could be implemented by recurrently connected probabilistic population codes. The relevant information flow in these networks will be most interpretable at the population level, particularly for redundant neural codes. We therefore outline a general approach to identify the essential features of a neural message-passing algorithm. Finally, we argue that to reveal the most important aspects of these neural computations, we must study large-scale activity patterns during moderately complex, naturalistic behaviors. PMID:28595050

What factors predict the passage of state-level e-cigarette regulations?

PubMed

Maclean, Johanna Catherine; Oney, Melissa; Marti, Joachim; Sindelar, Jody

2018-05-01

E-cigarettes are controversial products. They may help addicted smokers to consume nicotine in a less harmful manner or to quit tobacco cigarettes entirely, but these products may also entice youth into smoking. This controversy complicates e-cigarette regulation as any regulation may lead to health improvements for some populations, and health declines for other populations. Using data from 2007 to 2016, we examine factors that are plausibly linked with U.S. state e-cigarette regulations. We find that less conservative states are more likely to regulate e-cigarettes and that states with stronger tobacco lobbies are less likely to regulate e-cigarettes. This information can help policymakers as they determine how best to promote public health through regulation. Copyright © 2018 John Wiley & Sons, Ltd.

Evaluating disease management program effectiveness: an introduction to time-series analysis.

PubMed

Linden, Ariel; Adams, John L; Roberts, Nancy

2003-01-01

Currently, the most widely used method in the disease management (DM) industry for evaluating program effectiveness is referred to as the "total population approach." This model is a pretest-posttest design, with the most basic limitation being that without a control group, there may be sources of bias and/or competing extraneous confounding factors that offer a plausible rationale explaining the change from baseline. Furthermore, with the current inclination of DM programs to use financial indicators rather than program-specific utilization indicators as the principal measure of program success, additional biases are introduced that may cloud evaluation results. This paper presents a non-technical introduction to time-series analysis (using disease-specific utilization measures) as an alternative, and more appropriate, approach to evaluating DM program effectiveness than the current total population approach.

Genome-Wide Meta-Analysis Identifies Regions on 7p21 (AHR) and 15q24 (CYP1A2) As Determinants of Habitual Caffeine Consumption

PubMed Central

Azzato, Elizabeth M.; Bennett, Siiri N.; Berndt, Sonja I.; Boerwinkle, Eric; Chanock, Stephen; Chatterjee, Nilanjan; Couper, David; Curhan, Gary; Heiss, Gerardo; Hu, Frank B.; Hunter, David J.; Jacobs, Kevin; Jensen, Majken K.; Kraft, Peter; Landi, Maria Teresa; Nettleton, Jennifer A.; Purdue, Mark P.; Rajaraman, Preetha; Rimm, Eric B.; Rose, Lynda M.; Rothman, Nathaniel; Silverman, Debra; Stolzenberg-Solomon, Rachael; Subar, Amy; Yeager, Meredith; Chasman, Daniel I.; van Dam, Rob M.; Caporaso, Neil E.

2011-01-01

We report the first genome-wide association study of habitual caffeine intake. We included 47,341 individuals of European descent based on five population-based studies within the United States. In a meta-analysis adjusted for age, sex, smoking, and eigenvectors of population variation, two loci achieved genome-wide significance: 7p21 (P = 2.4×10−19), near AHR, and 15q24 (P = 5.2×10−14), between CYP1A1 and CYP1A2. Both the AHR and CYP1A2 genes are biologically plausible candidates as CYP1A2 metabolizes caffeine and AHR regulates CYP1A2. PMID:21490707

Reactive transport modeling in the subsurface environment with OGS-IPhreeqc

NASA Astrophysics Data System (ADS)

He, Wenkui; Beyer, Christof; Fleckenstein, Jan; Jang, Eunseon; Kalbacher, Thomas; Naumov, Dimitri; Shao, Haibing; Wang, Wenqing; Kolditz, Olaf

2015-04-01

Worldwide, sustainable water resource management becomes an increasingly challenging task due to the growth of population and extensive applications of fertilizer in agriculture. Moreover, climate change causes further stresses to both water quantity and quality. Reactive transport modeling in the coupled soil-aquifer system is a viable approach to assess the impacts of different land use and groundwater exploitation scenarios on the water resources. However, the application of this approach is usually limited in spatial scale and to simplified geochemical systems due to the huge computational expense involved. Such computational expense is not only caused by solving the high non-linearity of the initial boundary value problems of water flow in the unsaturated zone numerically with rather fine spatial and temporal discretization for the correct mass balance and numerical stability, but also by the intensive computational task of quantifying geochemical reactions. In the present study, a flexible and efficient tool for large scale reactive transport modeling in variably saturated porous media and its applications are presented. The open source scientific software OpenGeoSys (OGS) is coupled with the IPhreeqc module of the geochemical solver PHREEQC. The new coupling approach makes full use of advantages from both codes: OGS provides a flexible choice of different numerical approaches for simulation of water flow in the vadose zone such as the pressure-based or mixed forms of Richards equation; whereas the IPhreeqc module leads to a simplification of data storage and its communication with OGS, which greatly facilitates the coupling and code updating. Moreover, a parallelization scheme with MPI (Message Passing Interface) is applied, in which the computational task of water flow and mass transport is partitioned through domain decomposition, whereas the efficient parallelization of geochemical reactions is achieved by smart allocation of computational workload over multiple compute nodes. The plausibility of the new coupling is verified by several benchmark tests. In addition, the efficiency of the new coupling approach is demonstrated by its application in a large scale scenario, in which the environmental fate of pesticides in a complex soil-aquifer system is studied.

Reactive transport modeling in variably saturated porous media with OGS-IPhreeqc

NASA Astrophysics Data System (ADS)

He, W.; Beyer, C.; Fleckenstein, J. H.; Jang, E.; Kalbacher, T.; Shao, H.; Wang, W.; Kolditz, O.

2014-12-01

Worldwide, sustainable water resource management becomes an increasingly challenging task due to the growth of population and extensive applications of fertilizer in agriculture. Moreover, climate change causes further stresses to both water quantity and quality. Reactive transport modeling in the coupled soil-aquifer system is a viable approach to assess the impacts of different land use and groundwater exploitation scenarios on the water resources. However, the application of this approach is usually limited in spatial scale and to simplified geochemical systems due to the huge computational expense involved. Such computational expense is not only caused by solving the high non-linearity of the initial boundary value problems of water flow in the unsaturated zone numerically with rather fine spatial and temporal discretization for the correct mass balance and numerical stability, but also by the intensive computational task of quantifying geochemical reactions. In the present study, a flexible and efficient tool for large scale reactive transport modeling in variably saturated porous media and its applications are presented. The open source scientific software OpenGeoSys (OGS) is coupled with the IPhreeqc module of the geochemical solver PHREEQC. The new coupling approach makes full use of advantages from both codes: OGS provides a flexible choice of different numerical approaches for simulation of water flow in the vadose zone such as the pressure-based or mixed forms of Richards equation; whereas the IPhreeqc module leads to a simplification of data storage and its communication with OGS, which greatly facilitates the coupling and code updating. Moreover, a parallelization scheme with MPI (Message Passing Interface) is applied, in which the computational task of water flow and mass transport is partitioned through domain decomposition, whereas the efficient parallelization of geochemical reactions is achieved by smart allocation of computational workload over multiple compute nodes. The plausibility of the new coupling is verified by several benchmark tests. In addition, the efficiency of the new coupling approach is demonstrated by its application in a large scale scenario, in which the environmental fate of pesticides in a complex soil-aquifer system is studied.

The Time Course of Plausibility Effects on Eye Movements in Reading: Evidence from Noun-Noun Compounds

ERIC Educational Resources Information Center

Staub, Adrian; Rayner, Keith; Pollatsek, Alexander; Hyona, Jukka; Majewski, Helen

2007-01-01

Readers' eye movements were monitored as they read sentences containing noun-noun compounds that varied in frequency (e.g., elevator mechanic, mountain lion). The left constituent of the compound was either plausible or implausible as a head noun at the point at which it appeared, whereas the compound as a whole was always plausible. When the head…

Glioma and occupational exposure in Sweden, a case-control study.

PubMed Central

Rodvall, Y; Ahlbom, A; Spännare, B; Nise, G

1996-01-01

OBJECTIVES: The aim of the study was to analyse whether any job titles, industrial codes, and certain occupational exposures were associated with an increased risk of glioma. METHODS: A population based case-control study of incident primary brain tumours in adults was carried out in Uppsala, Sweden in the period 1987-90. The study included 192 cases of glioma and 192 matched controls. It also included cases with other tumours of the central nervous system with matched controls. Information from all 343 controls was used in this study. Information was collected by means of a questionnaire that was sent to all subjects. An occupational hygienist reviewed the questionnaires for self reported exposures to substances and assessed whether these reported exposures were plausible or not in the corresponding occupation. RESULTS: The kappa coefficient for those classified by the two methods ranged between 0.46 and 0.88, and they were almost the same for cases and controls. For men exposed to solvents a relative risk (RR) of 2.6 (95% CI 1.3 to 5.2) was found. For men exposed to pesticides the RR was 1.8 (95% CI 0.6 to 5.1), and for plastic materials the RR was 3.6 (95% CI 1.0 to 12.4). For men employed in forestry and logging the RR was 2.2 (95% CI 0.9 to 5.3) and in basic metal industries 2.0 (95% CI 1.0 to 4.0). CONCLUSION: An increased risk of glioma was associated with use of solvents, pesticides, and plastic materials but this should be interpreted with some caution. PMID:8983463

BRIP1 overexpression is correlated with clinical features and survival outcome of luminal breast cancer subtypes

PubMed Central

Gupta, Ishita; Ouhtit, Allal; Al-Ajmi, Adil; Rizvi, Syed Gauhar A; Al-Riyami, Hamad; Al-Riyami, Marwa

2018-01-01

In Oman, breast cancer is most common, representing approximately more than 25% of all cancers in women. Relatively younger populations of patients (25–40 years) present surprisingly with an aggressive phenotype and advanced tumor stages. In this study, we investigated differential gene expressions in Luminal A, Luminal B, triple-negative and Her2+ breast cancer subtypes and compared data to benign tumor samples. We identified a potential candidate gene BRIP1, showing differential expression in the four breast cancer subtypes examined, suggesting that BRIP1 has the profile of a useful diagnostic marker, suitable for targeted therapeutic intervention. RT-qPCR and Western blotting analysis showed higher BRIP1 expression in luminal samples as compared to triple-negative subtype patient’s samples. We further screened BRIP1 for eventual mutations/SNPs/deletions by sequencing the entire coding region. Four previously identified polymorphisms were detected, one within the 5′-UTR region (c.141-64G > A) and three in the BRCA-binding domain (c.2755T > C, c.2647G > A and c.3411T > C). Kaplan–Meier analysis revealed that patients with overexpression of BRIP1 displayed a poor survival rate (P < 0.05). BRIP1 has a dual function of an oncogene and a tumor suppressor gene in addition to its role as a potential biomarker to predict survival and prognosis. Data obtained in this study suggest that BRIP1 can plausibly have an oncogenic role in sporadic cancers. PMID:29138235

Constitutional CHEK2 mutations are infrequent in early-onset and familial breast/ovarian cancer patients from Pakistan

PubMed Central

2013-01-01

Background Less than 20% of Pakistani women with early-onset or familial breast/ovarian cancer harbor germ line mutations in the high-penetrance genes BRCA1, BRCA2 and TP53. Thus, mutations in other genes confer genetic susceptibility to breast cancer, of which CHEK2 is a plausible candidate. CHEK2 encodes a checkpoint kinase, involved in response to DNA damage. Methods In the present study we assessed the prevalence of CHEK2 germ line mutations in 145 BRCA1/2-negative early-onset and familial breast/ovarian cancer patients from Pakistan (Group 1). Mutation analysis of the complete CHEK2 coding region was performed using denaturing high-performance liquid chromatography analysis, followed by DNA sequencing of variant fragments. Results Two potentially deleterious missense mutations, c.275C>G (p.P92R) and c.1216C>T, (p.R406C), were identified (1.4%). The c.275C>G mutation is novel and has not been described in other populations. It was detected in a 30-year-old breast cancer patient with a family history of breast and multiple other cancers. The c.1216C>T mutation was found in a 34-year-old ovarian cancer patient from a family with two breast cancer cases. Both mutations were not detected in 229 recently recruited BRCA1/2-negative high risk patients (Group 2). Conclusion Our findings suggest that CHEK2 mutations may not contribute significantly to breast/ovarian cancer risk in Pakistani women. PMID:23806170

The functional spectrum of low-frequency coding variation.

PubMed

Marth, Gabor T; Yu, Fuli; Indap, Amit R; Garimella, Kiran; Gravel, Simon; Leong, Wen Fung; Tyler-Smith, Chris; Bainbridge, Matthew; Blackwell, Tom; Zheng-Bradley, Xiangqun; Chen, Yuan; Challis, Danny; Clarke, Laura; Ball, Edward V; Cibulskis, Kristian; Cooper, David N; Fulton, Bob; Hartl, Chris; Koboldt, Dan; Muzny, Donna; Smith, Richard; Sougnez, Carrie; Stewart, Chip; Ward, Alistair; Yu, Jin; Xue, Yali; Altshuler, David; Bustamante, Carlos D; Clark, Andrew G; Daly, Mark; DePristo, Mark; Flicek, Paul; Gabriel, Stacey; Mardis, Elaine; Palotie, Aarno; Gibbs, Richard

2011-09-14

Rare coding variants constitute an important class of human genetic variation, but are underrepresented in current databases that are based on small population samples. Recent studies show that variants altering amino acid sequence and protein function are enriched at low variant allele frequency, 2 to 5%, but because of insufficient sample size it is not clear if the same trend holds for rare variants below 1% allele frequency. The 1000 Genomes Exon Pilot Project has collected deep-coverage exon-capture data in roughly 1,000 human genes, for nearly 700 samples. Although medical whole-exome projects are currently afoot, this is still the deepest reported sampling of a large number of human genes with next-generation technologies. According to the goals of the 1000 Genomes Project, we created effective informatics pipelines to process and analyze the data, and discovered 12,758 exonic SNPs, 70% of them novel, and 74% below 1% allele frequency in the seven population samples we examined. Our analysis confirms that coding variants below 1% allele frequency show increased population-specificity and are enriched for functional variants. This study represents a large step toward detecting and interpreting low frequency coding variation, clearly lays out technical steps for effective analysis of DNA capture data, and articulates functional and population properties of this important class of genetic variation.

Polymorphism at the defensin gene in the Anopheles gambiae complex: testing different selection hypotheses

PubMed Central

Simard, Frédéric; Licht, Monica; Besansky, Nora J.; Lehmann, Tovi

2007-01-01

Genetic variation in defensin, a gene encoding a major effector molecule of insects immune response was analyzed within and between populations of three members of the Anopheles gambiae complex. The species selected included the two anthropophilic species, An. gambiae and An. arabiensis and the most zoophilic species of the complex, An. quadriannulatus. The first species was represented by four populations spanning its extreme genetic and geographical ranges, whereas each of the other two species was represented by a single population. We found (i) reduced overall polymorphism in the mature peptide region and in the total coding region, together with specific reductions in rare and moderately frequent mutations (sites) in the coding region compared with non coding regions, (ii) markedly reduced rate of nonsynonymous diversity compared with synonymous variation in the mature peptide and virtually identical mature peptide across the three species, and (iii) increased divergence between species in the mature peptide together with reduced differentiation between populations of An. gambiae in the same DNA region. These patterns suggest a strong purifying selection on the mature peptide and probably the whole coding region. Because An. quadriannulatus is not exposed to human pathogens, identical mature peptide and similar pattern of polymorphism across species implies that human pathogens played no role as selective agents on this peptide. PMID:17161659

Defining traumatic brain injury in children and youth using international classification of diseases version 10 codes: a systematic review protocol.

PubMed

Chan, Vincy; Thurairajah, Pravheen; Colantonio, Angela

2013-11-13

Although healthcare administrative data are commonly used for traumatic brain injury research, there is currently no consensus or consistency on using the International Classification of Diseases version 10 codes to define traumatic brain injury among children and youth. This protocol is for a systematic review of the literature to explore the range of International Classification of Diseases version 10 codes that are used to define traumatic brain injury in this population. The databases MEDLINE, MEDLINE In-Process, Embase, PsychINFO, CINAHL, SPORTDiscus, and Cochrane Database of Systematic Reviews will be systematically searched. Grey literature will be searched using Grey Matters and Google. Reference lists of included articles will also be searched. Articles will be screened using predefined inclusion and exclusion criteria and all full-text articles that meet the predefined inclusion criteria will be included for analysis. The study selection process and reasons for exclusion at the full-text level will be presented using a PRISMA study flow diagram. Information on the data source of included studies, year and location of study, age of study population, range of incidence, and study purpose will be abstracted into a separate table and synthesized for analysis. All International Classification of Diseases version 10 codes will be listed in tables and the codes that are used to define concussion, acquired traumatic brain injury, head injury, or head trauma will be identified. The identification of the optimal International Classification of Diseases version 10 codes to define this population in administrative data is crucial, as it has implications for policy, resource allocation, planning of healthcare services, and prevention strategies. It also allows for comparisons across countries and studies. This protocol is for a review that identifies the range and most common diagnoses used to conduct surveillance for traumatic brain injury in children and youth. This is an important first step in reaching an appropriate definition using International Classification of Diseases version 10 codes and can inform future work on reaching consensus on the codes to define traumatic brain injury for this vulnerable population.

Clinical and billing review of extracorporeal membrane oxygenation.

PubMed

Blum, James M; Lynch, William R; Coopersmith, Craig M

2015-06-01

Extracorporeal membrane oxygenation (ECMO) is a temporary technique for providing life support for cardiac dysfunction, pulmonary dysfunction, or both. The two forms of ECMO, veno-arterial (VA) and veno-venous (VV), are used to support cardiopulmonary and pulmonary dysfunction, respectively. Historically, ECMO was predominantly used in the neonatal and pediatric populations, as early adult studies failed to improve outcomes. ECMO has become far more common in the adult population because of positive results in published case series and clinical trials during the 2009 influenza A(H1N1) pandemic in 2009 to 2010. Advances in technology that make the technique much easier to implement likely fueled the renewed interest. Although exact criteria for ECMO are not available, patients who are good candidates are generally considered to be relatively young and suffering from acute illness that is believed to be reversible or organ dysfunction that is otherwise treatable. With the increase in the use in the adult population, a number of different codes have been generated to better identify the method of support with distinctly different relative value units assigned to each code from a very simple prior coding scheme. To effectively be reimbursed for use of the technique, it is imperative that the clinician understands the new coding scheme and works with payers to determine what is incorporated into each specific code.

Genetic diversity of the HLA-G coding region in Amerindian populations from the Brazilian Amazon: a possible role of natural selection.

PubMed

Mendes-Junior, C T; Castelli, E C; Meyer, D; Simões, A L; Donadi, E A

2013-12-01

HLA-G has an important role in the modulation of the maternal immune system during pregnancy, and evidence that balancing selection acts in the promoter and 3'UTR regions has been previously reported. To determine whether selection acts on the HLA-G coding region in the Amazon Rainforest, exons 2, 3 and 4 were analyzed in a sample of 142 Amerindians from nine villages of five isolated tribes that inhabit the Central Amazon. Six previously described single-nucleotide polymorphisms (SNPs) were identified and the Expectation-Maximization (EM) and PHASE algorithms were used to computationally reconstruct SNP haplotypes (HLA-G alleles). A new HLA-G allele, which originated in Amerindian populations by a crossing-over event between two widespread HLA-G alleles, was identified in 18 individuals. Neutrality tests evidenced that natural selection has a complex part in the HLA-G coding region. Although balancing selection is the type of selection that shapes variability at a local level (Native American populations), we have also shown that purifying selection may occur on a worldwide scale. Moreover, the balancing selection does not seem to act on the coding region as strongly as it acts on the flanking regulatory regions, and such coding signature may actually reflect a hitchhiking effect.

Estimating the Cost-Effectiveness of HIV Prevention Programmes in Vietnam, 2006-2010: A Modelling Study

PubMed Central

Pham, Quang Duy; Wilson, David P.; Kerr, Cliff C.; Shattock, Andrew J.; Do, Hoa Mai; Duong, Anh Thuy; Nguyen, Long Thanh; Zhang, Lei

2015-01-01

Introduction Vietnam has been largely reliant on international support in its HIV response. Over 2006-2010, a total of US$480 million was invested in its HIV programmes, more than 70% of which came from international sources. This study investigates the potential epidemiological impacts of these programmes and their cost-effectiveness. Methods We conducted a data synthesis of HIV programming, spending, epidemiological, and clinical outcomes. Counterfactual scenarios were defined based on assumed programme coverage and behaviours had the programmes not been implemented. An epidemiological model, calibrated to reflect the actual epidemiological trends, was used to estimate plausible ranges of programme impacts. The model was then used to estimate the costs per averted infection, death, and disability adjusted life-year (DALY). Results Based on observed prevalence reductions amongst most population groups, and plausible counterfactuals, modelling suggested that antiretroviral therapy (ART) and prevention programmes over 2006-2010 have averted an estimated 50,600 [95% uncertainty bound: 36,300–68,900] new infections and 42,600 [36,100–54,100] deaths, resulting in 401,600 [312,200–496,300] fewer DALYs across all population groups. HIV programmes in Vietnam have cost an estimated US$1,972 [1,447–2,747], US$2,344 [1,843–2,765], and US$248 [201–319] for each averted infection, death, and DALY, respectively. Conclusions Our evaluation suggests that HIV programmes in Vietnam have most likely had benefits that are cost-effective. ART and direct HIV prevention were the most cost-effective interventions in reducing HIV disease burden. PMID:26196290

Infectious Etiologies of Childhood Leukemia: Plausibility and Challenges to Proof

PubMed Central

O’Connor, Siobhán M.; Boneva, Roumiana S.

2007-01-01

Infections as well as environmental exposures are proposed determinants of childhood acute lymphoblastic leukemia (ALL), particularly common precursor B-cell ALL (cALL). Lines of investigation test hypotheses that cALL is a rarer result of common infection, that it results from uncommon infection, or that it ensues from abnormal immune development; perhaps it requires a preceding prenatal or early childhood insult. Ideally, studies should document that particular infections precede leukemia and induce malignant transformation. However, limited detection studies have not directly linked specific human or nonhuman infectious agents with ALL or cALL. Primarily based on surrogate markers of infectious exposure, indirect evidence from ecologic and epidemiologic studies varies widely, but some suggest that infancy or early childhood infectious exposures might protect against childhood ALL or cALL. Several others suggest that maternal infection during pregnancy might increase risk or that certain breast-feeding practices decrease risk. To date, evidence cannot confirm or refute whether at least one infection induces or is a major co-factor for developing ALL or cALL, or perhaps actually protects against disease. Differences in methodology and populations studied may explain some inconsistencies. Other challenges to proof include the likely time lag between infection and diagnosis, the ubiquity of many infections, the influence of age at infection, and the limitations in laboratory assays; small numbers of cases, inaccurate background leukemia rates, and difficulty tracking mobile populations further affect cluster investigations. Nevertheless, existing evidence partially supports plausibility and warrants further investigation into potential infectious determinants of ALL and cALL, particularly in the context of multifactorial or complex systems. PMID:17366835

Developing a climate adaptation strategy for vulnerable seabirds based on prioritisation of intervention options

NASA Astrophysics Data System (ADS)

Alderman, Rachael; Hobday, Alistair J.

2017-06-01

Conservation of marine species typically focuses on monitoring and mitigating demonstrated stressors where possible. Evidence is accumulating that some species will be negatively affected in the future by climate change and that reduction of existing stressors may not be sufficient to offset these impacts. Recent work suggests the shy albatross (Thalassarche cauta) will be adversely affected by projected changes in environmental conditions under plausible climate change scenarios. Furthermore, modelling shows that elimination of the principal present-day threat to albatrosses, fisheries bycatch, an achievable and critical priority, may not be sufficient to reverse projected population declines due to climate impacts, which cannot be directly eliminated. Here, a case study is presented in which a range of intervention options, in preparation for predicted climate change impacts, are identified and evaluated. A suite of 24 plausible climate adaptation options is first assessed using a semi-quantitative cost-benefit-risk tool, leading to a relative ranking of actions. Of these options, increasing chick survival via reduction of disease prevalence through control of vectors, was selected for field trials. Avian insecticide was applied to chicks' mid-way through their development and the effect on subsequent survival was evaluated. Survival of treated chicks after six weeks was significantly higher (92.7%) than those in control areas (82.1%). This approach shows that options to enhance albatross populations exist and we argue that testing interventions prior to serious impacts can formalise institutional processes and allow refinement of actions that offer some chance of mitigating the impacts of climate change on iconic marine species.

Effects of plausibility on structural priming.

PubMed

Christianson, Kiel; Luke, Steven G; Ferreira, Fernanda

2010-03-01

We report a replication and extension of Ferreira (2003), in which it was observed that native adult English speakers misinterpret passive sentences that relate implausible but not impossible semantic relationships (e.g., The angler was caught by the fish) significantly more often than they do plausible passives or plausible or implausible active sentences. In the experiment reported here, participants listened to the same plausible and implausible passive and active sentences as in Ferreira (2003), answered comprehension questions, and then orally described line drawings of simple transitive actions. The descriptions were analyzed as a measure of structural priming (Bock, 1986). Question accuracy data replicated Ferreira (2003). Production data yielded an interaction: Passive descriptions were produced more often after plausible passives and implausible actives. We interpret these results as indicative of a language processor that proceeds along differentiated morphosyntactic and semantic routes. The processor may end up adjudicating between conflicting outputs from these routes by settling on a "good enough" representation that is not completely faithful to the input.

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Cannabis and psychosis: an update on course and biological plausible mechanisms.

PubMed

Linszen, Don; van Amelsvoort, Therese

2007-03-01

Cannabis use is the most commonly abused illicit substance. Its relation with psychosis remains a topic of debate. Epidemiological studies suggest that cannabis is a component cause accounting for approximately 10% of cases. An increasing number of studies have been published on neurobiological effects of cannabis and vulnerability of psychosis. Acute cannabis administration can induce memory impairments, sometimes persisting months following abstinence. There is no evidence that residual effects on cognition remain after years of abstinence. The scarce literature on neuro-imaging mainly done in nonpsychotic populations, show little evidence that cannabis has effects on brain anatomy. Acute effects of cannabis include increases of cerebral blood flow, whereas long-term effects of cannabis include attenuation of cerebral blood flow. In animals Delta9-tetrahydrocannabinol enhances dopaminergic neurotransmission in brain regions known to be implicated in psychosis. Studies in humans show that genetic vulnerability may add to increased risk of developing psychosis and cognitive impairments following cannabis consumption. Delta9-tetrahydrocannabinol induces psychotic like states and memory impairments in healthy volunteers. Simultaneously with increasing understanding of neurobiological cannabis effects, there is a lack of studies in people with psychosis. There are plausible mechanisms that might explain the psychotogenic effects of cannabis.

The Plausibility of a String Quartet Performance in Virtual Reality.

PubMed

Bergstrom, Ilias; Azevedo, Sergio; Papiotis, Panos; Saldanha, Nuno; Slater, Mel

2017-04-01

We describe an experiment that explores the contribution of auditory and other features to the illusion of plausibility in a virtual environment that depicts the performance of a string quartet. 'Plausibility' refers to the component of presence that is the illusion that the perceived events in the virtual environment are really happening. The features studied were: Gaze (the musicians ignored the participant, the musicians sometimes looked towards and followed the participant's movements), Sound Spatialization (Mono, Stereo, Spatial), Auralization (no sound reflections, reflections corresponding to a room larger than the one perceived, reflections that exactly matched the virtual room), and Environment (no sound from outside of the room, birdsong and wind corresponding to the outside scene). We adopted the methodology based on color matching theory, where 20 participants were first able to assess their feeling of plausibility in the environment with each of the four features at their highest setting. Then five times participants started from a low setting on all features and were able to make transitions from one system configuration to another until they matched their original feeling of plausibility. From these transitions a Markov transition matrix was constructed, and also probabilities of a match conditional on feature configuration. The results show that Environment and Gaze were individually the most important factors influencing the level of plausibility. The highest probability transitions were to improve Environment and Gaze, and then Auralization and Spatialization. We present this work as both a contribution to the methodology of assessing presence without questionnaires, and showing how various aspects of a musical performance can influence plausibility.

What if? Neural activity underlying semantic and episodic counterfactual thinking.

PubMed

Parikh, Natasha; Ruzic, Luka; Stewart, Gregory W; Spreng, R Nathan; De Brigard, Felipe

2018-05-25

Counterfactual thinking (CFT) is the process of mentally simulating alternative versions of known facts. In the past decade, cognitive neuroscientists have begun to uncover the neural underpinnings of CFT, particularly episodic CFT (eCFT), which activates regions in the default network (DN) also activated by episodic memory (eM) recall. However, the engagement of DN regions is different for distinct kinds of eCFT. More plausible counterfactuals and counterfactuals about oneself show stronger activity in DN regions compared to implausible and other- or object-focused counterfactuals. The current study sought to identify a source for this difference in DN activity. Specifically, self-focused counterfactuals may also be more plausible, suggesting that DN core regions are sensitive to the plausibility of a simulation. On the other hand, plausible and self-focused counterfactuals may involve more episodic information than implausible and other-focused counterfactuals, which would imply DN sensitivity to episodic information. In the current study, we compared episodic and semantic counterfactuals generated to be plausible or implausible against episodic and semantic memory reactivation using fMRI. Taking multivariate and univariate approaches, we found that the DN is engaged more during episodic simulations, including eM and all eCFT, than during semantic simulations. Semantic simulations engaged more inferior temporal and lateral occipital regions. The only region that showed strong plausibility effects was the hippocampus, which was significantly engaged for implausible CFT but not for plausible CFT, suggestive of binding more disparate information. Consequences of these findings for the cognitive neuroscience of mental simulation are discussed. Published by Elsevier Inc.

The double crush syndrome revisited--a Delphi study to reveal current expert views on mechanisms underlying dual nerve disorders.

PubMed

Schmid, Annina B; Coppieters, Michel W

2011-12-01

A high prevalence of dual nerve disorders is frequently reported. How a secondary nerve disorder may develop following a primary nerve disorder remains largely unknown. Although still frequently cited, most explanatory theories were formulated many years ago. Considering recent advances in neuroscience, it is uncertain whether these theories still reflect current expert opinion. A Delphi study was conducted to update views on potential mechanisms underlying dual nerve disorders. In three rounds, seventeen international experts in the field of peripheral nerve disorders were asked to list possible mechanisms and rate their plausibility. Mechanisms with a median plausibility rating of ≥7 out of 10 were considered highly plausible. The experts identified fourteen mechanisms associated with a first nerve disorder that may predispose to the development of another nerve disorder. Of these fourteen mechanisms, nine have not previously been linked to double crush. Four mechanisms were considered highly plausible (impaired axonal transport, ion channel up or downregulation, inflammation in the dorsal root ganglia and neuroma-in-continuity). Eight additional mechanisms were listed which are not triggered by a primary nerve disorder, but may render the nervous system more vulnerable to multiple nerve disorders, such as systemic diseases and neurotoxic medication. Even though many mechanisms were classified as plausible or highly plausible, overall plausibility ratings varied widely. Experts indicated that a wide range of mechanisms has to be considered to better understand dual nerve disorders. Previously listed theories cannot be discarded, but may be insufficient to explain the high prevalence of dual nerve disorders. Copyright © 2011 Elsevier Ltd. All rights reserved.

Methods and feasibility of collecting occupational data for a large population-based cohort study in the United States: the reasons for geographic and racial differences in stroke study

PubMed Central

2014-01-01

Background Coronary heart disease and stroke are major contributors to preventable mortality. Evidence links work conditions to these diseases; however, occupational data are perceived to be difficult to collect for large population-based cohorts. We report methodological details and the feasibility of conducting an occupational ancillary study for a large U.S. prospective cohort being followed longitudinally for cardiovascular disease and stroke. Methods Current and historical occupational information were collected from active participants of the REasons for Geographic And Racial Differences in Stroke (REGARDS) Study. A survey was designed to gather quality occupational data among this national cohort of black and white men and women aged 45 years and older (enrolled 2003–2007). Trained staff conducted Computer-Assisted Telephone Interviews (CATI). After a brief pilot period, interviewers received additional training in the collection of narrative industry and occupation data before administering the survey to remaining cohort members. Trained coders used a computer-assisted coding system to assign U.S. Census codes for industry and occupation. All data were double coded; discrepant codes were independently resolved. Results Over a 2-year period, 17,648 participants provided consent and completed the occupational survey (87% response rate). A total of 20,427 jobs were assigned Census codes. Inter-rater reliability was 80% for industry and 74% for occupation. Less than 0.5% of the industry and occupation data were uncodable, compared with 12% during the pilot period. Concordance between the current and longest-held jobs was moderately high. The median time to collect employment status plus narrative and descriptive job information by CATI was 1.6 to 2.3 minutes per job. Median time to assign Census codes was 1.3 minutes per rater. Conclusions The feasibility of conducting high-quality occupational data collection and coding for a large heterogeneous population-based sample was demonstrated. We found that training for interview staff was important in ensuring that narrative responses for industry and occupation were adequately specified for coding. Estimates of survey administration time and coding from digital records provide an objective basis for planning future studies. The social and environmental conditions of work are important understudied risk factors that can be feasibly integrated into large population-based health studies. PMID:24512119

Methods and feasibility of collecting occupational data for a large population-based cohort study in the United States: the reasons for geographic and racial differences in stroke study.

PubMed

MacDonald, Leslie A; Pulley, LeaVonne; Hein, Misty J; Howard, Virginia J

2014-02-10

Coronary heart disease and stroke are major contributors to preventable mortality. Evidence links work conditions to these diseases; however, occupational data are perceived to be difficult to collect for large population-based cohorts. We report methodological details and the feasibility of conducting an occupational ancillary study for a large U.S. prospective cohort being followed longitudinally for cardiovascular disease and stroke. Current and historical occupational information were collected from active participants of the REasons for Geographic And Racial Differences in Stroke (REGARDS) Study. A survey was designed to gather quality occupational data among this national cohort of black and white men and women aged 45 years and older (enrolled 2003-2007). Trained staff conducted Computer-Assisted Telephone Interviews (CATI). After a brief pilot period, interviewers received additional training in the collection of narrative industry and occupation data before administering the survey to remaining cohort members. Trained coders used a computer-assisted coding system to assign U.S. Census codes for industry and occupation. All data were double coded; discrepant codes were independently resolved. Over a 2-year period, 17,648 participants provided consent and completed the occupational survey (87% response rate). A total of 20,427 jobs were assigned Census codes. Inter-rater reliability was 80% for industry and 74% for occupation. Less than 0.5% of the industry and occupation data were uncodable, compared with 12% during the pilot period. Concordance between the current and longest-held jobs was moderately high. The median time to collect employment status plus narrative and descriptive job information by CATI was 1.6 to 2.3 minutes per job. Median time to assign Census codes was 1.3 minutes per rater. The feasibility of conducting high-quality occupational data collection and coding for a large heterogeneous population-based sample was demonstrated. We found that training for interview staff was important in ensuring that narrative responses for industry and occupation were adequately specified for coding. Estimates of survey administration time and coding from digital records provide an objective basis for planning future studies. The social and environmental conditions of work are important understudied risk factors that can be feasibly integrated into large population-based health studies.

Phylogenetic Network for European mtDNA

PubMed Central

Finnilä, Saara; Lehtonen, Mervi S.; Majamaa, Kari

2001-01-01

The sequence in the first hypervariable segment (HVS-I) of the control region has been used as a source of evolutionary information in most phylogenetic analyses of mtDNA. Population genetic inference would benefit from a better understanding of the variation in the mtDNA coding region, but, thus far, complete mtDNA sequences have been rare. We determined the nucleotide sequence in the coding region of mtDNA from 121 Finns, by conformation-sensitive gel electrophoresis and subsequent sequencing and by direct sequencing of the D loop. Furthermore, 71 sequences from our previous reports were included, so that the samples represented all the mtDNA haplogroups present in the Finnish population. We found a total of 297 variable sites in the coding region, which allowed the compilation of unambiguous phylogenetic networks. The D loop harbored 104 variable sites, and, in most cases, these could be localized within the coding-region networks, without discrepancies. Interestingly, many homoplasies were detected in the coding region. Nucleotide variation in the rRNA and tRNA genes was 6%, and that in the third nucleotide positions of structural genes amounted to 22% of that in the HVS-I. The complete networks enabled the relationships between the mtDNA haplogroups to be analyzed. Phylogenetic networks based on the entire coding-region sequence in mtDNA provide a rich source for further population genetic studies, and complete sequences make it easier to differentiate between disease-causing mutations and rare polymorphisms. PMID:11349229

Direct observation of mother-child communication in pediatric cancer: assessment of verbal and non-verbal behavior and emotion.

PubMed

Dunn, Madeleine J; Rodriguez, Erin M; Miller, Kimberly S; Gerhardt, Cynthia A; Vannatta, Kathryn; Saylor, Megan; Scheule, C Melanie; Compas, Bruce E

2011-06-01

To examine the acceptability and feasibility of coding observed verbal and nonverbal behavioral and emotional components of mother-child communication among families of children with cancer. Mother-child dyads (N=33, children ages 5-17 years) were asked to engage in a videotaped 15-min conversation about the child's cancer. Coding was done using the Iowa Family Interaction Rating Scale (IFIRS). Acceptability and feasibility of direct observation in this population were partially supported: 58% consented and 81% of those (47% of all eligible dyads) completed the task; trained raters achieved 78% agreement in ratings across codes. The construct validity of the IFIRS was demonstrated by expected associations within and between positive and negative behavioral/emotional code ratings and between mothers' and children's corresponding code ratings. Direct observation of mother-child communication about childhood cancer has the potential to be an acceptable and feasible method of assessing verbal and nonverbal behavior and emotion in this population.

Using Prospect Theory to Investigate Decision-Making Bias Within an Information Security Context

DTIC Science & Technology

2005-12-01

risk was acceptable, 5 when to the CA the risk was so bad...Population Proportion Lower Tail: Risk Averse (A) Coded as 0. Risk Seeking (B) Coded as 1. Ho (indifferent in risk behavior): p = . 5 Ha ( risk averse...Averse (A) Coded as 0. Risk Seeking (B) Coded as 1. Ho (indifferent in risk behavior): p = . 5 Ha ( risk averse thus significantly below . 5 ): p < . 5

Efficient Coding and Statistically Optimal Weighting of Covariance among Acoustic Attributes in Novel Sounds

PubMed Central

Stilp, Christian E.; Kluender, Keith R.

2012-01-01

To the extent that sensorineural systems are efficient, redundancy should be extracted to optimize transmission of information, but perceptual evidence for this has been limited. Stilp and colleagues recently reported efficient coding of robust correlation (r = .97) among complex acoustic attributes (attack/decay, spectral shape) in novel sounds. Discrimination of sounds orthogonal to the correlation was initially inferior but later comparable to that of sounds obeying the correlation. These effects were attenuated for less-correlated stimuli (r = .54) for reasons that are unclear. Here, statistical properties of correlation among acoustic attributes essential for perceptual organization are investigated. Overall, simple strength of the principal correlation is inadequate to predict listener performance. Initial superiority of discrimination for statistically consistent sound pairs was relatively insensitive to decreased physical acoustic/psychoacoustic range of evidence supporting the correlation, and to more frequent presentations of the same orthogonal test pairs. However, increased range supporting an orthogonal dimension has substantial effects upon perceptual organization. Connectionist simulations and Eigenvalues from closed-form calculations of principal components analysis (PCA) reveal that perceptual organization is near-optimally weighted to shared versus unshared covariance in experienced sound distributions. Implications of reduced perceptual dimensionality for speech perception and plausible neural substrates are discussed. PMID:22292057

Dominant, open nonverbal displays are attractive at zero-acquaintance

PubMed Central

Vacharkulksemsuk, Tanya; Reit, Emily; Khambatta, Poruz; Eastwick, Paul W.; Finkel, Eli J.; Carney, Dana R.

2016-01-01

Across two field studies of romantic attraction, we demonstrate that postural expansiveness makes humans more romantically appealing. In a field study (n = 144 speed-dates), we coded nonverbal behaviors associated with liking, love, and dominance. Postural expansiveness—expanding the body in physical space—was most predictive of attraction, with each one-unit increase in coded behavior from the video recordings nearly doubling a person’s odds of getting a “yes” response from one’s speed-dating partner. In a subsequent field experiment (n = 3,000), we tested the causality of postural expansion (vs. contraction) on attraction using a popular Global Positioning System-based online-dating application. Mate-seekers rapidly flipped through photographs of potential sexual/date partners, selecting those they desired to meet for a date. Mate-seekers were significantly more likely to select partners displaying an expansive (vs. contractive) nonverbal posture. Mediation analyses demonstrate one plausible mechanism through which expansiveness is appealing: Expansiveness makes the dating candidate appear more dominant. In a dating world in which success sometimes is determined by a split-second decision rendered after a brief interaction or exposure to a static photograph, single persons have very little time to make a good impression. Our research suggests that a nonverbal dominance display increases a person’s chances of being selected as a potential mate. PMID:27035937

Dominant, open nonverbal displays are attractive at zero-acquaintance.

PubMed

Vacharkulksemsuk, Tanya; Reit, Emily; Khambatta, Poruz; Eastwick, Paul W; Finkel, Eli J; Carney, Dana R

2016-04-12

Across two field studies of romantic attraction, we demonstrate that postural expansiveness makes humans more romantically appealing. In a field study (n = 144 speed-dates), we coded nonverbal behaviors associated with liking, love, and dominance. Postural expansiveness-expanding the body in physical space-was most predictive of attraction, with each one-unit increase in coded behavior from the video recordings nearly doubling a person's odds of getting a "yes" response from one's speed-dating partner. In a subsequent field experiment (n = 3,000), we tested the causality of postural expansion (vs. contraction) on attraction using a popular Global Positioning System-based online-dating application. Mate-seekers rapidly flipped through photographs of potential sexual/date partners, selecting those they desired to meet for a date. Mate-seekers were significantly more likely to select partners displaying an expansive (vs. contractive) nonverbal posture. Mediation analyses demonstrate one plausible mechanism through which expansiveness is appealing: Expansiveness makes the dating candidate appear more dominant. In a dating world in which success sometimes is determined by a split-second decision rendered after a brief interaction or exposure to a static photograph, single persons have very little time to make a good impression. Our research suggests that a nonverbal dominance display increases a person's chances of being selected as a potential mate.

Disability Evaluation System Analysis and Research Annual Report 2015

DTIC Science & Technology

2016-03-11

that of the military population as a whole; exceeding weight and body fat standards (i.e. overweight or obesity ) was the most common condition listed...prevalent conditions in the general military applicant population [8].  The most common conditions noted at the MEPS, were: overweight, obesity , and...ICD-9 Diagnosis Code n % of Cond 1 % of App 2 ICD-9 Diagnosis Code n % of Cond 1 % of App 2 Overweight, obesity and other

Knowledge extraction from evolving spiking neural networks with rank order population coding.

PubMed

Soltic, Snjezana; Kasabov, Nikola

2010-12-01

This paper demonstrates how knowledge can be extracted from evolving spiking neural networks with rank order population coding. Knowledge discovery is a very important feature of intelligent systems. Yet, a disproportionally small amount of research is centered on the issue of knowledge extraction from spiking neural networks which are considered to be the third generation of artificial neural networks. The lack of knowledge representation compatibility is becoming a major detriment to end users of these networks. We show that a high-level knowledge can be obtained from evolving spiking neural networks. More specifically, we propose a method for fuzzy rule extraction from an evolving spiking network with rank order population coding. The proposed method was used for knowledge discovery on two benchmark taste recognition problems where the knowledge learnt by an evolving spiking neural network was extracted in the form of zero-order Takagi-Sugeno fuzzy IF-THEN rules.

Improving coding accuracy in an academic practice.

PubMed

Nguyen, Dana; O'Mara, Heather; Powell, Robert

2017-01-01

Practice management has become an increasingly important component of graduate medical education. This applies to every practice environment; private, academic, and military. One of the most critical aspects of practice management is documentation and coding for physician services, as they directly affect the financial success of any practice. Our quality improvement project aimed to implement a new and innovative method for teaching billing and coding in a longitudinal fashion in a family medicine residency. We hypothesized that implementation of a new teaching strategy would increase coding accuracy rates among residents and faculty. Design: single group, pretest-posttest. military family medicine residency clinic. Study populations: 7 faculty physicians and 18 resident physicians participated as learners in the project. Educational intervention: monthly structured coding learning sessions in the academic curriculum that involved learner-presented cases, small group case review, and large group discussion. overall coding accuracy (compliance) percentage and coding accuracy per year group for the subjects that were able to participate longitudinally. Statistical tests used: average coding accuracy for population; paired t test to assess improvement between 2 intervention periods, both aggregate and by year group. Overall coding accuracy rates remained stable over the course of time regardless of the modality of the educational intervention. A paired t test was conducted to compare coding accuracy rates at baseline (mean (M)=26.4%, SD=10%) to accuracy rates after all educational interventions were complete (M=26.8%, SD=12%); t24=-0.127, P=.90. Didactic teaching and small group discussion sessions did not improve overall coding accuracy in a residency practice. Future interventions could focus on educating providers at the individual level.

The impact of conventional dietary intake data coding methods on foods typically consumed by low-income African-American and White urban populations.

PubMed

Mason, Marc A; Fanelli Kuczmarski, Marie; Allegro, Deanne; Zonderman, Alan B; Evans, Michele K

2015-08-01

Analysing dietary data to capture how individuals typically consume foods is dependent on the coding variables used. Individual foods consumed simultaneously, like coffee with milk, are given codes to identify these combinations. Our literature review revealed a lack of discussion about using combination codes in analysis. The present study identified foods consumed at mealtimes and by race when combination codes were or were not utilized. Duplicate analysis methods were performed on separate data sets. The original data set consisted of all foods reported; each food was coded as if it was consumed individually. The revised data set was derived from the original data set by first isolating coded foods consumed as individual items from those foods consumed simultaneously and assigning a code to designate a combination. Foods assigned a combination code, like pancakes with syrup, were aggregated and associated with a food group, defined by the major food component (i.e. pancakes), and then appended to the isolated coded foods. Healthy Aging in Neighborhoods of Diversity across the Life Span study. African-American and White adults with two dietary recalls (n 2177). Differences existed in lists of foods most frequently consumed by mealtime and race when comparing results based on original and revised data sets. African Americans reported consumption of sausage/luncheon meat and poultry, while ready-to-eat cereals and cakes/doughnuts/pastries were reported by Whites on recalls. Use of combination codes provided more accurate representation of how foods were consumed by populations. This information is beneficial when creating interventions and exploring diet-health relationships.

Exome Sequencing in an Admixed Isolated Population Indicates NFXL1 Variants Confer a Risk for Specific Language Impairment

PubMed Central

Villanueva, Pía; Nudel, Ron; Hoischen, Alexander; Fernández, María Angélica; Simpson, Nuala H.; Gilissen, Christian; Reader, Rose H.; Jara, Lillian; Echeverry, Maria Magdalena; Francks, Clyde; Baird, Gillian; Conti-Ramsden, Gina; O’Hare, Anne; Bolton, Patrick F.; Hennessy, Elizabeth R.; Palomino, Hernán; Carvajal-Carmona, Luis; Veltman, Joris A.; Cazier, Jean-Baptiste; De Barbieri, Zulema

2015-01-01

Children affected by Specific Language Impairment (SLI) fail to acquire age appropriate language skills despite adequate intelligence and opportunity. SLI is highly heritable, but the understanding of underlying genetic mechanisms has proved challenging. In this study, we use molecular genetic techniques to investigate an admixed isolated founder population from the Robinson Crusoe Island (Chile), who are affected by a high incidence of SLI, increasing the power to discover contributory genetic factors. We utilize exome sequencing in selected individuals from this population to identify eight coding variants that are of putative significance. We then apply association analyses across the wider population to highlight a single rare coding variant (rs144169475, Minor Allele Frequency of 4.1% in admixed South American populations) in the NFXL1 gene that confers a nonsynonymous change (N150K) and is significantly associated with language impairment in the Robinson Crusoe population (p = 2.04 × 10–4, 8 variants tested). Subsequent sequencing of NFXL1 in 117 UK SLI cases identified four individuals with heterozygous variants predicted to be of functional consequence. We conclude that coding variants within NFXL1 confer an increased risk of SLI within a complex genetic model. PMID:25781923

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Aerosol Constraints on the Atmosphere of the Hot Saturn-mass Planet WASP-49b

NASA Astrophysics Data System (ADS)

Cubillos, Patricio E.; Fossati, Luca; Erkaev, Nikolai V.; Malik, Matej; Tokano, Tetsuya; Lendl, Monika; Johnstone, Colin P.; Lammer, Helmut; Wyttenbach, Aurélien

2017-11-01

The strong, nearly wavelength-independent absorption cross section of aerosols produces featureless exoplanet transmission spectra, limiting our ability to characterize their atmospheres. Here, we show that even in the presence of featureless spectra, we can still characterize certain atmospheric properties. Specifically, we constrain the upper and lower pressure boundaries of aerosol layers, and present plausible composition candidates. We study the case of the bloated Saturn-mass planet WASP-49 b, where near-infrared observations reveal a flat transmission spectrum between 0.7 and 1.0 μm. First, we use a hydrodynamic upper-atmosphere code to estimate the pressure reached by the ionizing stellar high-energy photons at {10}-8 bar, setting the upper pressure boundary where aerosols could exist. Then, we combine HELIOS and Pyrat Bay radiative-transfer models to constrain the temperature and photospheric pressure of atmospheric aerosols, in a Bayesian framework. For WASP-49 b, we constrain the transmission photosphere (hence, the aerosol deck boundaries) to pressures above {10}-5 bar (100× solar metallicity), {10}-4 bar (solar), and {10}-3 bar (0.1× solar) as the lower boundary, and below {10}-7 bar as the upper boundary. Lastly, we compare condensation curves of aerosol compounds with the planet’s pressure-temperature profile to identify plausible condensates responsible for the absorption. Under these circumstances, we find these candidates: {{Na}}2{{S}} (at 100× solar metallicity); Cr and MnS (at solar and 0.1× solar) and forsterite, enstatite, and alabandite (at 0.1× solar).

Azerbaijani-Russian Code-Switching and Code-Mixing: Form, Function, and Identity

ERIC Educational Resources Information Center

Zuercher, Kenneth

2009-01-01

From incorporation into the Russian Empire in 1828, through the collapse of the U.S.S.R. in 1991 governmental language policies and other socio/political forces influenced the Turkic population of the Republic of Azerbaijan to speak Russian. Even with changes since independence Russian use--including various kinds of code-switching and…

Code Switching among Bilingual and Limited English Proficient Students: Possible Indicators of Giftedness

ERIC Educational Resources Information Center

Hughes, Claire E.; Shaunessy, Elizabeth S.; Brice, Alejandro R.; Ratliff, Mary Anne; McHatton, Patricia Alvarez

2006-01-01

Code switching includes the use of complete sentences, phrases, and borrowed words from another language (Brice & Brice, 2000). It is a common linguistic phenomenon noted among bilingual populations. In order to code switch effectively, students must possess a high level of understanding of the 2 cultures, as well as a deep understanding of the…

Targeting the T-Lak cell originated protein kinase by OTS964 shrinks the size of power-law coded heterogeneous glioma stem cell populations

PubMed Central

Sugimori, Michiya; Hayakawa, Yumiko; Koh, Masaki; Hayashi, Tomohide; Tamura, Ryoi; Kuroda, Satoshi

2018-01-01

Glioblastoma resists chemoradiotherapy, then, recurs to be a fatal space-occupying lesion. The recurrence is caused by re-growing cell populations such as glioma stem cells (GSCs), suggesting that GSC populations should be targeted. This study addressed whether a novel anti-cancer drug, OTS964, an inhibitor for T-LAK cell originated protein kinase (TOPK), is effective in reducing the size of the heterogeneous GSC populations, a power-law coded heterogeneous GSC populations consisting of glioma sphere (GS) clones, by detailing quantitative growth properties. We found that OTS964 killed GS clones while suppressing the growth of surviving GS clones, thus identifying clone-eliminating and growth-disturbing efficacies of OTS964. The efficacies led to a significant size reduction in GS populations in a dose-dependent manner. The surviving GS clones reconstructed GS populations in the following generations; the recovery of GS populations fits a recurrence after the chemotherapy. The recovering GS clones resisted the clone-eliminating effect of OTS964 in sequential exposure during the growth recovery. However, surprisingly, the resistant properties of the recovered-GS clones had been plastically canceled during self-renewal, and then the GS clones had become re-sensitive to OTS964. Thus, OTS964 targets GSCs to eliminate them or suppress their growth, resulting in shrinkage of the power-law coded GSC populations. We propose a therapy focusing on long-term control in recurrence of glioblastoma via reducing the size of the GSC populations by OTS964. PMID:29423027

Targeting the T-Lak cell originated protein kinase by OTS964 shrinks the size of power-law coded heterogeneous glioma stem cell populations.

PubMed

Sugimori, Michiya; Hayakawa, Yumiko; Koh, Masaki; Hayashi, Tomohide; Tamura, Ryoi; Kuroda, Satoshi

2018-01-09

Glioblastoma resists chemoradiotherapy, then, recurs to be a fatal space-occupying lesion. The recurrence is caused by re-growing cell populations such as glioma stem cells (GSCs), suggesting that GSC populations should be targeted. This study addressed whether a novel anti-cancer drug, OTS964, an inhibitor for T-LAK cell originated protein kinase (TOPK), is effective in reducing the size of the heterogeneous GSC populations, a power-law coded heterogeneous GSC populations consisting of glioma sphere (GS) clones, by detailing quantitative growth properties. We found that OTS964 killed GS clones while suppressing the growth of surviving GS clones, thus identifying clone-eliminating and growth-disturbing efficacies of OTS964. The efficacies led to a significant size reduction in GS populations in a dose-dependent manner. The surviving GS clones reconstructed GS populations in the following generations; the recovery of GS populations fits a recurrence after the chemotherapy. The recovering GS clones resisted the clone-eliminating effect of OTS964 in sequential exposure during the growth recovery. However, surprisingly, the resistant properties of the recovered-GS clones had been plastically canceled during self-renewal, and then the GS clones had become re-sensitive to OTS964. Thus, OTS964 targets GSCs to eliminate them or suppress their growth, resulting in shrinkage of the power-law coded GSC populations. We propose a therapy focusing on long-term control in recurrence of glioblastoma via reducing the size of the GSC populations by OTS964.

Smartphone tool to collect repeated 24 h dietary recall data in Nepal.

PubMed

Harris-Fry, Helen; Beard, B James; Harrisson, Tom; Paudel, Puskar; Shrestha, Niva; Jha, Sonali; Shrestha, Bhim P; Manandhar, Dharma S; Costello, Anthony; Saville, Naomi M

2018-02-01

To outline the development of a smartphone-based tool to collect thrice-repeated 24 h dietary recall data in rural Nepal, and to describe energy intakes, common errors and researchers' experiences using the tool. We designed a novel tool to collect multi-pass 24 h dietary recalls in rural Nepal by combining the use of a CommCare questionnaire on smartphones, a paper form, a QR (quick response)-coded list of foods and a photographic atlas of portion sizes. Twenty interviewers collected dietary data on three non-consecutive days per respondent, with three respondents per household. Intakes were converted into nutrients using databases on nutritional composition of foods, recipes and portion sizes. Dhanusha and Mahottari districts, Nepal. Pregnant women, their mothers-in-law and male household heads. Energy intakes assessed in 150 households; data corrections and our experiences reported from 805 households and 6765 individual recalls. Dietary intake estimates gave plausible values, with male household heads appearing to have higher energy intakes (median (25th-75th centile): 12 079 (9293-14 108) kJ/d) than female members (8979 (7234-11 042) kJ/d for pregnant women). Manual editing of data was required when interviewers mistook portions for food codes and for coding items not on the food list. Smartphones enabled quick monitoring of data and interviewer performance, but we initially faced technical challenges with CommCare forms crashing. With sufficient time dedicated to development and pre-testing, this novel smartphone-based tool provides a useful method to collect data. Future work is needed to further validate this tool and adapt it for other contexts.

Estimating numbers of females with cubs-of-the-year in the Yellowstone grizzly bear population

USGS Publications Warehouse

Keating, K.A.; Schwartz, C.C.; Haroldson, M.A.; Moody, D.

2001-01-01

For grizzly bears (Ursus arctos horribilis) in the Greater Yellowstone Ecosystem (GYE), minimum population size and allowable numbers of human-caused mortalities have been calculated as a function of the number of unique females with cubs-of-the-year (FCUB) seen during a 3- year period. This approach underestimates the total number of FCUB, thereby biasing estimates of population size and sustainable mortality. Also, it does not permit calculation of valid confidence bounds. Many statistical methods can resolve or mitigate these problems, but there is no universal best method. Instead, relative performances of different methods can vary with population size, sample size, and degree of heterogeneity among sighting probabilities for individual animals. We compared 7 nonparametric estimators, using Monte Carlo techniques to assess performances over the range of sampling conditions deemed plausible for the Yellowstone population. Our goal was to estimate the number of FCUB present in the population each year. Our evaluation differed from previous comparisons of such estimators by including sample coverage methods and by treating individual sightings, rather than sample periods, as the sample unit. Consequently, our conclusions also differ from earlier studies. Recommendations regarding estimators and necessary sample sizes are presented, together with estimates of annual numbers of FCUB in the Yellowstone population with bootstrap confidence bounds.

Populations of weedy crop–wild hybrid beets show contrasting variation in mating system and population genetic structure

PubMed Central

Arnaud, Jean-François; Fénart, Stéphane; Cordellier, Mathilde; Cuguen, Joël

2010-01-01

Reproductive traits are key parameters for the evolution of invasiveness in weedy crop–wild hybrids. In Beta vulgaris, cultivated beets hybridize with their wild relatives in the seed production areas, giving rise to crop–wild hybrid weed beets. We investigated the genetic structure, the variation in first-year flowering and the variation in mating system among weed beet populations occurring within sugar beet production fields. No spatial genetic structure was found for first-year populations composed of F1 crop–wild hybrid beets. In contrast, populations composed of backcrossed weed beets emerging from the seed bank showed a strong isolation-by-distance pattern. Whereas gametophytic self-incompatibility prevents selfing in wild beet populations, all studied weed beet populations had a mixed-mating system, plausibly because of the introgression of the crop-derived Sf gene that disrupts self-incompatibility. No significant relationship between outcrossing rate and local weed beet density was found, suggesting no trends for a shift in the mating system because of environmental effects. We further reveal that increased invasiveness of weed beets may stem from positive selection on first-year flowering induction depending on the B gene inherited from the wild. Finally, we discuss the practical and applied consequences of our findings for crop-weed management. PMID:25567926

Residential exposure to aircraft noise and hospital admissions for cardiovascular diseases: multi-airport retrospective study.

PubMed

Correia, Andrew W; Peters, Junenette L; Levy, Jonathan I; Melly, Steven; Dominici, Francesca

2013-10-08

To investigate whether exposure to aircraft noise increases the risk of hospitalization for cardiovascular diseases in older people (≥ 65 years) residing near airports. Multi-airport retrospective study of approximately 6 million older people residing near airports in the United States. We superimposed contours of aircraft noise levels (in decibels, dB) for 89 airports for 2009 provided by the US Federal Aviation Administration on census block resolution population data to construct two exposure metrics applicable to zip code resolution health insurance data: population weighted noise within each zip code, and 90th centile of noise among populated census blocks within each zip code. 2218 zip codes surrounding 89 airports in the contiguous states. 6 027 363 people eligible to participate in the national medical insurance (Medicare) program (aged ≥ 65 years) residing near airports in 2009. Percentage increase in the hospitalization admission rate for cardiovascular disease associated with a 10 dB increase in aircraft noise, for each airport and on average across airports adjusted by individual level characteristics (age, sex, race), zip code level socioeconomic status and demographics, zip code level air pollution (fine particulate matter and ozone), and roadway density. Averaged across all airports and using the 90th centile noise exposure metric, a zip code with 10 dB higher noise exposure had a 3.5% higher (95% confidence interval 0.2% to 7.0%) cardiovascular hospital admission rate, after controlling for covariates. Despite limitations related to potential misclassification of exposure, we found a statistically significant association between exposure to aircraft noise and risk of hospitalization for cardiovascular diseases among older people living near airports.

Normative Database and Color-code Agreement of Peripapillary Retinal Nerve Fiber Layer and Macular Ganglion Cell-inner Plexiform Layer Thickness in a Vietnamese Population.

PubMed

Perez, Claudio I; Chansangpetch, Sunee; Thai, Andy; Nguyen, Anh-Hien; Nguyen, Anwell; Mora, Marta; Nguyen, Ngoc; Lin, Shan C

2018-06-05

Evaluate the distribution and the color probability codes of the peripapillary retinal nerve fiber layer (RNFL) and macular ganglion cell-inner plexiform layer (GCIPL) thickness in a healthy Vietnamese population and compare them with the original color-codes provided by the Cirrus spectral domain OCT. Cross-sectional study. We recruited non-glaucomatous Vietnamese subjects and constructed a normative database for peripapillary RNFL and macular GCIPL thickness. The probability color-codes for each decade of age were calculated. We evaluated the agreement with Kappa coefficient (κ) between OCT color probability codes with Cirrus built-in original normative database and the Vietnamese normative database. 149 eyes of 149 subjects were included. The mean age of enrollees was 60.77 (±11.09) years, with a mean spherical equivalent of +0.65 (±1.58) D and mean axial length of 23.4 (±0.87) mm. Average RNFL thickness was 97.86 (±9.19) microns and average macular GCIPL was 82.49 (±6.09) microns. Agreement between original and adjusted normative database for RNFL was fair for average and inferior quadrant (κ=0.25 and 0.2, respectively); and good for other quadrants (range: κ=0.63-0.73). For macular GCIPL κ agreement ranged between 0.39 and 0.69. After adjusting with the normative Vietnamese database, the percent of yellow and red color-codes increased significantly for peripapillary RNFL thickness. Vietnamese population has a thicker RNFL in comparison with Cirrus normative database. This leads to a poor color-code agreement in average and inferior quadrant between the original and adjusted database. These findings should encourage to create a peripapillary RNFL normative database for each ethnicity.

The Sign Rule and Beyond: Boundary Effects, Flexibility, and Noise Correlations in Neural Population Codes

PubMed Central

Hu, Yu; Zylberberg, Joel; Shea-Brown, Eric

2014-01-01

Over repeat presentations of the same stimulus, sensory neurons show variable responses. This “noise” is typically correlated between pairs of cells, and a question with rich history in neuroscience is how these noise correlations impact the population's ability to encode the stimulus. Here, we consider a very general setting for population coding, investigating how information varies as a function of noise correlations, with all other aspects of the problem – neural tuning curves, etc. – held fixed. This work yields unifying insights into the role of noise correlations. These are summarized in the form of theorems, and illustrated with numerical examples involving neurons with diverse tuning curves. Our main contributions are as follows. (1) We generalize previous results to prove a sign rule (SR) — if noise correlations between pairs of neurons have opposite signs vs. their signal correlations, then coding performance will improve compared to the independent case. This holds for three different metrics of coding performance, and for arbitrary tuning curves and levels of heterogeneity. This generality is true for our other results as well. (2) As also pointed out in the literature, the SR does not provide a necessary condition for good coding. We show that a diverse set of correlation structures can improve coding. Many of these violate the SR, as do experimentally observed correlations. There is structure to this diversity: we prove that the optimal correlation structures must lie on boundaries of the possible set of noise correlations. (3) We provide a novel set of necessary and sufficient conditions, under which the coding performance (in the presence of noise) will be as good as it would be if there were no noise present at all. PMID:24586128

Residential exposure to aircraft noise and hospital admissions for cardiovascular diseases: multi-airport retrospective study

PubMed Central

Correia, Andrew W; Peters, Junenette L; Levy, Jonathan I; Melly, Steven

2013-01-01

Objective To investigate whether exposure to aircraft noise increases the risk of hospitalization for cardiovascular diseases in older people (≥65 years) residing near airports. Design Multi-airport retrospective study of approximately 6 million older people residing near airports in the United States. We superimposed contours of aircraft noise levels (in decibels, dB) for 89 airports for 2009 provided by the US Federal Aviation Administration on census block resolution population data to construct two exposure metrics applicable to zip code resolution health insurance data: population weighted noise within each zip code, and 90th centile of noise among populated census blocks within each zip code. Setting 2218 zip codes surrounding 89 airports in the contiguous states. Participants 6 027 363 people eligible to participate in the national medical insurance (Medicare) program (aged ≥65 years) residing near airports in 2009. Main outcome measures Percentage increase in the hospitalization admission rate for cardiovascular disease associated with a 10 dB increase in aircraft noise, for each airport and on average across airports adjusted by individual level characteristics (age, sex, race), zip code level socioeconomic status and demographics, zip code level air pollution (fine particulate matter and ozone), and roadway density. Results Averaged across all airports and using the 90th centile noise exposure metric, a zip code with 10 dB higher noise exposure had a 3.5% higher (95% confidence interval 0.2% to 7.0%) cardiovascular hospital admission rate, after controlling for covariates. Conclusions Despite limitations related to potential misclassification of exposure, we found a statistically significant association between exposure to aircraft noise and risk of hospitalization for cardiovascular diseases among older people living near airports. PMID:24103538

Assessment of tissue allograft safety monitoring with administrative healthcare databases: a pilot project using Medicare data.

PubMed

Dhakal, Sanjaya; Burwen, Dale R; Polakowski, Laura L; Zinderman, Craig E; Wise, Robert P

2014-03-01

Assess whether Medicare data are useful for monitoring tissue allograft safety and utilization. We used health care claims (billing) data from 2007 for 35 million fee-for-service Medicare beneficiaries, a predominantly elderly population. Using search terms for transplant-related procedures, we generated lists of ICD-9-CM and CPT(®) codes and assessed the frequency of selected allograft procedures. Step 1 used inpatient data and ICD-9-CM procedure codes. Step 2 added non-institutional provider (e.g., physician) claims, outpatient institutional claims, and CPT codes. We assembled preliminary lists of diagnosis codes for infections after selected allograft procedures. Many ICD-9-CM codes were ambiguous as to whether the procedure involved an allograft. Among 1.3 million persons with a procedure ascertained using the list of ICD-9-CM codes, only 1,886 claims clearly involved an allograft. CPT codes enabled better ascertainment of some allograft procedures (over 17,000 persons had corneal transplants and over 2,700 had allograft skin transplants). For spinal fusion procedures, CPT codes improved specificity for allografts; of nearly 100,000 patients with ICD-9-CM codes for spinal fusions, more than 34,000 had CPT codes indicating allograft use. Monitoring infrequent events (infections) after infrequent exposures (tissue allografts) requires large study populations. A strength of the large Medicare databases is the substantial number of certain allograft procedures. Limitations include lack of clinical detail and donor information. Medicare data can potentially augment passive reporting systems and may be useful for monitoring tissue allograft safety and utilization where codes clearly identify allograft use and coding algorithms can effectively screen for infections.

Molecular characterization of a long range haplotype affecting protein yield and mastitis susceptibility in Norwegian Red cattle.

PubMed

Sodeland, Marte; Grove, Harald; Kent, Matthew; Taylor, Simon; Svendsen, Morten; Hayes, Ben J; Lien, Sigbjørn

2011-08-11

Previous fine mapping studies in Norwegian Red cattle (NRC) in the region 86-90.4 Mb on Bos taurus chromosome 6 (BTA6) has revealed a quantitative trait locus (QTL) for protein yield (PY) around 88 Mb and a QTL for clinical mastitis (CM) around 90 Mb. The close proximity of these QTLs may partly explain the unfavorable genetic correlation between these two traits in NRC. A long range haplotype covering this region was introduced into the NRC population through the importation of a Holstein-Friesian bull (1606 Frasse) from Sweden in the 1970s. It has been suggested that this haplotype has a favorable effect on milk protein content but an unfavorable effect on mastitis susceptibility. Selective breeding for milk production traits is likely to have increased the frequency of this haplotype in the NRC population. Association mapping for PY and CM in NRC was performed using genotypes from 556 SNPs throughout the region 86-97 Mb on BTA6 and daughter-yield-deviations (DYDs) from 2601 bulls made available from the Norwegian dairy herd recording system. Highest test scores for PY were found for single-nucleotide polymorphisms (SNPs) within and surrounding the genes CSN2 and CSN1S2, coding for the β-casein and α(S2)-casein proteins. High coverage re-sequencing by high throughput sequencing technology enabled molecular characterization of a long range haplotype from 1606 Frasse encompassing these two genes. Haplotype analysis of a large number of descendants from this bull indicated that the haplotype was not markedly disrupted by recombination in this region. The haplotype was associated with both increased milk protein content and increased susceptibility to mastitis, which might explain parts of the observed genetic correlation between PY and CM in NRC. Plausible causal polymorphisms affecting PY were detected in the promoter region and in the 5'-flanking UTR of CSN1S2. These polymorphisms could affect transcription or translation of CSN1S2 and thereby affect the amount of α(S2)-casein in milk. Highest test scores for CM were found in the region 89-91 Mb on BTA6, very close to a cluster of genes coding for CXC chemokines. Expression levels of some of these CXC chemokines have previously been shown to increase in bovine mammary gland cell lines after exposure to bacterial cell wall components. Molecular characterization of the long range haplotype from the Holstein-Friesian bull 1606 Frasse, imported into NRC in the 1970s, revealed polymorphisms that could affect transcription or translation of the casein gene CSN1S2. Sires with this haplotype had daughters with significantly elevated milk protein content and selection for milk production traits is likely to have increased the frequency of this haplotype in the NRC population. The haplotype was also associated with increased mastitis susceptibility, which might explain parts of the genetic correlation between PY and CM in NRC.

YORP and collisional shaping of the sub-populations, rotation rate and size-frequency distributions in the main-belt

NASA Astrophysics Data System (ADS)

Rossi, A.; Marzari, F.; Scheeres, D.; Jacobson, S.; Davis, D.

In the last several years a comprehensive asteroid-population-evolution model was developed incorporating both the YORP effect and collisional evolution \\citep{rossi_2009}, \\citep{marz_2011}, \\citep{jac_mnras}. From the results of this model we were able to match the observed main belt rotation rate distribution and to give a first plausible explanation of the observed excess of slow rotators, through a random walk-like evolution of the spin, induced by repeated collisions with small projectiles. Moreover, adding to the model the rotational fission hypothesis (i.e. when the rotation rate exceeds a critical value, erosion and binary formation occur; \\citealt{sch_2007}) and binary-asteroid evolution \\citep{jac_sch}, we first showed that the YORP-induced rotational-fission hypothesis has strong repercussions for the small size end of the main-belt asteroid size-frequency distribution. We also concluded that this hypothesis is consistent with observed asteroid-population statistics and with the observed sub-populations of binary asteroids, asteroid pairs and contact binaries. An overview of the results obtained, the modelling uncertainties and the ongoing work will be given.

Feed-forward segmentation of figure-ground and assignment of border-ownership.

PubMed

Supèr, Hans; Romeo, August; Keil, Matthias

2010-05-19

Figure-ground is the segmentation of visual information into objects and their surrounding backgrounds. Two main processes herein are boundary assignment and surface segregation, which rely on the integration of global scene information. Recurrent processing either by intrinsic horizontal connections that connect surrounding neurons or by feedback projections from higher visual areas provide such information, and are considered to be the neural substrate for figure-ground segmentation. On the contrary, a role of feedforward projections in figure-ground segmentation is unknown. To have a better understanding of a role of feedforward connections in figure-ground organization, we constructed a feedforward spiking model using a biologically plausible neuron model. By means of surround inhibition our simple 3-layered model performs figure-ground segmentation and one-sided border-ownership coding. We propose that the visual system uses feed forward suppression for figure-ground segmentation and border-ownership assignment.

Using Grid Cells for Navigation

PubMed Central

Bush, Daniel; Barry, Caswell; Manson, Daniel; Burgess, Neil

2015-01-01

Summary Mammals are able to navigate to hidden goal locations by direct routes that may traverse previously unvisited terrain. Empirical evidence suggests that this “vector navigation” relies on an internal representation of space provided by the hippocampal formation. The periodic spatial firing patterns of grid cells in the hippocampal formation offer a compact combinatorial code for location within large-scale space. Here, we consider the computational problem of how to determine the vector between start and goal locations encoded by the firing of grid cells when this vector may be much longer than the largest grid scale. First, we present an algorithmic solution to the problem, inspired by the Fourier shift theorem. Second, we describe several potential neural network implementations of this solution that combine efficiency of search and biological plausibility. Finally, we discuss the empirical predictions of these implementations and their relationship to the anatomy and electrophysiology of the hippocampal formation. PMID:26247860

An automated approach to magnetic divertor configuration design

NASA Astrophysics Data System (ADS)

Blommaert, M.; Dekeyser, W.; Baelmans, M.; Gauger, N. R.; Reiter, D.

2015-01-01

Automated methods based on optimization can greatly assist computational engineering design in many areas. In this paper an optimization approach to the magnetic design of a nuclear fusion reactor divertor is proposed and applied to a tokamak edge magnetic configuration in a first feasibility study. The approach is based on reduced models for magnetic field and plasma edge, which are integrated with a grid generator into one sensitivity code. The design objective chosen here for demonstrative purposes is to spread the divertor target heat load as much as possible over the entire target area. Constraints on the separatrix position are introduced to eliminate physically irrelevant magnetic field configurations during the optimization cycle. A gradient projection method is used to ensure stable cost function evaluations during optimization. The concept is applied to a configuration with typical Joint European Torus (JET) parameters and it automatically provides plausible configurations with reduced heat load.

Preparing for rectal microbicides: sociocultural factors affecting product uptake among potential South American users.

PubMed

Galea, Jerome T; Kinsler, Janni J; Imrie, John; Nureña, César R; Ruiz, Lucía; Galarza, Luis Fernando; Sánchez, Jorge; Cunningham, William E

2014-06-01

We examined views on rectal microbicides (RMs), a potential HIV prevention option, among men who have sex with men and transgender women in 3 South American cities. During September 2009 to September 2010, we conducted 10 focus groups and 36 in-depth interviews (n = 140) in Lima and Iquitos, Peru, and Guayaquil, Ecuador, to examine 5 RM domains: knowledge, thoughts and opinions about RM as an HIV prevention tool, use, condoms, and social concerns. We coded emergent themes in recorded and transcribed data sets and extracted representative quotes. We collected sociodemographic information with a self-administered questionnaire. RM issues identified included limited knowledge; concerns regarding plausibility, side effects, and efficacy; impact on condom use; target users (insertive vs receptive partners); and access concerns. Understanding the sociocultural issues affecting RMs is critical to their uptake and should be addressed prior to product launch.

Unsupervised segmentation with dynamical units.

PubMed

Rao, A Ravishankar; Cecchi, Guillermo A; Peck, Charles C; Kozloski, James R

2008-01-01

In this paper, we present a novel network to separate mixtures of inputs that have been previously learned. A significant capability of the network is that it segments the components of each input object that most contribute to its classification. The network consists of amplitude-phase units that can synchronize their dynamics, so that separation is determined by the amplitude of units in an output layer, and segmentation by phase similarity between input and output layer units. Learning is unsupervised and based on a Hebbian update, and the architecture is very simple. Moreover, efficient segmentation can be achieved even when there is considerable superposition of the inputs. The network dynamics are derived from an objective function that rewards sparse coding in the generalized amplitude-phase variables. We argue that this objective function can provide a possible formal interpretation of the binding problem and that the implementation of the network architecture and dynamics is biologically plausible.

Profiling of Virulence Determinants in Cronobacter sakazakii Isolates from Different Plant and Environmental Commodities.

PubMed

Singh, Niharika; Raghav, Mamta; Narula, Shifa; Tandon, Simran; Goel, Gunjan

2017-05-01

Cronobacter sakazakii is an emerging pathogen causing meningitis, sepsis and necrotizing enterocolitis in neonates and immune-compromised adults. The present study describes the profiling of different virulence factors associated with C. sakazakii isolates derived from plant-based materials and environmental samples (soil, water, and vacuum dust). All the isolates exhibited β-hemolysis and chitinase activity, and were able to utilize inositol. Among the nine virulence-associated genes, hly gene coding for hemolysin was detected in all the isolates followed by ompA (outer membrane protein); however, plasmid-borne genes were detected at a level of 60% for both cpa (cronobacter plasminogen activator) and eitA (Ferric ion transporter protein) gene, respectively. Furthermore, the isolate C. sakazakii N81 showed cytotoxicity for Caco-2 cells. The presence of the virulence determinants investigated in this study indicates the pathogenic potential of C. sakazakii with their plausible connection with clinical manifestations.

Preparing for Rectal Microbicides: Sociocultural Factors Affecting Product Uptake Among Potential South American Users

PubMed Central

Kinsler, Janni J.; Imrie, John; Nureña, César R.; Ruiz, Lucía; Galarza, Luis Fernando; Sánchez, Jorge; Cunningham, William E.

2014-01-01

Objectives. We examined views on rectal microbicides (RMs), a potential HIV prevention option, among men who have sex with men and transgender women in 3 South American cities. Methods. During September 2009 to September 2010, we conducted 10 focus groups and 36 in-depth interviews (n = 140) in Lima and Iquitos, Peru, and Guayaquil, Ecuador, to examine 5 RM domains: knowledge, thoughts and opinions about RM as an HIV prevention tool, use, condoms, and social concerns. We coded emergent themes in recorded and transcribed data sets and extracted representative quotes. We collected sociodemographic information with a self-administered questionnaire. Results. RM issues identified included limited knowledge; concerns regarding plausibility, side effects, and efficacy; impact on condom use; target users (insertive vs receptive partners); and access concerns. Conclusions. Understanding the sociocultural issues affecting RMs is critical to their uptake and should be addressed prior to product launch. PMID:24825222

Towards biological plausibility of electronic noses: A spiking neural network based approach for tea odour classification.

PubMed

Sarkar, Sankho Turjo; Bhondekar, Amol P; Macaš, Martin; Kumar, Ritesh; Kaur, Rishemjit; Sharma, Anupma; Gulati, Ashu; Kumar, Amod

2015-11-01

The paper presents a novel encoding scheme for neuronal code generation for odour recognition using an electronic nose (EN). This scheme is based on channel encoding using multiple Gaussian receptive fields superimposed over the temporal EN responses. The encoded data is further applied to a spiking neural network (SNN) for pattern classification. Two forms of SNN, a back-propagation based SpikeProp and a dynamic evolving SNN are used to learn the encoded responses. The effects of information encoding on the performance of SNNs have been investigated. Statistical tests have been performed to determine the contribution of the SNN and the encoding scheme to overall odour discrimination. The approach has been implemented in odour classification of orthodox black tea (Kangra-Himachal Pradesh Region) thereby demonstrating a biomimetic approach for EN data analysis. Copyright © 2015 Elsevier Ltd. All rights reserved.

Feed-Forward Segmentation of Figure-Ground and Assignment of Border-Ownership

PubMed Central

Supèr, Hans; Romeo, August; Keil, Matthias

2010-01-01

Figure-ground is the segmentation of visual information into objects and their surrounding backgrounds. Two main processes herein are boundary assignment and surface segregation, which rely on the integration of global scene information. Recurrent processing either by intrinsic horizontal connections that connect surrounding neurons or by feedback projections from higher visual areas provide such information, and are considered to be the neural substrate for figure-ground segmentation. On the contrary, a role of feedforward projections in figure-ground segmentation is unknown. To have a better understanding of a role of feedforward connections in figure-ground organization, we constructed a feedforward spiking model using a biologically plausible neuron model. By means of surround inhibition our simple 3-layered model performs figure-ground segmentation and one-sided border-ownership coding. We propose that the visual system uses feed forward suppression for figure-ground segmentation and border-ownership assignment. PMID:20502718

Population Coding of Visual Space: Modeling

PubMed Central

Lehky, Sidney R.; Sereno, Anne B.

2011-01-01

We examine how the representation of space is affected by receptive field (RF) characteristics of the encoding population. Spatial responses were defined by overlapping Gaussian RFs. These responses were analyzed using multidimensional scaling to extract the representation of global space implicit in population activity. Spatial representations were based purely on firing rates, which were not labeled with RF characteristics (tuning curve peak location, for example), differentiating this approach from many other population coding models. Because responses were unlabeled, this model represents space using intrinsic coding, extracting relative positions amongst stimuli, rather than extrinsic coding where known RF characteristics provide a reference frame for extracting absolute positions. Two parameters were particularly important: RF diameter and RF dispersion, where dispersion indicates how broadly RF centers are spread out from the fovea. For large RFs, the model was able to form metrically accurate representations of physical space on low-dimensional manifolds embedded within the high-dimensional neural population response space, suggesting that in some cases the neural representation of space may be dimensionally isomorphic with 3D physical space. Smaller RF sizes degraded and distorted the spatial representation, with the smallest RF sizes (present in early visual areas) being unable to recover even a topologically consistent rendition of space on low-dimensional manifolds. Finally, although positional invariance of stimulus responses has long been associated with large RFs in object recognition models, we found RF dispersion rather than RF diameter to be the critical parameter. In fact, at a population level, the modeling suggests that higher ventral stream areas with highly restricted RF dispersion would be unable to achieve positionally-invariant representations beyond this narrow region around fixation. PMID:21344012

Semantics-based plausible reasoning to extend the knowledge coverage of medical knowledge bases for improved clinical decision support.

PubMed

Mohammadhassanzadeh, Hossein; Van Woensel, William; Abidi, Samina Raza; Abidi, Syed Sibte Raza

2017-01-01

Capturing complete medical knowledge is challenging-often due to incomplete patient Electronic Health Records (EHR), but also because of valuable, tacit medical knowledge hidden away in physicians' experiences. To extend the coverage of incomplete medical knowledge-based systems beyond their deductive closure, and thus enhance their decision-support capabilities, we argue that innovative, multi-strategy reasoning approaches should be applied. In particular, plausible reasoning mechanisms apply patterns from human thought processes, such as generalization, similarity and interpolation, based on attributional, hierarchical, and relational knowledge. Plausible reasoning mechanisms include inductive reasoning , which generalizes the commonalities among the data to induce new rules, and analogical reasoning , which is guided by data similarities to infer new facts. By further leveraging rich, biomedical Semantic Web ontologies to represent medical knowledge, both known and tentative, we increase the accuracy and expressivity of plausible reasoning, and cope with issues such as data heterogeneity, inconsistency and interoperability. In this paper, we present a Semantic Web-based, multi-strategy reasoning approach, which integrates deductive and plausible reasoning and exploits Semantic Web technology to solve complex clinical decision support queries. We evaluated our system using a real-world medical dataset of patients with hepatitis, from which we randomly removed different percentages of data (5%, 10%, 15%, and 20%) to reflect scenarios with increasing amounts of incomplete medical knowledge. To increase the reliability of the results, we generated 5 independent datasets for each percentage of missing values, which resulted in 20 experimental datasets (in addition to the original dataset). The results show that plausibly inferred knowledge extends the coverage of the knowledge base by, on average, 2%, 7%, 12%, and 16% for datasets with, respectively, 5%, 10%, 15%, and 20% of missing values. This expansion in the KB coverage allowed solving complex disease diagnostic queries that were previously unresolvable, without losing the correctness of the answers. However, compared to deductive reasoning, data-intensive plausible reasoning mechanisms yield a significant performance overhead. We observed that plausible reasoning approaches, by generating tentative inferences and leveraging domain knowledge of experts, allow us to extend the coverage of medical knowledge bases, resulting in improved clinical decision support. Second, by leveraging OWL ontological knowledge, we are able to increase the expressivity and accuracy of plausible reasoning methods. Third, our approach is applicable to clinical decision support systems for a range of chronic diseases.

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Of Pesticides and Men: A California Story of Genes and Environment in Parkinson’s Disease

PubMed Central

Ritz, BR; Paul, KC; Bronstein, JM

2018-01-01

At the start of the post-genomics era, most Parkinson’s disease (PD) etiology cannot be explained by our knowledge of genetic or environmental factors alone. For more than a decade, we have explored gene-environment (GxE) interactions possibly responsible for the heterogeneity of genetic as well as environmental results across populations. We developed three pesticide exposure measures (ambient due to agricultural applications, home and garden use, occupational use) in a large population-based case-control study of incident PD in central California. Specifically, we assessed interactions with genes responsible for pesticide metabolism (PON1); transport across the blood brain barrier (ABCB1); pesticides interfering with or depending on dopamine transporter activity (DAT) and dopamine metabolism (ALDH2); impacting mitochondrial function via oxidative/nitrosative stress (NOS1) or proteasome inhibition (SKP1); and contributing to immune dysregulation (HLA-DR). These studies established some specificity for pesticides’ neurodegenerative actions, contributed biologic plausibility to epidemiologic findings, and identified genetically susceptible populations. PMID:26857251

The population genetics of the alpha-2 globin locus of orangutans (Pongo pygmaeus).

PubMed

Steiper, Michael E; Wolfe, Nathan D; Karesh, William B; Kilbourn, Annelisa M; Bosi, Edwin J; Ruvolo, Maryellen

2005-03-01

In this study, the molecular population genetics of the orangutan's alpha-2 globin (HBA2) gene were investigated in order to test for the action of natural selection. Haplotypes from 28 orangutan chromosomes were collected from a 1.46-kilobase region of the alpha-2 globin locus. While many aspects of the data were consistent with neutrality, the observed heterogeneous distribution of polymorphisms was inconsistent with neutral expectations. Furthermore, a single amino acid variant, found in both the Bornean and the Sumatran orangutan subspecies, was associated with different alternative synonymous variants in each subspecies, suggesting that the allele may have spread separately through the two subspecies after two distinct origination events. This variant is not in Hardy-Weinberg equilibrium (HWE). These observations are consistent with neutral models that incorporate population structure and models that invoke selection. The orangutan Plasmodium parasite is a plausible selective agent that may underlie the variation at alpha-2 globin in orangutans.

Application of plausible reasoning to AI-based control systems

NASA Technical Reports Server (NTRS)

Berenji, Hamid; Lum, Henry, Jr.

1987-01-01

Some current approaches to plausible reasoning in artificial intelligence are reviewed and discussed. Some of the most significant recent advances in plausible and approximate reasoning are examined. A synergism among the techniques of uncertainty management is advocated, and brief discussions on the certainty factor approach, probabilistic approach, Dempster-Shafer theory of evidence, possibility theory, linguistic variables, and fuzzy control are presented. Some extensions to these methods are described, and the applications of the methods are considered.

Mathematical Modelling as a Tool to Understand Cell Self-renewal and Differentiation.

PubMed

Getto, Philipp; Marciniak-Czochra, Anna

2015-01-01

Mathematical modeling is a powerful technique to address key questions and paradigms in a variety of complex biological systems and can provide quantitative insights into cell kinetics, fate determination and development of cell populations. The chapter is devoted to a review of modeling of the dynamics of stem cell-initiated systems using mathematical methods of ordinary differential equations. Some basic concepts and tools for cell population dynamics are summarized and presented as a gentle introduction to non-mathematicians. The models take into account different plausible mechanisms regulating homeostasis. Two mathematical frameworks are proposed reflecting, respectively, a discrete (punctuated by division events) and a continuous character of transitions between differentiation stages. Advantages and constraints of the mathematical approaches are presented on examples of models of blood systems and compared to patients data on healthy hematopoiesis.

The impact of regime type on health: does redistribution explain everything?

PubMed

Wigley, Simon; Akkoyunlu-Wigley, Arzu

2011-01-01

Many scholars claim that democracy improves population health. The prevailing explanation for this is that democratic regimes distribute health-promoting resources more widely than autocratic regimes. The central contention of this article is that democracies also have a significant pro-health effect regardless of public redistributive policies. After establishing the theoretical plausibility of the nondistributive effect, a panel of 153 countries for the years 1972 to 2000 is used to examine the relationship between extent of democratic experience and life expectancy. The authors find that democratic governance continues to have a salutary effect on population health even when controls are introduced for the distribution of health-enhancing resources. Data for fifty autocratic countries for the years 1994 to 2007 are then used to examine whether media freedom—independent of government responsiveness—has a positive impact on life expectancy.

Fertility, Human Capital, and Economic Growth over the Demographic Transition

PubMed Central

Mason, Andrew

2009-01-01

Do low fertility and population aging lead to economic decline if couples have fewer children, but invest more in each child? By addressing this question, this article extends previous work in which the authors show that population aging leads to an increased demand for wealth that can, under some conditions, lead to increased capital per worker and higher per capita consumption. This article is based on an overlapping generations (OLG) model which highlights the quantity–quality tradeoff and the links between human capital investment and economic growth. It incorporates new national level estimates of human capital investment produced by the National Transfer Accounts project. Simulation analysis is employed to show that, even in the absence of the capital dilution effect, low fertility leads to higher per capita consumption through human capital accumulation, given plausible model parameters. PMID:20495605

Severe mortality of a population of threatened Agassiz’s desert tortoises: the American badger as a potential predator

USGS Publications Warehouse

Emblidge, Patrick G.; Nussear, Ken E.; Esque, Todd C.; Aiello, Christina M.; Walde, Andrew D.

2015-01-01

In the Mojave Desert of the southwestern United States, adult Agassiz’s desert tortoises Gopherus agassizii typically experience high survival, but population declines associated with anthropogenic impacts led to their listing as a threatened Species under the US Endangered Species Act in 1990. Predation of adult tortoises is not often considered a significant threat as they are adapted to deter most predation attempts. Despite these adaptations, some populations have experienced elevated mortality attributed to predators, suggesting that predation pressure may occasionally increase. During the tortoise activity seasons of 2012 and 2013, we observed unsustainably high mortality in 1 of 4 populations of adult desert tortoises (22 and 84%, respectively) in the western Mojave Desert in the vicinity of Barstow, CA. Photographic evidence from trail cameras and examination of carcass condition suggest that American badgers Taxidea taxus— a sometimes cited but unconfirmed predator of adult tortoises — may have been responsible for some of the mortality observed. We discuss the American badger as a plausible predator of a local tortoise population, but recommend further investigation into these events and the impacts such mortality can have on tortoise persistence.

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Whole-genome sequencing identifies EN1 as a determinant of bone density and fracture

PubMed Central

Zheng, Hou-Feng; Forgetta, Vincenzo; Hsu, Yi-Hsiang; Estrada, Karol; Rosello-Diez, Alberto; Leo, Paul J; Dahia, Chitra L; Park-Min, Kyung Hyun; Tobias, Jonathan H; Kooperberg, Charles; Kleinman, Aaron; Styrkarsdottir, Unnur; Liu, Ching-Ti; Uggla, Charlotta; Evans, Daniel S; Nielson, Carrie M; Walter, Klaudia; Pettersson-Kymmer, Ulrika; McCarthy, Shane; Eriksson, Joel; Kwan, Tony; Jhamai, Mila; Trajanoska, Katerina; Memari, Yasin; Min, Josine; Huang, Jie; Danecek, Petr; Wilmot, Beth; Li, Rui; Chou, Wen-Chi; Mokry, Lauren E; Moayyeri, Alireza; Claussnitzer, Melina; Cheng, Chia-Ho; Cheung, Warren; Medina-Gómez, Carolina; Ge, Bing; Chen, Shu-Huang; Choi, Kwangbom; Oei, Ling; Fraser, James; Kraaij, Robert; Hibbs, Matthew A; Gregson, Celia L; Paquette, Denis; Hofman, Albert; Wibom, Carl; Tranah, Gregory J; Marshall, Mhairi; Gardiner, Brooke B; Cremin, Katie; Auer, Paul; Hsu, Li; Ring, Sue; Tung, Joyce Y; Thorleifsson, Gudmar; Enneman, Anke W; van Schoor, Natasja M; de Groot, Lisette C.P.G.M.; van der Velde, Nathalie; Melin, Beatrice; Kemp, John P; Christiansen, Claus; Sayers, Adrian; Zhou, Yanhua; Calderari, Sophie; van Rooij, Jeroen; Carlson, Chris; Peters, Ulrike; Berlivet, Soizik; Dostie, Josée; Uitterlinden, Andre G; Williams, Stephen R.; Farber, Charles; Grinberg, Daniel; LaCroix, Andrea Z; Haessler, Jeff; Chasman, Daniel I; Giulianini, Franco; Rose, Lynda M; Ridker, Paul M; Eisman, John A; Nguyen, Tuan V; Center, Jacqueline R; Nogues, Xavier; Garcia-Giralt, Natalia; Launer, Lenore L; Gudnason, Vilmunder; Mellström, Dan; Vandenput, Liesbeth; Karlsson, Magnus K; Ljunggren, Östen; Svensson, Olle; Hallmans, Göran; Rousseau, François; Giroux, Sylvie; Bussière, Johanne; Arp, Pascal P; Koromani, Fjorda; Prince, Richard L; Lewis, Joshua R; Langdahl, Bente L; Hermann, A Pernille; Jensen, Jens-Erik B; Kaptoge, Stephen; Khaw, Kay-Tee; Reeve, Jonathan; Formosa, Melissa M; Xuereb-Anastasi, Angela; Åkesson, Kristina; McGuigan, Fiona E; Garg, Gaurav; Olmos, Jose M; Zarrabeitia, Maria T; Riancho, Jose A; Ralston, Stuart H; Alonso, Nerea; Jiang, Xi; Goltzman, David; Pastinen, Tomi; Grundberg, Elin; Gauguier, Dominique; Orwoll, Eric S; Karasik, David; Davey-Smith, George; Smith, Albert V; Siggeirsdottir, Kristin; Harris, Tamara B; Zillikens, M Carola; van Meurs, Joyce BJ; Thorsteinsdottir, Unnur; Maurano, Matthew T; Timpson, Nicholas J; Soranzo, Nicole; Durbin, Richard; Wilson, Scott G; Ntzani, Evangelia E; Brown, Matthew A; Stefansson, Kari; Hinds, David A; Spector, Tim; Cupples, L Adrienne; Ohlsson, Claes; Greenwood, Celia MT; Jackson, Rebecca D; Rowe, David W; Loomis, Cynthia A; Evans, David M; Ackert-Bicknell, Cheryl L; Joyner, Alexandra L; Duncan, Emma L; Kiel, Douglas P; Rivadeneira, Fernando; Richards, J Brent

2016-01-01

SUMMARY The extent to which low-frequency (minor allele frequency [MAF] between 1–5%) and rare (MAF ≤ 1%) variants contribute to complex traits and disease in the general population is largely unknown. Bone mineral density (BMD) is highly heritable, is a major predictor of osteoporotic fractures and has been previously associated with common genetic variants1–8, and rare, population-specific, coding variants9. Here we identify novel non-coding genetic variants with large effects on BMD (ntotal = 53,236) and fracture (ntotal = 508,253) in individuals of European ancestry from the general population. Associations for BMD were derived from whole-genome sequencing (n=2,882 from UK10K), whole-exome sequencing (n= 3,549), deep imputation of genotyped samples using a combined UK10K/1000Genomes reference panel (n=26,534), and de-novo replication genotyping (n= 20,271). We identified a low-frequency non-coding variant near a novel locus, EN1, with an effect size 4-fold larger than the mean of previously reported common variants for lumbar spine BMD8 (rs11692564[T], MAF = 1.7%, replication effect size = +0.20 standard deviations [SD], Pmeta = 2×10−14), which was also associated with a decreased risk of fracture (OR = 0.85; P = 2×10−11; ncases = 98,742 and ncontrols = 409,511). Using an En1Cre/flox mouse model, we observed that conditional loss of En1 results in low bone mass, likely as a consequence of high bone turn-over. We also identified a novel low-frequency non-coding variant with large effects on BMD near WNT16 (rs148771817[T], MAF = 1.1%, replication effect size = +0.39 SD, Pmeta = 1×10−11). In general, there was an excess of association signals arising from deleterious coding and conserved non-coding variants. These findings provide evidence that low-frequency non-coding variants have large effects on BMD and fracture, thereby providing rationale for whole-genome sequencing and improved imputation reference panels to study the genetic architecture of complex traits and disease in the general population. PMID:26367794

Hippocampal Remapping Is Constrained by Sparseness rather than Capacity

PubMed Central

Kammerer, Axel; Leibold, Christian

2014-01-01

Grid cells in the medial entorhinal cortex encode space with firing fields that are arranged on the nodes of spatial hexagonal lattices. Potential candidates to read out the space information of this grid code and to combine it with other sensory cues are hippocampal place cells. In this paper, we investigate a population of grid cells providing feed-forward input to place cells. The capacity of the underlying synaptic transformation is determined by both spatial acuity and the number of different spatial environments that can be represented. The codes for different environments arise from phase shifts of the periodical entorhinal cortex patterns that induce a global remapping of hippocampal place fields, i.e., a new random assignment of place fields for each environment. If only a single environment is encoded, the grid code can be read out at high acuity with only few place cells. A surplus in place cells can be used to store a space code for more environments via remapping. The number of stored environments can be increased even more efficiently by stronger recurrent inhibition and by partitioning the place cell population such that learning affects only a small fraction of them in each environment. We find that the spatial decoding acuity is much more resilient to multiple remappings than the sparseness of the place code. Since the hippocampal place code is sparse, we thus conclude that the projection from grid cells to the place cells is not using its full capacity to transfer space information. Both populations may encode different aspects of space. PMID:25474570

The impact of conventional dietary intake data coding methods on foods typically consumed by low-income African-American and White urban populations

PubMed Central

Mason, Marc A; Kuczmarski, Marie Fanelli; Allegro, Deanne; Zonderman, Alan B; Evans, Michele K

2016-01-01

Objective Analysing dietary data to capture how individuals typically consume foods is dependent on the coding variables used. Individual foods consumed simultaneously, like coffee with milk, are given codes to identify these combinations. Our literature review revealed a lack of discussion about using combination codes in analysis. The present study identified foods consumed at mealtimes and by race when combination codes were or were not utilized. Design Duplicate analysis methods were performed on separate data sets. The original data set consisted of all foods reported; each food was coded as if it was consumed individually. The revised data set was derived from the original data set by first isolating coded foods consumed as individual items from those foods consumed simultaneously and assigning a code to designate a combination. Foods assigned a combination code, like pancakes with syrup, were aggregated and associated with a food group, defined by the major food component (i.e. pancakes), and then appended to the isolated coded foods. Setting Healthy Aging in Neighborhoods of Diversity across the Life Span study. Subjects African-American and White adults with two dietary recalls (n 2177). Results Differences existed in lists of foods most frequently consumed by mealtime and race when comparing results based on original and revised data sets. African Americans reported consumption of sausage/luncheon meat and poultry, while ready-to-eat cereals and cakes/doughnuts/pastries were reported by Whites on recalls. Conclusions Use of combination codes provided more accurate representation of how foods were consumed by populations. This information is beneficial when creating interventions and exploring diet–health relationships. PMID:25435191

Two Perspectives on the Origin of the Standard Genetic Code

NASA Astrophysics Data System (ADS)

Sengupta, Supratim; Aggarwal, Neha; Bandhu, Ashutosh Vishwa

2014-12-01

The origin of a genetic code made it possible to create ordered sequences of amino acids. In this article we provide two perspectives on code origin by carrying out simulations of code-sequence coevolution in finite populations with the aim of examining how the standard genetic code may have evolved from more primitive code(s) encoding a small number of amino acids. We determine the efficacy of the physico-chemical hypothesis of code origin in the absence and presence of horizontal gene transfer (HGT) by allowing a diverse collection of code-sequence sets to compete with each other. We find that in the absence of horizontal gene transfer, natural selection between competing codes distinguished by differences in the degree of physico-chemical optimization is unable to explain the structure of the standard genetic code. However, for certain probabilities of the horizontal transfer events, a universal code emerges having a structure that is consistent with the standard genetic code.

Stable and Dynamic Coding for Working Memory in Primate Prefrontal Cortex

PubMed Central

Watanabe, Kei; Funahashi, Shintaro; Stokes, Mark G.

2017-01-01

Working memory (WM) provides the stability necessary for high-level cognition. Influential theories typically assume that WM depends on the persistence of stable neural representations, yet increasing evidence suggests that neural states are highly dynamic. Here we apply multivariate pattern analysis to explore the population dynamics in primate lateral prefrontal cortex (PFC) during three variants of the classic memory-guided saccade task (recorded in four animals). We observed the hallmark of dynamic population coding across key phases of a working memory task: sensory processing, memory encoding, and response execution. Throughout both these dynamic epochs and the memory delay period, however, the neural representational geometry remained stable. We identified two characteristics that jointly explain these dynamics: (1) time-varying changes in the subpopulation of neurons coding for task variables (i.e., dynamic subpopulations); and (2) time-varying selectivity within neurons (i.e., dynamic selectivity). These results indicate that even in a very simple memory-guided saccade task, PFC neurons display complex dynamics to support stable representations for WM. SIGNIFICANCE STATEMENT Flexible, intelligent behavior requires the maintenance and manipulation of incoming information over various time spans. For short time spans, this faculty is labeled “working memory” (WM). Dominant models propose that WM is maintained by stable, persistent patterns of neural activity in prefrontal cortex (PFC). However, recent evidence suggests that neural activity in PFC is dynamic, even while the contents of WM remain stably represented. Here, we explored the neural dynamics in PFC during a memory-guided saccade task. We found evidence for dynamic population coding in various task epochs, despite striking stability in the neural representational geometry of WM. Furthermore, we identified two distinct cellular mechanisms that contribute to dynamic population coding. PMID:28559375

Survey of Business Owners and Self-Employed Persons (SBO)

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LACEwING: A New Moving Group Analysis Code

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

Riedel, Adric R.; Blunt, Sarah C.; Faherty, Jacqueline K.

We present a new nearby young moving group (NYMG) kinematic membership analysis code, LocAting Constituent mEmbers In Nearby Groups (LACEwING), a new Catalog of Suspected Nearby Young Stars, a new list of bona fide members of moving groups, and a kinematic traceback code. LACEwING is a convergence-style algorithm with carefully vetted membership statistics based on a large numerical simulation of the Solar Neighborhood. Given spatial and kinematic information on stars, LACEwING calculates membership probabilities in 13 NYMGs and three open clusters within 100 pc. In addition to describing the inputs, methods, and products of the code, we provide comparisons ofmore » LACEwING to other popular kinematic moving group membership identification codes. As a proof of concept, we use LACEwING to reconsider the membership of 930 stellar systems in the Solar Neighborhood (within 100 pc) that have reported measurable lithium equivalent widths. We quantify the evidence in support of a population of young stars not attached to any NYMGs, which is a possible sign of new as-yet-undiscovered groups or of a field population of young stars.« less

The Solid Rocket Motor Slag Population: Results of a Radar-based Regressive Statistical Evaluation

NASA Technical Reports Server (NTRS)

Horstman, Matthew F.; Xu, Yu-Lin

2008-01-01

Solid rocket motor (SRM) slag has been identified as a significant source of man-made orbital debris. The propensity of SRMs to generate particles of 100 m and larger has caused concern regarding their contribution to the debris environment. Radar observation, rather than in-situ gathered evidence, is currently the only measurable source for the NASA/ODPO model of the on-orbit slag population. This simulated model includes the time evolution of the resultant orbital populations using a historical database of SRM launches, propellant masses, and estimated locations and times of tail-off. However, due to the small amount of observational evidence, there can be no direct comparison to check the validity of this model. Rather than using the assumed population developed from purely historical and physical assumptions, a regressional approach was used which utilized the populations observed by the Haystack radar from 1996 to present. The estimated trajectories from the historical model of slag sources, and the corresponding plausible detections by the Haystack radar, were identified. Comparisons with observational data from the ensuing years were made, and the SRM model was altered with respect to size and mass production of slag particles to reflect the historical data obtained. The result is a model SRM population that fits within the bounds of the observed environment.

Role of a plausible nuisance contributor in the declining obesity-mortality risks over time.

PubMed

Mehta, Tapan; Pajewski, Nicholas M; Keith, Scott W; Fontaine, Kevin; Allison, David B

2016-12-15

Recent analyses of epidemiological data including the National Health and Nutrition Examination Survey (NHANES) have suggested that the harmful effects of obesity may have decreased over calendar time. The shifting BMI distribution over time coupled with the application of fixed broad BMI categories in these analyses could be a plausible "nuisance contributor" to this observed change in the obesity-associated mortality over calendar time. To evaluate the extent to which observed temporal changes in the obesity-mortality association may be due to a shifting population distribution for body mass index (BMI), coupled with analyses based on static, broad BMI categories. Simulations were conducted using data from NHANES I and III linked with mortality data. Data from NHANES I were used to fit a "true" model treating BMI as a continuous variable. Coefficients estimated from this model were used to simulate mortality for participants in NHANES III. Hence, the population-level association between BMI and mortality in NHANES III was fixed to be identical to the association estimated in NHANES I. Hazard ratios (HRs) for obesity categories based on BMI for NHANES III with simulated mortality data were compared to the corresponding estimated HRs from NHANES I. Change in hazard ratios for simulated data in NHANES III compared to observed estimates from NHANES I. On average, hazard ratios for NHANES III based on simulated mortality data were 29.3% lower than the estimates from NHANES I using observed mortality follow-up. This reduction accounted for roughly three-fourths of the apparent decrease in the obesity-mortality association observed in a previous analysis of these data. Some of the apparent diminution of the association between obesity and mortality may be an artifact of treating BMI as a categorical variable. Copyright © 2016. Published by Elsevier Inc.

UV SEDs of early-type cluster galaxies: a new look at the UV upturn

NASA Astrophysics Data System (ADS)

Ali, S. S.; Bremer, M. N.; Phillipps, S.; De Propris, R.

2018-05-01

Using GALEX, Ultraviolet Optical Telescope (UVOT), and optical photometry, we explore the prevalence and strength of the Ultraviolet (UV) upturn in the spectra of quiescent early-type galaxies in several nearby clusters. Even for galaxies with completely passive optical colours, there is a large spread in vacuum UV colour consistent with almost all having some UV upturn component. Combining GALEX and UVOT data below 3000 Å, we generate for the first time comparatively detailed UV spectral energy distributions for Coma cluster galaxies. Fitting the UV upturn component with a blackbody, 26 of these show a range of characteristic temperatures (10 000-21 000K) for the UV upturn population. Assuming a single temperature to explain GALEX-optical colours could underestimate the fraction of galaxies with UV upturns and mis-classify some as systems with residual star formation. The UV upturn phenomenon is not an exclusive feature found only in giant galaxies; we identify galaxies with similar (or even bluer) FUV - V colours to the giants with upturns over a range of fainter luminosities. The temperature and strength of the UV upturn are correlated with galaxy mass. Under the plausible hypothesis that the sources of the UV upturn are blue horizontal branch stars, the most likely mechanism for this is the presence of a substantial (between 4 per cent and 20 per cent) Helium-rich (Y > 0.3) population of stars in these galaxies, potentially formed at z ˜ 4 and certainly at z > 2; this plausibly sets a lower limit of {˜ } {0.3- 0.8} × 10^{10} M⊙ to the in situ stellar mass of ˜L* galaxies at this redshift.

LZW-Kernel: fast kernel utilizing variable length code blocks from LZW compressors for protein sequence classification.

PubMed

Filatov, Gleb; Bauwens, Bruno; Kertész-Farkas, Attila

2018-05-07

Bioinformatics studies often rely on similarity measures between sequence pairs, which often pose a bottleneck in large-scale sequence analysis. Here, we present a new convolutional kernel function for protein sequences called the LZW-Kernel. It is based on code words identified with the Lempel-Ziv-Welch (LZW) universal text compressor. The LZW-Kernel is an alignment-free method, it is always symmetric, is positive, always provides 1.0 for self-similarity and it can directly be used with Support Vector Machines (SVMs) in classification problems, contrary to normalized compression distance (NCD), which often violates the distance metric properties in practice and requires further techniques to be used with SVMs. The LZW-Kernel is a one-pass algorithm, which makes it particularly plausible for big data applications. Our experimental studies on remote protein homology detection and protein classification tasks reveal that the LZW-Kernel closely approaches the performance of the Local Alignment Kernel (LAK) and the SVM-pairwise method combined with Smith-Waterman (SW) scoring at a fraction of the time. Moreover, the LZW-Kernel outperforms the SVM-pairwise method when combined with BLAST scores, which indicates that the LZW code words might be a better basis for similarity measures than local alignment approximations found with BLAST. In addition, the LZW-Kernel outperforms n-gram based mismatch kernels, hidden Markov model based SAM and Fisher kernel, and protein family based PSI-BLAST, among others. Further advantages include the LZW-Kernel's reliance on a simple idea, its ease of implementation, and its high speed, three times faster than BLAST and several magnitudes faster than SW or LAK in our tests. LZW-Kernel is implemented as a standalone C code and is a free open-source program distributed under GPLv3 license and can be downloaded from https://github.com/kfattila/LZW-Kernel. akerteszfarkas@hse.ru. Supplementary data are available at Bioinformatics Online.

Terrorism-related fear and avoidance behavior in a multiethnic urban population.

PubMed

Eisenman, David P; Glik, Deborah; Ong, Michael; Zhou, Qiong; Tseng, Chi-Hong; Long, Anna; Fielding, Jonathan; Asch, Steven

2009-01-01

We sought to determine whether groups traditionally most vulnerable to disasters would be more likely than would be others to perceive population-level risk as high (as measured by the estimated color-coded alert level) would worry more about terrorism, and would avoid activities because of terrorism concerns. We conducted a random digit dial survey of the Los Angeles County population October 2004 through January 2005 in 6 languages. We asked respondents what color alert level the country was under, how often they worry about terrorist attacks, and how often they avoid activities because of terrorism. Multivariate regression modeled correlates of worry and avoidance, including mental illness, disability, demographic factors, and estimated color-coded alert level. Persons who are mentally ill, those who are disabled, African Americans, Latinos, Chinese Americans, Korean Americans, and non-US citizens were more likely to perceive population-level risk as high, as measured by the estimated color-coded alert level. These groups also reported more worry and avoidance behaviors because of concerns about terrorism. Vulnerable populations experience a disproportionate burden of the psychosocial impact of terrorism threats and our national response. Further studies should investigate the specific behaviors affected and further elucidate disparities in the disaster burden associated with terrorism and terrorism policies.

Terrorism-Related Fear and Avoidance Behavior in a Multiethnic Urban Population

PubMed Central

Glik, Deborah; Ong, Michael; Zhou, Qiong; Tseng, Chi-Hong; Long, Anna; Fielding, Jonathan; Asch, Steven

2009-01-01

Objectives. We sought to determine whether groups traditionally most vulnerable to disasters would be more likely than would be others to perceive population-level risk as high (as measured by the estimated color-coded alert level) would worry more about terrorism, and would avoid activities because of terrorism concerns. Methods. We conducted a random digit dial survey of the Los Angeles County population October 2004 through January 2005 in 6 languages. We asked respondents what color alert level the country was under, how often they worry about terrorist attacks, and how often they avoid activities because of terrorism. Multivariate regression modeled correlates of worry and avoidance, including mental illness, disability, demographic factors, and estimated color-coded alert level. Results. Persons who are mentally ill, those who are disabled, African Americans, Latinos, Chinese Americans, Korean Americans, and non-US citizens were more likely to perceive population-level risk as high, as measured by the estimated color-coded alert level. These groups also reported more worry and avoidance behaviors because of concerns about terrorism. Conclusions. Vulnerable populations experience a disproportionate burden of the psychosocial impact of terrorism threats and our national response. Further studies should investigate the specific behaviors affected and further elucidate disparities in the disaster burden associated with terrorism and terrorism policies. PMID:19008521

Spatial Tuning Shifts Increase the Discriminability and Fidelity of Population Codes in Visual Cortex

PubMed Central

2017-01-01

Selective visual attention enables organisms to enhance the representation of behaviorally relevant stimuli by altering the encoding properties of single receptive fields (RFs). Yet we know little about how the attentional modulations of single RFs contribute to the encoding of an entire visual scene. Addressing this issue requires (1) measuring a group of RFs that tile a continuous portion of visual space, (2) constructing a population-level measurement of spatial representations based on these RFs, and (3) linking how different types of RF attentional modulations change the population-level representation. To accomplish these aims, we used fMRI to characterize the responses of thousands of voxels in retinotopically organized human cortex. First, we found that the response modulations of voxel RFs (vRFs) depend on the spatial relationship between the RF center and the visual location of the attended target. Second, we used two analyses to assess the spatial encoding quality of a population of voxels. We found that attention increased fine spatial discriminability and representational fidelity near the attended target. Third, we linked these findings by manipulating the observed vRF attentional modulations and recomputing our measures of the fidelity of population codes. Surprisingly, we discovered that attentional enhancements of population-level representations largely depend on position shifts of vRFs, rather than changes in size or gain. Our data suggest that position shifts of single RFs are a principal mechanism by which attention enhances population-level representations in visual cortex. SIGNIFICANCE STATEMENT Although changes in the gain and size of RFs have dominated our view of how attention modulates visual information codes, such hypotheses have largely relied on the extrapolation of single-cell responses to population responses. Here we use fMRI to relate changes in single voxel receptive fields (vRFs) to changes in population-level representations. We find that vRF position shifts contribute more to population-level enhancements of visual information than changes in vRF size or gain. This finding suggests that position shifts are a principal mechanism by which spatial attention enhances population codes for relevant visual information. This poses challenges for labeled line theories of information processing, suggesting that downstream regions likely rely on distributed inputs rather than single neuron-to-neuron mappings. PMID:28242794

nIFTY galaxy cluster simulations - III. The similarity and diversity of galaxies and subhaloes

NASA Astrophysics Data System (ADS)

Elahi, Pascal J.; Knebe, Alexander; Pearce, Frazer R.; Power, Chris; Yepes, Gustavo; Cui, Weiguang; Cunnama, Daniel; Kay, Scott T.; Sembolini, Federico; Beck, Alexander M.; Davé, Romeel; February, Sean; Huang, Shuiyao; Katz, Neal; McCarthy, Ian G.; Murante, Giuseppe; Perret, Valentin; Puchwein, Ewald; Saro, Alexandro; Teyssier, Romain

2016-05-01

We examine subhaloes and galaxies residing in a simulated Λ cold dark matter galaxy cluster (M^crit_{200}=1.1× 10^{15} h^{-1} M_{⊙}) produced by hydrodynamical codes ranging from classic smooth particle hydrodynamics (SPH), newer SPH codes, adaptive and moving mesh codes. These codes use subgrid models to capture galaxy formation physics. We compare how well these codes reproduce the same subhaloes/galaxies in gravity-only, non-radiative hydrodynamics and full feedback physics runs by looking at the overall subhalo/galaxy distribution and on an individual object basis. We find that the subhalo population is reproduced to within ≲10 per cent for both dark matter only and non-radiative runs, with individual objects showing code-to-code scatter of ≲0.1 dex, although the gas in non-radiative simulations shows significant scatter. Including feedback physics significantly increases the diversity. Subhalo mass and Vmax distributions vary by ≈20 per cent. The galaxy populations also show striking code-to-code variations. Although the Tully-Fisher relation is similar in almost all codes, the number of galaxies with 109 h- 1 M⊙ ≲ M* ≲ 1012 h- 1 M⊙ can differ by a factor of 4. Individual galaxies show code-to-code scatter of ˜0.5 dex in stellar mass. Moreover, systematic differences exist, with some codes producing galaxies 70 per cent smaller than others. The diversity partially arises from the inclusion/absence of active galactic nucleus feedback. Our results combined with our companion papers demonstrate that subgrid physics is not just subject to fine-tuning, but the complexity of building galaxies in all environments remains a challenge. We argue that even basic galaxy properties, such as stellar mass to halo mass, should be treated with errors bars of ˜0.2-0.4 dex.

Glyphosate Use Predicts ADHD Hospital Discharges in the Healthcare Cost and Utilization Project Net (HCUPnet): A Two-Way Fixed-Effects Analysis

PubMed Central

Fluegge, Keith R.; Fluegge, Kyle R.

2015-01-01

There has been considerable international study on the etiology of rising mental disorders, such as attention-deficit hyperactivity disorder (ADHD), in human populations. As glyphosate is the most commonly used herbicide in the world, we sought to test the hypothesis that glyphosate use in agriculture may be a contributing environmental factor to the rise of ADHD in human populations. State estimates for glyphosate use and nitrogen fertilizer use were obtained from the U.S. Geological Survey (USGS). We queried the Healthcare Cost and Utilization Project net (HCUPNET) for state-level hospitalization discharge data in all patients for all-listed ADHD from 2007 to 2010. We used rural-urban continuum codes from the USDA-Economic Research Service when exploring the effect of urbanization on the relationship between herbicide use and ADHD. Least squares dummy variable (LSDV) method and within method using two-way fixed effects was used to elucidate the relationship between glyphosate use and all-listed ADHD hospital discharges. We show that a one kilogram increase in glyphosate use, in particular, in one year significantly positively predicts state-level all-listed ADHD discharges, expressed as a percent of total mental disorders, the following year (coefficient = 5.54E-08, p<.01). A study on the effect of urbanization on the relationship between glyphosate and ADHD indicates that the relationship is marginally significantly positive after multiple comparison correction only in urban U.S. counties (p<.025). Furthermore, total glyphosate use is strongly positively associated with total farm use of nitrogen fertilizers from 1992 to 2006 (p<.001). We present evidence from the biomedical research literature of a plausible link among glyphosate, nitrogen dysbiosis and ADHD. Glyphosate use is a significant predictor of state hospitalizations for all-listed ADHD hospital discharges, with the effect concentrated in urban U.S. counties. This effect is seen even after controlling for individual state characteristics, strong correlations over time, and other significant associations with ADHD in the literature. We draw upon the econometric results to propose unique mechanisms, borrowing principles from soil and atmospheric sciences, for how glyphosate-based herbicides may be contributing to the rise of ADHD in all populations. PMID:26287729

Would a madman have been so wise as this?" The effects of source credibility and message credibility on validation.

PubMed

Foy, Jeffrey E; LoCasto, Paul C; Briner, Stephen W; Dyar, Samantha

2017-02-01

Readers rapidly check new information against prior knowledge during validation, but research is inconsistent as to whether source credibility affects validation. We argue that readers are likely to accept highly plausible assertions regardless of source, but that high source credibility may boost acceptance of claims that are less plausible based on general world knowledge. In Experiment 1, participants read narratives with assertions for which the plausibility varied depending on the source. For high credibility sources, we found that readers were faster to read information confirming these assertions relative to contradictory information. We found the opposite patterns for low credibility characters. In Experiment 2, readers read claims from the same high or low credibility sources, but the claims were always plausible based on general world knowledge. Readers consistently took longer to read contradictory information, regardless of source. In Experiment 3, participants read modified versions of "The Tell-Tale Heart," which was narrated entirely by an unreliable source. We manipulated the plausibility of a target event, as well as whether high credibility characters within the story provided confirmatory or contradictory information about the narrator's description of the target event. Though readers rated the narrator as being insane, they were more likely to believe the narrator's assertions about the target event when it was plausible and corroborated by other characters. We argue that sourcing research would benefit from focusing on the relationship between source credibility, message credibility, and multiple sources within a text.

Population-specific variation in haplotype composition and heterozygosity at the POLB locus.

PubMed

Yamtich, Jennifer; Speed, William C; Straka, Eva; Kidd, Judith R; Sweasy, Joann B; Kidd, Kenneth K

2009-05-01

DNA polymerase beta plays a central role in base excision repair (BER), which removes large numbers of endogenous DNA lesions from each cell on a daily basis. Little is currently known about germline polymorphisms within the POLB locus, making it difficult to study the association of variants at this locus with human diseases such as cancer. Yet, approximately thirty percent of human tumor types show variants of DNA polymerase beta. We have assessed the global frequency distributions of coding and common non-coding SNPs in and flanking the POLB gene for a total of 14 sites typed in approximately 2400 individuals from anthropologically defined human populations worldwide. We have found a marked difference between haplotype frequencies in African populations and in non-African populations.

Illuminating heterogeneous anisotropic upper mantle: testing a new anisotropic teleseismic body-wave tomography code - part II: Inversion mode

NASA Astrophysics Data System (ADS)

Munzarova, Helena; Plomerova, Jaroslava; Kissling, Edi

2015-04-01

Considering only isotropic wave propagation and neglecting anisotropy in teleseismic tomography studies is a simplification obviously incongruous with current understanding of the mantle-lithosphere plate dynamics. Furthermore, in solely isotropic high-resolution tomography results, potentially significant artefacts (i.e., amplitude and/or geometry distortions of 3D velocity heterogeneities) may result from such neglect. Therefore, we have undertaken to develop a code for anisotropic teleseismic tomography (AniTomo), which will allow us to invert the relative P-wave travel time residuals simultaneously for coupled isotropic-anisotropic P-wave velocity models of the upper mantle. To accomplish that, we have modified frequently-used isotropic teleseismic tomography code Telinv (e.g., Weiland et al., JGR, 1995; Lippitsch, JGR, 2003; Karousova et al., GJI, 2013). Apart from isotropic velocity heterogeneities, a weak hexagonal anisotropy is assumed as well to be responsible for the observed P-wave travel-time residuals. Moreover, no limitations to orientation of the symmetry axis are prescribed in the code. We allow a search for anisotropy oriented generally in 3D, which represents a unique approach among recent trials that otherwise incorporate only azimuthal anisotopy into the body-wave tomography. The presented code for retrieving anisotropy in 3D thus enables its direct applications to datasets from tectonically diverse regions. In this contribution, we outline the theoretical background of the AniTomo anisotropic tomography code. We parameterize the mantle lithosphere and asthenosphere with an orthogonal grid of nodes with various values of isotropic velocities, as well as of strength and orientation of anisotropy in 3D, which is defined by azimuth and inclination of either fast or slow symmetry axis of the hexagonal approximation of the media. Careful testing of the new code on synthetics, concentrating on code functionality, strength and weaknesses, is a necessary step before AniTomo is applied to real datasets. We examine various aspects coming along with anisotropic tomography such as setting a starting anisotropic model and parameters controlling the inversion, and particularly influence of a ray coverage on resolvability of individual anisotropic parameters. Synthetic testing also allows investigation of the well-known trade-off between effects of P-wave anisotropy and isotropic heterogeneities. Therefore, the target synthetic models are designed to represent schematically different heterogeneous anisotropic structures of the upper mantle. Testing inversion mode of the AniTomo code, considering an azimuthally quasi-equal distribution of rays and teleseismic P-wave incidences, shows that a separation of seismic anisotropy and isotropic velocity heterogeneities is plausible and that the correct orientation of the symmetry axes in a model can be found within three iterations for well-tuned damping factors.

Identifying personal microbiomes using metagenomic codes

PubMed Central

Franzosa, Eric A.; Huang, Katherine; Meadow, James F.; Gevers, Dirk; Lemon, Katherine P.; Bohannan, Brendan J. M.; Huttenhower, Curtis

2015-01-01

Community composition within the human microbiome varies across individuals, but it remains unknown if this variation is sufficient to uniquely identify individuals within large populations or stable enough to identify them over time. We investigated this by developing a hitting set-based coding algorithm and applying it to the Human Microbiome Project population. Our approach defined body site-specific metagenomic codes: sets of microbial taxa or genes prioritized to uniquely and stably identify individuals. Codes capturing strain variation in clade-specific marker genes were able to distinguish among 100s of individuals at an initial sampling time point. In comparisons with follow-up samples collected 30–300 d later, ∼30% of individuals could still be uniquely pinpointed using metagenomic codes from a typical body site; coincidental (false positive) matches were rare. Codes based on the gut microbiome were exceptionally stable and pinpointed >80% of individuals. The failure of a code to match its owner at a later time point was largely explained by the loss of specific microbial strains (at current limits of detection) and was only weakly associated with the length of the sampling interval. In addition to highlighting patterns of temporal variation in the ecology of the human microbiome, this work demonstrates the feasibility of microbiome-based identifiability—a result with important ethical implications for microbiome study design. The datasets and code used in this work are available for download from huttenhower.sph.harvard.edu/idability. PMID:25964341

Transition from Target to Gaze Coding in Primate Frontal Eye Field during Memory Delay and Memory-Motor Transformation.

PubMed

Sajad, Amirsaman; Sadeh, Morteza; Yan, Xiaogang; Wang, Hongying; Crawford, John Douglas

2016-01-01

The frontal eye fields (FEFs) participate in both working memory and sensorimotor transformations for saccades, but their role in integrating these functions through time remains unclear. Here, we tracked FEF spatial codes through time using a novel analytic method applied to the classic memory-delay saccade task. Three-dimensional recordings of head-unrestrained gaze shifts were made in two monkeys trained to make gaze shifts toward briefly flashed targets after a variable delay (450-1500 ms). A preliminary analysis of visual and motor response fields in 74 FEF neurons eliminated most potential models for spatial coding at the neuron population level, as in our previous study (Sajad et al., 2015). We then focused on the spatiotemporal transition from an eye-centered target code (T; preferred in the visual response) to an eye-centered intended gaze position code (G; preferred in the movement response) during the memory delay interval. We treated neural population codes as a continuous spatiotemporal variable by dividing the space spanning T and G into intermediate T-G models and dividing the task into discrete steps through time. We found that FEF delay activity, especially in visuomovement cells, progressively transitions from T through intermediate T-G codes that approach, but do not reach, G. This was followed by a final discrete transition from these intermediate T-G delay codes to a "pure" G code in movement cells without delay activity. These results demonstrate that FEF activity undergoes a series of sensory-memory-motor transformations, including a dynamically evolving spatial memory signal and an imperfect memory-to-motor transformation.

A system for household enumeration and re-identification in densely populated slums to facilitate community research, education, and advocacy.

PubMed

Thomson, Dana R; Shitole, Shrutika; Shitole, Tejal; Sawant, Kiran; Subbaraman, Ramnath; Bloom, David E; Patil-Deshmukh, Anita

2014-01-01

We devised and implemented an innovative Location-Based Household Coding System (LBHCS) appropriate to a densely populated informal settlement in Mumbai, India. LBHCS codes were designed to double as unique household identifiers and as walking directions; when an entire community is enumerated, LBHCS codes can be used to identify the number of households located per road (or lane) segment. LBHCS was used in community-wide biometric, mental health, diarrheal disease, and water poverty studies. It also facilitated targeted health interventions by a research team of youth from Mumbai, including intensive door-to-door education of residents, targeted follow-up meetings, and a full census. In addition, LBHCS permitted rapid and low-cost preparation of GIS mapping of all households in the slum, and spatial summation and spatial analysis of survey data. LBHCS was an effective, easy-to-use, affordable approach to household enumeration and re-identification in a densely populated informal settlement where alternative satellite imagery and GPS technologies could not be used.

Optimizing Distribution of Pandemic Influenza Antiviral Drugs

PubMed Central

Huang, Hsin-Chan; Morton, David P.; Johnson, Gregory P.; Gutfraind, Alexander; Galvani, Alison P.; Clements, Bruce; Meyers, Lauren A.

2015-01-01

We provide a data-driven method for optimizing pharmacy-based distribution of antiviral drugs during an influenza pandemic in terms of overall access for a target population and apply it to the state of Texas, USA. We found that during the 2009 influenza pandemic, the Texas Department of State Health Services achieved an estimated statewide access of 88% (proportion of population willing to travel to the nearest dispensing point). However, access reached only 34.5% of US postal code (ZIP code) areas containing <1,000 underinsured persons. Optimized distribution networks increased expected access to 91% overall and 60% in hard-to-reach regions, and 2 or 3 major pharmacy chains achieved near maximal coverage in well-populated areas. Independent pharmacies were essential for reaching ZIP code areas containing <1,000 underinsured persons. This model was developed during a collaboration between academic researchers and public health officials and is available as a decision support tool for Texas Department of State Health Services at a Web-based interface. PMID:25625858

Complementary codes for odor identity and intensity in olfactory cortex

PubMed Central

Bolding, Kevin A; Franks, Kevin M

2017-01-01

The ability to represent both stimulus identity and intensity is fundamental for perception. Using large-scale population recordings in awake mice, we find distinct coding strategies facilitate non-interfering representations of odor identity and intensity in piriform cortex. Simply knowing which neurons were activated is sufficient to accurately represent odor identity, with no additional information about identity provided by spike time or spike count. Decoding analyses indicate that cortical odor representations are not sparse. Odorant concentration had no systematic effect on spike counts, indicating that rate cannot encode intensity. Instead, odor intensity can be encoded by temporal features of the population response. We found a subpopulation of rapid, largely concentration-invariant responses was followed by another population of responses whose latencies systematically decreased at higher concentrations. Cortical inhibition transforms olfactory bulb output to sharpen these dynamics. Our data therefore reveal complementary coding strategies that can selectively represent distinct features of a stimulus. DOI: http://dx.doi.org/10.7554/eLife.22630.001 PMID:28379135

Documentation of ethnicity.

PubMed

Brasić, James Robert

2004-12-01

The comparison of the ethnic composition of an intermediate care facility with several Hispanic residents and the general population was hindered by the absence of categorization of ethnicity according to the United States Census. If all Hispanic residents of the facility were white, then 55% of the facility population were white, a proportion comparable to the 58.2% white population of the general population. On the other hand, if all the Hispanic residents were not white, then 27.5% of the facility residents were white. In that case, the proportion of white residents of the facility is much less than in the general population. Therefore, a Demographic Coding Form was developed to capture the essential data to make direct comparisons and contrasts with the general population recorded by the United States Census. Since the United States Census records Hispanic ethnic minority status as a separate category independent from all other ethnic groups, the design of experiments to investigate the possible effects of ethnicity on populations wisely incorporates the administration of a Demographic Coding Form to capture the key ethnic data to permit direct comparison with the general population.

Simultaneous gene finding in multiple genomes.

PubMed

König, Stefanie; Romoth, Lars W; Gerischer, Lizzy; Stanke, Mario

2016-11-15

As the tree of life is populated with sequenced genomes ever more densely, the new challenge is the accurate and consistent annotation of entire clades of genomes. We address this problem with a new approach to comparative gene finding that takes a multiple genome alignment of closely related species and simultaneously predicts the location and structure of protein-coding genes in all input genomes, thereby exploiting negative selection and sequence conservation. The model prefers potential gene structures in the different genomes that are in agreement with each other, or-if not-where the exon gains and losses are plausible given the species tree. We formulate the multi-species gene finding problem as a binary labeling problem on a graph. The resulting optimization problem is NP hard, but can be efficiently approximated using a subgradient-based dual decomposition approach. The proposed method was tested on whole-genome alignments of 12 vertebrate and 12 Drosophila species. The accuracy was evaluated for human, mouse and Drosophila melanogaster and compared to competing methods. Results suggest that our method is well-suited for annotation of (a large number of) genomes of closely related species within a clade, in particular, when RNA-Seq data are available for many of the genomes. The transfer of existing annotations from one genome to another via the genome alignment is more accurate than previous approaches that are based on protein-spliced alignments, when the genomes are at close to medium distances. The method is implemented in C ++ as part of Augustus and available open source at http://bioinf.uni-greifswald.de/augustus/ CONTACT: stefaniekoenig@ymail.com or mario.stanke@uni-greifswald.deSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Evidence of evolutionary history and selective sweeps in the genome of Meishan pig reveals its genetic and phenotypic characterization.

PubMed

Zhao, Pengju; Yu, Ying; Feng, Wen; Du, Heng; Yu, Jian; Kang, Huimin; Zheng, Xianrui; Wang, Zhiquan; Liu, George E; Ernst, Catherine W; Ran, Xueqin; Wang, Jiafu; Liu, Jian-Feng

2018-05-01

Meishan is a pig breed indigenous to China and famous for its high fecundity. The traits of Meishan are strongly associated with its distinct evolutionary history and domestication. However, the genomic evidence linking the domestication of Meishan pigs with its unique features is still poorly understood. The goal of this study is to investigate the genomic signatures and evolutionary evidence related to the phenotypic traits of Meishan via large-scale sequencing. We found that the unique domestication of Meishan pigs occurred in the Taihu Basin area between the Majiabang and Liangzhu Cultures, during which 300 protein-coding genes have underwent positive selection. Notably, enrichment of the FoxO signaling pathway with significant enrichment signal and the harbored gene IGF1R were likely associated with the high fertility of Meishan pigs. Moreover, NFKB1 exhibited strong selective sweep signals and positively participated in hyaluronan biosynthesis as the key gene of NF-kB signaling, which may have resulted in the wrinkled skin and face of Meishan pigs. Particularly, three population-specific synonymous single-nucleotide variants occurred in PYROXD1, MC1R, and FAM83G genes; the T305C substitution in the MCIR gene explained the black coat of the Meishan pigs well. In addition, the shared haplotypes between Meishan and Duroc breeds confirmed the previous Asian-derived introgression and demonstrated the specific contribution of Meishan pigs. These findings will help us explain the unique genetic and phenotypic characteristics of Meishan pigs and offer a plausible method for their utilization of Meishan pigs as valuable genetic resources in pig breeding and as an animal model for human wrinkled skin disease research.

Neural coding in graphs of bidirectional associative memories.

PubMed

Bouchain, A David; Palm, Günther

2012-01-24

In the last years we have developed large neural network models for the realization of complex cognitive tasks in a neural network architecture that resembles the network of the cerebral cortex. We have used networks of several cortical modules that contain two populations of neurons (one excitatory, one inhibitory). The excitatory populations in these so-called "cortical networks" are organized as a graph of Bidirectional Associative Memories (BAMs), where edges of the graph correspond to BAMs connecting two neural modules and nodes of the graph correspond to excitatory populations with associative feedback connections (and inhibitory interneurons). The neural code in each of these modules consists essentially of the firing pattern of the excitatory population, where mainly it is the subset of active neurons that codes the contents to be represented. The overall activity can be used to distinguish different properties of the patterns that are represented which we need to distinguish and control when performing complex tasks like language understanding with these cortical networks. The most important pattern properties or situations are: exactly fitting or matching input, incomplete information or partially matching pattern, superposition of several patterns, conflicting information, and new information that is to be learned. We show simple simulations of these situations in one area or module and discuss how to distinguish these situations based on the overall internal activation of the module. This article is part of a Special Issue entitled "Neural Coding". Copyright © 2011 Elsevier B.V. All rights reserved.

Impact of population growth and population ethics on climate change mitigation policy

PubMed Central

Scovronick, Noah; Budolfson, Mark B.; Dennig, Francis; Fleurbaey, Marc; Siebert, Asher; Socolow, Robert H.; Spears, Dean; Wagner, Fabian

2017-01-01

Future population growth is uncertain and matters for climate policy: higher growth entails more emissions and means more people will be vulnerable to climate-related impacts. We show that how future population is valued importantly determines mitigation decisions. Using the Dynamic Integrated Climate-Economy model, we explore two approaches to valuing population: a discounted version of total utilitarianism (TU), which considers total wellbeing and is standard in social cost of carbon dioxide (SCC) models, and of average utilitarianism (AU), which ignores population size and sums only each time period’s discounted average wellbeing. Under both approaches, as population increases the SCC increases, but optimal peak temperature decreases. The effect is larger under TU, because it responds to the fact that a larger population means climate change hurts more people: for example, in 2025, assuming the United Nations (UN)-high rather than UN-low population scenario entails an increase in the SCC of 85% under TU vs. 5% under AU. The difference in the SCC between the two population scenarios under TU is comparable to commonly debated decisions regarding time discounting. Additionally, we estimate the avoided mitigation costs implied by plausible reductions in population growth, finding that large near-term savings ($billions annually) occur under TU; savings under AU emerge in the more distant future. These savings are larger than spending shortfalls for human development policies that may lower fertility. Finally, we show that whether lowering population growth entails overall improvements in wellbeing—rather than merely cost savings—again depends on the ethical approach to valuing population. PMID:29087298

Impact of population growth and population ethics on climate change mitigation policy.

PubMed

Scovronick, Noah; Budolfson, Mark B; Dennig, Francis; Fleurbaey, Marc; Siebert, Asher; Socolow, Robert H; Spears, Dean; Wagner, Fabian

2017-11-14

Future population growth is uncertain and matters for climate policy: higher growth entails more emissions and means more people will be vulnerable to climate-related impacts. We show that how future population is valued importantly determines mitigation decisions. Using the Dynamic Integrated Climate-Economy model, we explore two approaches to valuing population: a discounted version of total utilitarianism (TU), which considers total wellbeing and is standard in social cost of carbon dioxide (SCC) models, and of average utilitarianism (AU), which ignores population size and sums only each time period's discounted average wellbeing. Under both approaches, as population increases the SCC increases, but optimal peak temperature decreases. The effect is larger under TU, because it responds to the fact that a larger population means climate change hurts more people: for example, in 2025, assuming the United Nations (UN)-high rather than UN-low population scenario entails an increase in the SCC of 85% under TU vs. 5% under AU. The difference in the SCC between the two population scenarios under TU is comparable to commonly debated decisions regarding time discounting. Additionally, we estimate the avoided mitigation costs implied by plausible reductions in population growth, finding that large near-term savings ($billions annually) occur under TU; savings under AU emerge in the more distant future. These savings are larger than spending shortfalls for human development policies that may lower fertility. Finally, we show that whether lowering population growth entails overall improvements in wellbeing-rather than merely cost savings-again depends on the ethical approach to valuing population. Copyright © 2017 the Author(s). Published by PNAS.

Density dependence and risk of extinction in a small population of sea otters

USGS Publications Warehouse

Gerber, L.R.; Buenau, K.E.; VanBlaricom, G.

2004-01-01

Sea otters (Enhydra lutris (L.)) were hunted to extinction off the coast of Washington State early in the 20th century. A new population was established by translocations from Alaska in 1969 and 1970. The population, currently numbering at least 550 animals, A major threat to the population is the ongoing risk of majour oil spills in sea otter habitat. We apply population models to census and demographic data in order to evaluate the status of the population. We fit several density dependent models to test for density dependence and determine plausible values for the carrying capacity (K) by comparing model goodness of fit to an exponential model. Model fits were compared using Akaike Information Criterion (AIC). A significant negative relationship was found between the population growth rate and population size (r2=0.27, F=5.57, df=16, p<0.05), suggesting density dependence in Washington state sea otters. Information criterion statistics suggest that the model is the most parsimonious, followed closely by the logistic Beverton-Holt model. Values of K ranged from 612 to 759 with best-fit parameter estimates for the Beverton-Holt model including 0.26 for r and 612 for K. The latest (2001) population index count (555) puts the population at 87-92% of the estimated carrying capacity, above the suggested range for optimum sustainable population (OSP). Elasticity analysis was conducted to examine the effects of proportional changes in vital rates on the population growth rate (??). The elasticity values indicate the population is most sensitive to changes in survival rates (particularly adult survival).

Phthalates impact human health: Epidemiological evidences and plausible mechanism of action.

PubMed

Benjamin, Sailas; Masai, Eiji; Kamimura, Naofumi; Takahashi, Kenji; Anderson, Robin C; Faisal, Panichikkal Abdul

2017-10-15

Disregarding the rising alarm on the hazardous nature of various phthalates and their metabolites, ruthless usage of phthalates as plasticizer in plastics and as additives in innumerable consumer products continues due low their cost, attractive properties, and lack of suitable alternatives. Globally, in silico computational, in vitro mechanistic, in vivo preclinical and limited clinical or epidemiological human studies showed that over a dozen phthalates and their metabolites ingested passively by man from the general environment, foods, drinks, breathing air, and routine household products cause various dysfunctions. Thus, this review addresses the health hazards posed by phthalates on children and adolescents, epigenetic modulation, reproductive toxicity in women and men; insulin resistance and type II diabetes; overweight and obesity, skeletal anomalies, allergy and asthma, cancer, etc., coupled with the description of major phthalates and their general uses, phthalate exposure routes, biomonitoring and risk assessment, special account on endocrine disruption; and finally, a plausible molecular cross-talk with a unique mechanism of action. This clinically focused comprehensive review on the hazards of phthalates would benefit the general population, academia, scientists, clinicians, environmentalists, and law or policy makers to decide upon whether usage of phthalates to be continued swiftly without sufficient deceleration or regulated by law or to be phased out from earth forever. Copyright © 2017. Published by Elsevier B.V.

Effects of isoflurane anesthesia on ensemble patterns of Ca2+ activity in mouse v1: reduced direction selectivity independent of increased correlations in cellular activity.

PubMed

Goltstein, Pieter M; Montijn, Jorrit S; Pennartz, Cyriel M A

2015-01-01

Anesthesia affects brain activity at the molecular, neuronal and network level, but it is not well-understood how tuning properties of sensory neurons and network connectivity change under its influence. Using in vivo two-photon calcium imaging we matched neuron identity across episodes of wakefulness and anesthesia in the same mouse and recorded spontaneous and visually evoked activity patterns of neuronal ensembles in these two states. Correlations in spontaneous patterns of calcium activity between pairs of neurons were increased under anesthesia. While orientation selectivity remained unaffected by anesthesia, this treatment reduced direction selectivity, which was attributable to an increased response to the null-direction. As compared to anesthesia, populations of V1 neurons coded more mutual information on opposite stimulus directions during wakefulness, whereas information on stimulus orientation differences was lower. Increases in correlations of calcium activity during visual stimulation were correlated with poorer population coding, which raised the hypothesis that the anesthesia-induced increase in correlations may be causal to degrading directional coding. Visual stimulation under anesthesia, however, decorrelated ongoing activity patterns to a level comparable to wakefulness. Because visual stimulation thus appears to 'break' the strength of pairwise correlations normally found in spontaneous activity under anesthesia, the changes in correlational structure cannot explain the awake-anesthesia difference in direction coding. The population-wide decrease in coding for stimulus direction thus occurs independently of anesthesia-induced increments in correlations of spontaneous activity.

Effects of Isoflurane Anesthesia on Ensemble Patterns of Ca2+ Activity in Mouse V1: Reduced Direction Selectivity Independent of Increased Correlations in Cellular Activity

PubMed Central

Goltstein, Pieter M.; Montijn, Jorrit S.; Pennartz, Cyriel M. A.

2015-01-01

Anesthesia affects brain activity at the molecular, neuronal and network level, but it is not well-understood how tuning properties of sensory neurons and network connectivity change under its influence. Using in vivo two-photon calcium imaging we matched neuron identity across episodes of wakefulness and anesthesia in the same mouse and recorded spontaneous and visually evoked activity patterns of neuronal ensembles in these two states. Correlations in spontaneous patterns of calcium activity between pairs of neurons were increased under anesthesia. While orientation selectivity remained unaffected by anesthesia, this treatment reduced direction selectivity, which was attributable to an increased response to the null-direction. As compared to anesthesia, populations of V1 neurons coded more mutual information on opposite stimulus directions during wakefulness, whereas information on stimulus orientation differences was lower. Increases in correlations of calcium activity during visual stimulation were correlated with poorer population coding, which raised the hypothesis that the anesthesia-induced increase in correlations may be causal to degrading directional coding. Visual stimulation under anesthesia, however, decorrelated ongoing activity patterns to a level comparable to wakefulness. Because visual stimulation thus appears to ‘break’ the strength of pairwise correlations normally found in spontaneous activity under anesthesia, the changes in correlational structure cannot explain the awake-anesthesia difference in direction coding. The population-wide decrease in coding for stimulus direction thus occurs independently of anesthesia-induced increments in correlations of spontaneous activity. PMID:25706867

Was Wright Right? The Canonical Genetic Code is an Empirical Example of an Adaptive Peak in Nature; Deviant Genetic Codes Evolved Using Adaptive Bridges

PubMed Central

2010-01-01

The canonical genetic code is on a sub-optimal adaptive peak with respect to its ability to minimize errors, and is close to, but not quite, optimal. This is demonstrated by the near-total adjacency of synonymous codons, the similarity of adjacent codons, and comparisons of frequency of amino acid usage with number of codons in the code for each amino acid. As a rare empirical example of an adaptive peak in nature, it shows adaptive peaks are real, not merely theoretical. The evolution of deviant genetic codes illustrates how populations move from a lower to a higher adaptive peak. This is done by the use of “adaptive bridges,” neutral pathways that cross over maladaptive valleys by virtue of masking of the phenotypic expression of some maladaptive aspects in the genotype. This appears to be the general mechanism by which populations travel from one adaptive peak to another. There are multiple routes a population can follow to cross from one adaptive peak to another. These routes vary in the probability that they will be used, and this probability is determined by the number and nature of the mutations that happen along each of the routes. A modification of the depiction of adaptive landscapes showing genetic distances and probabilities of travel along their multiple possible routes would throw light on this important concept. PMID:20711776

Understanding large SEP events with the PATH code: Modeling of the 13 December 2006 SEP event

NASA Astrophysics Data System (ADS)

Verkhoglyadova, O. P.; Li, G.; Zank, G. P.; Hu, Q.; Cohen, C. M. S.; Mewaldt, R. A.; Mason, G. M.; Haggerty, D. K.; von Rosenvinge, T. T.; Looper, M. D.

2010-12-01

The Particle Acceleration and Transport in the Heliosphere (PATH) numerical code was developed to understand solar energetic particle (SEP) events in the near-Earth environment. We discuss simulation results for the 13 December 2006 SEP event. The PATH code includes modeling a background solar wind through which a CME-driven oblique shock propagates. The code incorporates a mixed population of both flare and shock-accelerated solar wind suprathermal particles. The shock parameters derived from ACE measurements at 1 AU and observational flare characteristics are used as input into the numerical model. We assume that the diffusive shock acceleration mechanism is responsible for particle energization. We model the subsequent transport of particles originated at the flare site and particles escaping from the shock and propagating in the equatorial plane through the interplanetary medium. We derive spectra for protons, oxygen, and iron ions, together with their time-intensity profiles at 1 AU. Our modeling results show reasonable agreement with in situ measurements by ACE, STEREO, GOES, and SAMPEX for this event. We numerically estimate the Fe/O abundance ratio and discuss the physics underlying a mixed SEP event. We point out that the flare population is as important as shock geometry changes during shock propagation for modeling time-intensity profiles and spectra at 1 AU. The combined effects of seed population and shock geometry will be examined in the framework of an extended PATH code in future modeling efforts.

Surface acoustic wave coding for orthogonal frequency coded devices

NASA Technical Reports Server (NTRS)

Malocha, Donald (Inventor); Kozlovski, Nikolai (Inventor)

2011-01-01

Methods and systems for coding SAW OFC devices to mitigate code collisions in a wireless multi-tag system. Each device producing plural stepped frequencies as an OFC signal with a chip offset delay to increase code diversity. A method for assigning a different OCF to each device includes using a matrix based on the number of OFCs needed and the number chips per code, populating each matrix cell with OFC chip, and assigning the codes from the matrix to the devices. The asynchronous passive multi-tag system includes plural surface acoustic wave devices each producing a different OFC signal having the same number of chips and including a chip offset time delay, an algorithm for assigning OFCs to each device, and a transceiver to transmit an interrogation signal and receive OFC signals in response with minimal code collisions during transmission.

Census Bureau Reports at Least 350 Languages Spoken in U.S. Homes

Science.gov Websites

United States Census Bureau Topics Population Latest Information Age and Sex Ancestry Children Mobility Population Estimates Population Projections Race Veterans Economy Latest Information Portal Other Economic Programs Business Latest Information Business Characteristics Classification Codes

The effect of clumped population structure on the variability of spreading dynamics.

PubMed

Black, Andrew J; House, Thomas; Keeling, Matt J; Ross, Joshua V

2014-10-21

Processes that spread through local contact, including outbreaks of infectious diseases, are inherently noisy, and are frequently observed to be far noisier than predicted by standard stochastic models that assume homogeneous mixing. One way to reproduce the observed levels of noise is to introduce significant individual-level heterogeneity with respect to infection processes, such that some individuals are expected to generate more secondary cases than others. Here we consider a population where individuals can be naturally aggregated into clumps (subpopulations) with stronger interaction within clumps than between them. This clumped structure induces significant increases in the noisiness of a spreading process, such as the transmission of infection, despite complete homogeneity at the individual level. Given the ubiquity of such clumped aggregations (such as homes, schools and workplaces for humans or farms for livestock) we suggest this as a plausible explanation for noisiness of many epidemic time series. Copyright © 2014 Elsevier Ltd. All rights reserved.

An Age Old Problem? Estimating the Impact of Dementia on Past Human Populations.

PubMed

Smith, Martin; Atkin, Alison; Cutler, Clare

2017-02-01

To model the impact of dementia on past societies. We consider multiple lines of evidence indicating elderly individuals to have been more common throughout the past than is frequently accepted. We then apply known dementia incidence/prevalence rates to plausible assumptions of past population structures to suggest prevalence in the past. Dementia prevalence in premodern societies is likely to have been around 5% of the rate seen in modern, developed countries but with a total past incidence running into billions. Dementia is often seen as a "modern" challenge that humans have not had to contend with before. We argue that this condition has had considerably greater effects than previously envisaged and is a challenge that humans have already withstood successfully, on one hand at a lower incidence but on the other without the considerable clinical, technological, and social advances that have been made in recent times.

Male circumcision and HIV infection risk.

PubMed

Krieger, John N

2012-02-01

Male circumcision is being promoted to reduce human immunodeficiency virus type 1 (HIV) infection rates. This review evaluates the scientific evidence suggesting that male circumcision reduces HIV infection risk in high-risk heterosexual populations. We followed the updated International Consultation on Urological Diseases evidence-based medicine recommendations to critically review the scientific evidence on male circumcision and HIV infection risk. Level 1 evidence supports the concept that male circumcision substantially reduces the risk of HIV infection. Three major lines of evidence support this conclusion: biological data suggesting that this concept is plausible, data from observational studies supported by high-quality meta-analyses, and three randomized clinical trials supported by high-quality meta-analyses. The evidence from these biological studies, observational studies, randomized controlled clinical trials, meta-analyses, and cost-effectiveness studies is conclusive. The challenges to implementation of male circumcision as a public health measure in high-risk populations must now be faced.

A method to identify drivers of societal change likely to affect natural assets in the future, illustrated with Australia's native biodiversity.

PubMed

Pepper, D A; Lada, Hania; Thomson, James R; Bakar, K Shuvo; Lake, P S; Mac Nally, Ralph

2017-03-01

Human society has a profound adverse effect on natural assets as human populations increase and as global climate changes. We need to envisage different futures that encompass plausible human responses to threats and change, and become more mindful of their likely impacts on natural assets. We describe a method for developing a set of future scenarios for a natural asset at national scale under ongoing human population growth and climate change. The method involves expansive consideration of potential drivers of societal change, a reduction of these to form a small set of key drivers to which contrasting settings are assigned, which we use to develop a set of different scenarios. We use Australia's native biodiversity as the focus to illustrate the method. Copyright © 2016 Elsevier B.V. All rights reserved.

Dreissenid mussels are not a "dead end" in Great Lakes food webs

USGS Publications Warehouse

Madenijan, Charles P.; Pothoven, Steven A.; Schneeberger, Philip J.; Ebener, Mark P.; Mohr, Lloyd C.; Nalepa, Thomas F.; Bence, James R.

2010-01-01

Dreissenid mussels have been regarded as a “dead end” in Great Lakes food webs because the degree of predation on dreissenid mussels, on a lakewide basis, is believed to be low. Waterfowl predation on dreissenid mussels in the Great Lakes has primarily been confined to bays, and therefore its effects on the dreissenid mussel population have been localized rather than operating on a lakewide level. Based on results from a previous study, annual consumption of dreissenid mussels by the round goby (Neogobius melanostomus) population in central Lake Erie averaged only 6 kilotonnes (kt; 1 kt = one thousand metric tons) during 1995–2002. In contrast, our coupling of lake whitefish (Coregonus clupeaformis) population models with a lake whitefish bioenergetics model revealed that lake whitefish populations in Lakes Michigan and Huron consumed 109 and 820 kt, respectively, of dreissenid mussels each year. Our results indicated that lake whitefish can be an important predator on dreissenid mussels in the Great Lakes, and that dreissenid mussels do not represent a “dead end” in Great Lakes food webs. The Lake Michigan dreissenid mussel population has been estimated to be growing more than three times faster than the Lake Huron dreissenid mussel population during the 2000s. One plausible explanation for the higher population growth rate in Lake Michigan would be the substantially higher predation rate by lake whitefish on dreissenid mussels in Lake Huron.

Not an ancient relic: the endemic Livistona palms of arid central Australia could have been introduced by humans

PubMed Central

Kondo, Toshiaki; Crisp, Michael D.; Linde, Celeste; Bowman, David M. J. S.; Kawamura, Kensuke; Kaneko, Shingo; Isagi, Yuji

2012-01-01

Livistona mariae is an endemic palm localized in arid central Australia. This species is separated by about 1000 km from its congener L. rigida, which grows distantly in the Roper River and Nicholson–Gregory River catchments in northern Australia. Such an isolated distribution of L. mariae has been assumed to have resulted from contraction of ancestral populations as Australia aridified from the Mid-Miocene (ca 15 Ma). To test this hypothesis at the population level, we examined the genetic relationships among 14 populations of L. mariae and L. rigida using eight nuclear microsatellite loci. Our population tree and Bayesian clustering revealed that these populations comprised two genetically distinct groups that did not correspond to the current classification at species rank, and L. mariae showed closest affinity with L. rigida from Roper River. Furthermore, coalescent divergence-time estimations suggested that the disjunction between the northern populations (within L. rigida) could have originated by intermittent colonization along an ancient river that has been drowned repeatedly by marine transgression. During that time, L. mariae populations could have been established by opportunistic immigrants from Roper River about 15 000 years ago, concurrently with the settlement of indigenous Australians in central Australia, who are thus plausible vectors. Thus, our results rule out the ancient relic hypothesis for the origin of L. mariae. PMID:22398168

With or without you: predictive coding and Bayesian inference in the brain

PubMed Central

Aitchison, Laurence; Lengyel, Máté

2018-01-01

Two theoretical ideas have emerged recently with the ambition to provide a unifying functional explanation of neural population coding and dynamics: predictive coding and Bayesian inference. Here, we describe the two theories and their combination into a single framework: Bayesian predictive coding. We clarify how the two theories can be distinguished, despite sharing core computational concepts and addressing an overlapping set of empirical phenomena. We argue that predictive coding is an algorithmic / representational motif that can serve several different computational goals of which Bayesian inference is but one. Conversely, while Bayesian inference can utilize predictive coding, it can also be realized by a variety of other representations. We critically evaluate the experimental evidence supporting Bayesian predictive coding and discuss how to test it more directly. PMID:28942084

Photoionization and High Density Gas

NASA Technical Reports Server (NTRS)

Kallman, T.; Bautista, M.; White, Nicholas E. (Technical Monitor)

2002-01-01

We present results of calculations using the XSTAR version 2 computer code. This code is loosely based on the XSTAR v.1 code which has been available for public use for some time. However it represents an improvement and update in several major respects, including atomic data, code structure, user interface, and improved physical description of ionization/excitation. In particular, it now is applicable to high density situations in which significant excited atomic level populations are likely to occur. We describe the computational techniques and assumptions, and present sample runs with particular emphasis on high density situations.

Potential Effects of a Scenario Earthquake on the Economy of Southern California: Small Business Exposure and Sensitivity Analysis to a Magnitude 7.8 Earthquake

USGS Publications Warehouse

Sherrouse, Benson C.; Hester, David J.; Wein, Anne M.

2008-01-01

The Multi-Hazards Demonstration Project (MHDP) is a collaboration between the U.S. Geological Survey (USGS) and various partners from the public and private sectors and academia, meant to improve Southern California's resiliency to natural hazards (Jones and others, 2007). In support of the MHDP objectives, the ShakeOut Scenario was developed. It describes a magnitude 7.8 (M7.8) earthquake along the southernmost 300 kilometers (200 miles) of the San Andreas Fault, identified by geoscientists as a plausible event that will cause moderate to strong shaking over much of the eight-county (Imperial, Kern, Los Angeles, Orange, Riverside, San Bernardino, San Diego, and Ventura) Southern California region. This report contains an exposure and sensitivity analysis of small businesses in terms of labor and employment statistics. Exposure is measured as the absolute counts of labor market variables anticipated to experience each level of Instrumental Intensity (a proxy measure of damage). Sensitivity is the percentage of the exposure of each business establishment size category to each Instrumental Intensity level. The analysis concerns the direct effect of the earthquake on small businesses. The analysis is inspired by the Bureau of Labor Statistics (BLS) report that analyzed the labor market losses (exposure) of a M6.9 earthquake on the Hayward fault by overlaying geocoded labor market data on Instrumental Intensity values. The method used here is influenced by the ZIP-code-level data provided by the California Employment Development Department (CA EDD), which requires the assignment of Instrumental Intensities to ZIP codes. The ZIP-code-level labor market data includes the number of business establishments, employees, and quarterly payroll categorized by business establishment size.

Fusimotor control of spindle sensitivity regulates central and peripheral coding of joint angles.

PubMed

Lan, Ning; He, Xin

2012-01-01

Proprioceptive afferents from muscle spindles encode information about peripheral joint movements for the central nervous system (CNS). The sensitivity of muscle spindle is nonlinearly dependent on the activation of gamma (γ) motoneurons in the spinal cord that receives inputs from the motor cortex. How fusimotor control of spindle sensitivity affects proprioceptive coding of joint position is not clear. Furthermore, what information is carried in the fusimotor signal from the motor cortex to the muscle spindle is largely unknown. In this study, we addressed the issue of communication between the central and peripheral sensorimotor systems using a computational approach based on the virtual arm (VA) model. In simulation experiments within the operational range of joint movements, the gamma static commands (γ(s)) to the spindles of both mono-articular and bi-articular muscles were hypothesized (1) to remain constant, (2) to be modulated with joint angles linearly, and (3) to be modulated with joint angles nonlinearly. Simulation results revealed a nonlinear landscape of Ia afferent with respect to both γ(s) activation and joint angle. Among the three hypotheses, the constant and linear strategies did not yield Ia responses that matched the experimental data, and therefore, were rejected as plausible strategies of spindle sensitivity control. However, if γ(s) commands were quadratically modulated with joint angles, a robust linear relation between Ia afferents and joint angles could be obtained in both mono-articular and bi-articular muscles. With the quadratic strategy of spindle sensitivity control, γ(s) commands may serve as the CNS outputs that inform the periphery of central coding of joint angles. The results suggest that the information of joint angles may be communicated between the CNS and muscles via the descending γ(s) efferent and Ia afferent signals.

Inequality and adolescent violence: an exploration of community, family, and individual factors.

PubMed Central

Bruce, Marino A.

2004-01-01

PURPOSE: The study seeks to examine whether the relationships among community, family, individual factors, and violent behavior are parallel across race- and gender-specific segments of the adolescent population. METHODS: Data from the National Longitudinal Study of Adolescent Health are analyzed to highlight the complex relationships between inequality, community, family, individual behavior, and violence. RESULTS: The results from robust regression analysis provide evidence that social environmental factors can influence adolescent violence in race- and gender-specific ways. CONCLUSIONS: Findings from this study establish the plausibility of multidimensional models that specify a complex relationship between inequality and adolescent violence. PMID:15101669

Exogenous hormone use, reproductive history and risk of adult myeloid leukaemia.

PubMed

Poynter, J N; Fonstad, R; Blair, C K; Roesler, M; Cerhan, J R; Hirsch, B; Nguyen, P; Ross, J A

2013-10-01

A hormonal aetiology is one explanation for the lower incidence of myeloid leukaemia in women compared with men. In this population-based case-control study, we evaluated associations between exogenous hormone use and reproductive history and myeloid leukaemia, overall and by disease subtype. We observed a suggestive association between oral contraceptive use and acute myeloid leukaemia (odds ratio=0.55, 95% confidence interval=0.32-0.96). Hormone replacement therapy and reproductive factors were not associated with risk. Despite the biological plausibility for a role of oestrogen in leukaemogenesis, other aetiologic factors are likely to explain the differing incidence rates in males and females.

Efficiency turns the table on neural encoding, decoding and noise.

PubMed

Deneve, Sophie; Chalk, Matthew

2016-04-01

Sensory neurons are usually described with an encoding model, for example, a function that predicts their response from the sensory stimulus using a receptive field (RF) or a tuning curve. However, central to theories of sensory processing is the notion of 'efficient coding'. We argue here that efficient coding implies a completely different neural coding strategy. Instead of a fixed encoding model, neural populations would be described by a fixed decoding model (i.e. a model reconstructing the stimulus from the neural responses). Because the population solves a global optimization problem, individual neurons are variable, but not noisy, and have no truly invariant tuning curve or receptive field. We review recent experimental evidence and implications for neural noise correlations, robustness and adaptation. Copyright © 2016. Published by Elsevier Ltd.

Phylogenetic incongruence in the Drosophila melanogaster species group

PubMed Central

Wong, Alex; Jensen, Jeffrey D.; Pool, John E.; Aquadro, Charles F.

2007-01-01

Drosophila melanogaster and its close relatives are used extensively in comparative biology. Despite the importance of phylogenetic information for such studies, relationships between some melanogaster species group members are unclear due to conflicting phylogenetic signals at different loci. In this study, we use twelve nuclear loci (eleven coding and one non-coding) to assess the degree of phylogenetic incongruence in this model system. We focus on two nodes: (1) The node joining the D. erecta-D. orena, D. melanogaster-D. simulans, and D. yakuba-D. teissieri lineages, and (2) The node joining the lineages leading to the melanogaster, takahashii, and eugracilis subgroups. We find limited evidence for incongruence at the first node; our data, as well as those of several previous studies, strongly support monophyly of a clade consisting of D. erecta-D. orena and D. yakuba-D. teissieri. By contrast, using likelihood based tests of congruence, we find robust evidence for topological incongruence at the second node. Different loci support different relationships among the melanogaster, takahashii and eugracilis subgroups, and the observed incongruence is not easily attributable to homoplasy, non-equilibrium base composition, or positive selection on a subset of loci. We argue that lineage sorting in the common ancestor of these three subgroups is the most plausible explanation for our observations. Such lineage sorting may lead to biased estimation of tree topology and evolutionary rates, and may confound inferences of positive selection. PMID:17071113

Does case misclassification threaten the validity of studies investigating the relationship between neck manipulation and vertebral artery dissection stroke? Yes.

PubMed

Paulus, Jessica K; Thaler, David E

2016-01-01

For patients and health care providers who are considering spinal manipulative therapy of the neck, it is crucial to establish if it is a trigger for cervical artery dissection and/or stroke, and if it is, the magnitude of the risk. We discuss the biological plausibility of how neck manipulation could cause cervical artery dissection. We also discuss how case misclassification threatens the validity of influential published studies that have investigated the relationship between neck manipulation and dissection. Our position is supported by the fact that the largest epidemiologic studies of neck manipulation safety with respect to neurological outcomes have relied on International Classification of Diseases-9 codes for case identification. However, the application of these codes in prior studies failed to identify dissections (rather than strokes in general) and so conclusions from those studies are invalid. There are several methodological challenges to understanding the association between neck manipulation and vertebral artery dissection. Addressing these issues is critical because even a modest association between neck manipulation and cervical artery dissection could translate into a significant number of avoidable dissections given the widespread use of neck manipulation by providers from various backgrounds. We believe that valid case classification, accurate measurement of manipulative procedures, and addressing reverse causation bias should be top priorities for future research.

Evaluating and minimizing noise impact due to aircraft flyover

NASA Technical Reports Server (NTRS)

Jacobson, I. D.; Cook, G.

1979-01-01

Existing techniques were used to assess the noise impact on a community due to aircraft operation and to optimize the flight paths of an approaching aircraft with respect to the annoyance produced. Major achievements are: (1) the development of a population model suitable for determining the noise impact, (2) generation of a numerical computer code which uses this population model along with the steepest descent algorithm to optimize approach/landing trajectories, (3) implementation of this optimization code in several fictitious cases as well as for the community surrounding Patrick Henry International Airport, Virginia.

SecPop Version 4: Sector Population Land Fraction and Economic Estimation Program: Users? Guide Model Manual and Verification Report.

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

Weber, Scott; Bixler, Nathan E.; McFadden, Katherine Letizia

In 1973 the U.S. Environmental Protection Agency (EPA) developed SecPop to calculate population estimates to support a study on air quality. The Nuclear Regulatory Commission (NRC) adopted this program to support siting reviews for nuclear power plant construction and license applications. Currently SecPop is used to prepare site data input files for offsite consequence calculations with the MELCOR Accident Consequence Code System (MACCS). SecPop enables the use of site-specific population, land use, and economic data for a polar grid defined by the user. Updated versions of SecPop have been released to use U.S. decennial census population data. SECPOP90 was releasedmore » in 1997 to use 1990 population and economic data. SECPOP2000 was released in 2003 to use 2000 population data and 1997 economic data. This report describes the current code version, SecPop version 4.3, which uses 2010 population data and both 2007 and 2012 economic data. It is also compatible with 2000 census and 2002 economic data. At the time of this writing, the current version of SecPop is 4.3.0, and that version is described herein. This report contains guidance for the installation and use of the code as well as a description of the theory, models, and algorithms involved. This report contains appendices which describe the development of the 2010 census file, 2007 county file, and 2012 county file. Finally, an appendix is included that describes the validation assessments performed.« less

Parameter and model uncertainty in a life-table model for fine particles (PM2.5): a statistical modeling study

PubMed Central

Tainio, Marko; Tuomisto, Jouni T; Hänninen, Otto; Ruuskanen, Juhani; Jantunen, Matti J; Pekkanen, Juha

2007-01-01

Background The estimation of health impacts involves often uncertain input variables and assumptions which have to be incorporated into the model structure. These uncertainties may have significant effects on the results obtained with model, and, thus, on decision making. Fine particles (PM2.5) are believed to cause major health impacts, and, consequently, uncertainties in their health impact assessment have clear relevance to policy-making. We studied the effects of various uncertain input variables by building a life-table model for fine particles. Methods Life-expectancy of the Helsinki metropolitan area population and the change in life-expectancy due to fine particle exposures were predicted using a life-table model. A number of parameter and model uncertainties were estimated. Sensitivity analysis for input variables was performed by calculating rank-order correlations between input and output variables. The studied model uncertainties were (i) plausibility of mortality outcomes and (ii) lag, and parameter uncertainties (iii) exposure-response coefficients for different mortality outcomes, and (iv) exposure estimates for different age groups. The monetary value of the years-of-life-lost and the relative importance of the uncertainties related to monetary valuation were predicted to compare the relative importance of the monetary valuation on the health effect uncertainties. Results The magnitude of the health effects costs depended mostly on discount rate, exposure-response coefficient, and plausibility of the cardiopulmonary mortality. Other mortality outcomes (lung cancer, other non-accidental and infant mortality) and lag had only minor impact on the output. The results highlight the importance of the uncertainties associated with cardiopulmonary mortality in the fine particle impact assessment when compared with other uncertainties. Conclusion When estimating life-expectancy, the estimates used for cardiopulmonary exposure-response coefficient, discount rate, and plausibility require careful assessment, while complicated lag estimates can be omitted without this having any major effect on the results. PMID:17714598

Parameter and model uncertainty in a life-table model for fine particles (PM2.5): a statistical modeling study.

PubMed

Tainio, Marko; Tuomisto, Jouni T; Hänninen, Otto; Ruuskanen, Juhani; Jantunen, Matti J; Pekkanen, Juha

2007-08-23

The estimation of health impacts involves often uncertain input variables and assumptions which have to be incorporated into the model structure. These uncertainties may have significant effects on the results obtained with model, and, thus, on decision making. Fine particles (PM2.5) are believed to cause major health impacts, and, consequently, uncertainties in their health impact assessment have clear relevance to policy-making. We studied the effects of various uncertain input variables by building a life-table model for fine particles. Life-expectancy of the Helsinki metropolitan area population and the change in life-expectancy due to fine particle exposures were predicted using a life-table model. A number of parameter and model uncertainties were estimated. Sensitivity analysis for input variables was performed by calculating rank-order correlations between input and output variables. The studied model uncertainties were (i) plausibility of mortality outcomes and (ii) lag, and parameter uncertainties (iii) exposure-response coefficients for different mortality outcomes, and (iv) exposure estimates for different age groups. The monetary value of the years-of-life-lost and the relative importance of the uncertainties related to monetary valuation were predicted to compare the relative importance of the monetary valuation on the health effect uncertainties. The magnitude of the health effects costs depended mostly on discount rate, exposure-response coefficient, and plausibility of the cardiopulmonary mortality. Other mortality outcomes (lung cancer, other non-accidental and infant mortality) and lag had only minor impact on the output. The results highlight the importance of the uncertainties associated with cardiopulmonary mortality in the fine particle impact assessment when compared with other uncertainties. When estimating life-expectancy, the estimates used for cardiopulmonary exposure-response coefficient, discount rate, and plausibility require careful assessment, while complicated lag estimates can be omitted without this having any major effect on the results.

Drug-Induced Acute Myocardial Infarction: Identifying ‘Prime Suspects’ from Electronic Healthcare Records-Based Surveillance System

PubMed Central

Coloma, Preciosa M.; Schuemie, Martijn J.; Trifirò, Gianluca; Furlong, Laura; van Mulligen, Erik; Bauer-Mehren, Anna; Avillach, Paul; Kors, Jan; Sanz, Ferran; Mestres, Jordi; Oliveira, José Luis; Boyer, Scott; Helgee, Ernst Ahlberg; Molokhia, Mariam; Matthews, Justin; Prieto-Merino, David; Gini, Rosa; Herings, Ron; Mazzaglia, Giampiero; Picelli, Gino; Scotti, Lorenza; Pedersen, Lars; van der Lei, Johan; Sturkenboom, Miriam

2013-01-01

Background Drug-related adverse events remain an important cause of morbidity and mortality and impose huge burden on healthcare costs. Routinely collected electronic healthcare data give a good snapshot of how drugs are being used in ‘real-world’ settings. Objective To describe a strategy that identifies potentially drug-induced acute myocardial infarction (AMI) from a large international healthcare data network. Methods Post-marketing safety surveillance was conducted in seven population-based healthcare databases in three countries (Denmark, Italy, and the Netherlands) using anonymised demographic, clinical, and prescription/dispensing data representing 21,171,291 individuals with 154,474,063 person-years of follow-up in the period 1996–2010. Primary care physicians’ medical records and administrative claims containing reimbursements for filled prescriptions, laboratory tests, and hospitalisations were evaluated using a three-tier triage system of detection, filtering, and substantiation that generated a list of drugs potentially associated with AMI. Outcome of interest was statistically significant increased risk of AMI during drug exposure that has not been previously described in current literature and is biologically plausible. Results Overall, 163 drugs were identified to be associated with increased risk of AMI during preliminary screening. Of these, 124 drugs were eliminated after adjustment for possible bias and confounding. With subsequent application of criteria for novelty and biological plausibility, association with AMI remained for nine drugs (‘prime suspects’): azithromycin; erythromycin; roxithromycin; metoclopramide; cisapride; domperidone; betamethasone; fluconazole; and megestrol acetate. Limitations Although global health status, co-morbidities, and time-invariant factors were adjusted for, residual confounding cannot be ruled out. Conclusion A strategy to identify potentially drug-induced AMI from electronic healthcare data has been proposed that takes into account not only statistical association, but also public health relevance, novelty, and biological plausibility. Although this strategy needs to be further evaluated using other healthcare data sources, the list of ‘prime suspects’ makes a good starting point for further clinical, laboratory, and epidemiologic investigation. PMID:24015213

Epidemiological causality.

PubMed

Morabia, Alfredo

2005-01-01

Epidemiological methods, which combine population thinking and group comparisons, can primarily identify causes of disease in populations. There is therefore a tension between our intuitive notion of a cause, which we want to be deterministic and invariant at the individual level, and the epidemiological notion of causes, which are invariant only at the population level. Epidemiologists have given heretofore a pragmatic solution to this tension. Causal inference in epidemiology consists in checking the logical coherence of a causality statement and determining whether what has been found grossly contradicts what we think we already know: how strong is the association? Is there a dose-response relationship? Does the cause precede the effect? Is the effect biologically plausible? Etc. This approach to causal inference can be traced back to the English philosophers David Hume and John Stuart Mill. On the other hand, the mode of establishing causality, devised by Jakob Henle and Robert Koch, which has been fruitful in bacteriology, requires that in every instance the effect invariably follows the cause (e.g., inoculation of Koch bacillus and tuberculosis). This is incompatible with epidemiological causality which has to deal with probabilistic effects (e.g., smoking and lung cancer), and is therefore invariant only for the population.

Evidence for a sex-segregated migration in the humpback whale (Megaptera novaeangliae).

PubMed

Brown, M R; Corkeron, P J; Hale, P T; Schultz, K W; Bryden, M M

1995-02-22

Existing population models for humpback whales assume that all individuals within a population undertake the annual migration from feeding areas in high latitudes to breeding areas in tropical waters. An excess of males was recorded in the commercial whaling catches near breeding areas in the southern hemisphere, but no account of this was taken in developing population models, because it was believed that this bias was a result of whalers selecting against females with young calves. Here we demonstrate that the sex ratio of migrating humpback whales near a breeding area is highly skewed towards males. A biopsy study carried out in 1992 throughout the northward and southward migrations revealed a sex ratio of 2.4 males: 1 female in the population of humpback whales migrating along the east Australian coast (n = 180). A reanalysis of the catches made during commercial whaling in this and other areas of the southern hemisphere gave a sex ratio of the same order. The most plausible explanation, supported by some evidence, is that some females remain in the feeding areas throughout winter. The results reported here show that existing management models require major revision to take account of these findings.

Detection Trend of Helminth Eggs in the Strata Soil Samples from Ancient Historic Places of Korea

PubMed Central

Seo, Min; Chai, Jong-Yil; Kim, Myeung Ju; Shim, Sang Yuk; Ki, Ho Chul; Shin, Dong Hoon

2016-01-01

For several years, we have conducted a series of studies on the patterns of ancient parasitism prevailing in the soil of rural and urban areas of past Kingdom of Korea. Actually, during our survey of paleoparasitology in archaeological sites of Korean peninsula, numerous ancient parasite eggs were discovered in the samples from the city districts of Hansung (Joseon) and Buyeo (Baikje), the palace moat at Gyeongju (Silla), shell-midden site at Bonghwang-dong (Silla to Joseon), and the reservoir found in Hwawangsansung fortress (Silla). By the paleoparasitological studies, with respect to parasitism in the high-density populations of ancient towns and cities, we have managed to catch glimpses of the patterns prevalent therein: a serious parasitic contamination of the soil in ancient urban areas, but not in rural areas of the past. Our historical research also proposed the plausible mechanism of parasite infection very serious indeed among urban populations in Korean history. Although city dwelling doubtless has accrued significant benefits for people and populations with agriculture, it can be equally supposed that living in such highly populated areas might have facilitated the spread of parasite infection. PMID:27853112

Impacts of changing rainfall regime on the demography of tropical birds

NASA Astrophysics Data System (ADS)

Brawn, Jeffrey D.; Benson, Thomas J.; Stager, Maria; Sly, Nicholas D.; Tarwater, Corey E.

2017-02-01

Biodiversity in tropical regions is particularly high and may be highly sensitive to climate change. Unfortunately, a lack of long-term data hampers understanding of how tropical species, especially animals, may react to projected environmental changes. The amount and timing of rainfall is key to the function of tropical ecosystems and, although specific model predictions differ, there is general agreement that rainfall regimes will change over large areas of the tropics. Here, we estimate associations between dry season length (DSL) and the population biology of 20 bird species sampled in central Panama over a 33-year period. Longer dry seasons decreased the population growth rates and viability of nearly one-third of the species sampled. Simulations with modest increases in DSL suggest that consistently longer dry seasons will change the structure of tropical bird communities. Such change may occur even without direct loss of habitat--a finding with fundamental implications for conservation planning. Systematic changes in rainfall regime may threaten some populations and communities of tropical animals even in large tracts of protected habitat. These findings suggest the need for collaboration between climate scientists and conservation biologists to identify areas where rainfall regimes will be able to plausibly maintain wildlife populations.

Detection Trend of Helminth Eggs in the Strata Soil Samples from Ancient Historic Places of Korea.

PubMed

Seo, Min; Chai, Jong-Yil; Kim, Myeung Ju; Shim, Sang Yuk; Ki, Ho Chul; Shin, Dong Hoon

2016-10-01

For several years, we have conducted a series of studies on the patterns of ancient parasitism prevailing in the soil of rural and urban areas of past Kingdom of Korea. Actually, during our survey of paleoparasitology in archaeological sites of Korean peninsula, numerous ancient parasite eggs were discovered in the samples from the city districts of Hansung (Joseon) and Buyeo (Baikje), the palace moat at Gyeongju (Silla), shell-midden site at Bonghwang-dong (Silla to Joseon), and the reservoir found in Hwawangsansung fortress (Silla). By the paleoparasitological studies, with respect to parasitism in the high-density populations of ancient towns and cities, we have managed to catch glimpses of the patterns prevalent therein: a serious parasitic contamination of the soil in ancient urban areas, but not in rural areas of the past. Our historical research also proposed the plausible mechanism of parasite infection very serious indeed among urban populations in Korean history. Although city dwelling doubtless has accrued significant benefits for people and populations with agriculture, it can be equally supposed that living in such highly populated areas might have facilitated the spread of parasite infection.

Genetic markers and population history: Finland revisited.

PubMed

Palo, Jukka U; Ulmanen, Ismo; Lukka, Matti; Ellonen, Pekka; Sajantila, Antti

2009-10-01

The Finnish population in Northern Europe has been a target of extensive genetic studies during the last decades. The population is considered as a homogeneous isolate, well suited for gene mapping studies because of its reduced diversity and homogeneity. However, several studies have shown substantial differences between the eastern and western parts of the country, especially in the male-mediated Y chromosome. This divergence is evident in non-neutral genetic variation also and it is usually explained to stem from founder effects occurring in the settlement of eastern Finland as late as in the 16th century. Here, we have reassessed this population historical scenario using Y-chromosomal, mitochondrial and autosomal markers and geographical sampling covering entire Finland. The obtained results suggest substantial Scandinavian gene flow into south-western, but not into the eastern, Finland. Male-biased Scandinavian gene flow into the south-western parts of the country would plausibly explain the large inter-regional differences observed in the Y-chromosome, and the relative homogeneity in the mitochondrial and autosomal data. On the basis of these results, we suggest that the expression of 'Finnish Disease Heritage' illnesses, more common in the eastern/north-eastern Finland, stems from long-term drift, rather than from relatively recent founder effects.

Transition from Target to Gaze Coding in Primate Frontal Eye Field during Memory Delay and Memory–Motor Transformation123

PubMed Central

Sajad, Amirsaman; Sadeh, Morteza; Yan, Xiaogang; Wang, Hongying

2016-01-01

Abstract The frontal eye fields (FEFs) participate in both working memory and sensorimotor transformations for saccades, but their role in integrating these functions through time remains unclear. Here, we tracked FEF spatial codes through time using a novel analytic method applied to the classic memory-delay saccade task. Three-dimensional recordings of head-unrestrained gaze shifts were made in two monkeys trained to make gaze shifts toward briefly flashed targets after a variable delay (450-1500 ms). A preliminary analysis of visual and motor response fields in 74 FEF neurons eliminated most potential models for spatial coding at the neuron population level, as in our previous study (Sajad et al., 2015). We then focused on the spatiotemporal transition from an eye-centered target code (T; preferred in the visual response) to an eye-centered intended gaze position code (G; preferred in the movement response) during the memory delay interval. We treated neural population codes as a continuous spatiotemporal variable by dividing the space spanning T and G into intermediate T–G models and dividing the task into discrete steps through time. We found that FEF delay activity, especially in visuomovement cells, progressively transitions from T through intermediate T–G codes that approach, but do not reach, G. This was followed by a final discrete transition from these intermediate T–G delay codes to a “pure” G code in movement cells without delay activity. These results demonstrate that FEF activity undergoes a series of sensory–memory–motor transformations, including a dynamically evolving spatial memory signal and an imperfect memory-to-motor transformation. PMID:27092335

Autistic traits are linked to reduced adaptive coding of face identity and selectively poorer face recognition in men but not women.

PubMed

Rhodes, Gillian; Jeffery, Linda; Taylor, Libby; Ewing, Louise

2013-11-01

Our ability to discriminate and recognize thousands of faces despite their similarity as visual patterns relies on adaptive, norm-based, coding mechanisms that are continuously updated by experience. Reduced adaptive coding of face identity has been proposed as a neurocognitive endophenotype for autism, because it is found in autism and in relatives of individuals with autism. Autistic traits can also extend continuously into the general population, raising the possibility that reduced adaptive coding of face identity may be more generally associated with autistic traits. In the present study, we investigated whether adaptive coding of face identity decreases as autistic traits increase in an undergraduate population. Adaptive coding was measured using face identity aftereffects, and autistic traits were measured using the Autism-Spectrum Quotient (AQ) and its subscales. We also measured face and car recognition ability to determine whether autistic traits are selectively related to face recognition difficulties. We found that men who scored higher on levels of autistic traits related to social interaction had reduced adaptive coding of face identity. This result is consistent with the idea that atypical adaptive face-coding mechanisms are an endophenotype for autism. Autistic traits were also linked with face-selective recognition difficulties in men. However, there were some unexpected sex differences. In women, autistic traits were linked positively, rather than negatively, with adaptive coding of identity, and were unrelated to face-selective recognition difficulties. These sex differences indicate that autistic traits can have different neurocognitive correlates in men and women and raise the intriguing possibility that endophenotypes of autism can differ in males and females. © 2013 Elsevier Ltd. All rights reserved.

Heuristic rules embedded genetic algorithm for in-core fuel management optimization

NASA Astrophysics Data System (ADS)

Alim, Fatih

The objective of this study was to develop a unique methodology and a practical tool for designing loading pattern (LP) and burnable poison (BP) pattern for a given Pressurized Water Reactor (PWR) core. Because of the large number of possible combinations for the fuel assembly (FA) loading in the core, the design of the core configuration is a complex optimization problem. It requires finding an optimal FA arrangement and BP placement in order to achieve maximum cycle length while satisfying the safety constraints. Genetic Algorithms (GA) have been already used to solve this problem for LP optimization for both PWR and Boiling Water Reactor (BWR). The GA, which is a stochastic method works with a group of solutions and uses random variables to make decisions. Based on the theories of evaluation, the GA involves natural selection and reproduction of the individuals in the population for the next generation. The GA works by creating an initial population, evaluating it, and then improving the population by using the evaluation operators. To solve this optimization problem, a LP optimization package, GARCO (Genetic Algorithm Reactor Code Optimization) code is developed in the framework of this thesis. This code is applicable for all types of PWR cores having different geometries and structures with an unlimited number of FA types in the inventory. To reach this goal, an innovative GA is developed by modifying the classical representation of the genotype. To obtain the best result in a shorter time, not only the representation is changed but also the algorithm is changed to use in-core fuel management heuristics rules. The improved GA code was tested to demonstrate and verify the advantages of the new enhancements. The developed methodology is explained in this thesis and preliminary results are shown for the VVER-1000 reactor hexagonal geometry core and the TMI-1 PWR. The improved GA code was tested to verify the advantages of new enhancements. The core physics code used for VVER in this research is Moby-Dick, which was developed to analyze the VVER by SKODA Inc. The SIMULATE-3 code, which is an advanced two-group nodal code, is used to analyze the TMI-1.

The Relationship Between Financial Incentives and Quality of Diabetes Care in Ontario, Canada

PubMed Central

Kiran, Tara; Victor, J. Charles; Kopp, Alexander; Shah, Baiju R.; Glazier, Richard H.

2012-01-01

OBJECTIVE We assessed the impact of a diabetes incentive code introduced for primary care physicians in Ontario, Canada, in 2002 on quality of diabetes care at the population and patient level. RESEARCH DESIGN AND METHODS We analyzed administrative data for 757,928 Ontarians with diabetes to examine the use of the code and receipt of three evidence-based monitoring tests from 2006 to 2008. We assessed testing rates over time and before and after billing of the incentive code. RESULTS One-quarter of Ontarians with diabetes had an incentive code billed by their physician. The proportion receiving the optimal number of all three monitoring tests (HbA1c, cholesterol, and eye tests) rose gradually from 16% in 2000 to 27% in 2008. Individuals who were younger, lived in rural areas, were not enrolled in a primary care model, or had a mental illness were less likely to receive all three recommended tests. Patients with higher numbers of incentive code billings in 2006–2008 were more likely to receive recommended testing but also were more likely to have received the highest level of recommended testing prior to introduction of the incentive code. Following the same patients over time, improvement in recommended testing was no greater after billing of the first incentive code than before. CONCLUSIONS The diabetes incentive code led to minimal improvement in quality of diabetes care at the population and patient level. Our findings suggest that physicians who provide the highest quality care prior to incentives may be those most likely to claim incentive payments. PMID:22456866

Inaccuracies in oral cavity-pharynx cancer coded as the underlying cause of death on U.S. death certificates, and trends in mortality rates (1999-2010).

PubMed

Polednak, Anthony P

2014-08-01

To enhance surveillance of mortality from oral cavity-pharynx cancer (OCPC) by considering inaccuracies in the cancer site coded as the underlying cause of death on death certificates vs. cancer site in a population-based cancer registry (as the gold standard). A database was used for 9 population-based cancer registries of the Surveillance, Epidemiology and End Results (SEER) Program, including deaths in 1999-2010 for patients diagnosed in 1973-2010. Numbers of deaths and death rates for OCPC in the SEER population were modified for apparent inaccuracies in the cancer site coded as the underlying cause of death. For age groups <65 years, deaths from OCPC were underestimated by 22-35% by using unmodified (vs. modified) numbers, but temporal declines in death rates were still evident in the SEER population and were similar to declines using routine mortality data for the entire U.S. population. Deaths were underestimated by about 70-80% using underlying cause for tonsillar cancers, strongly associated with human papillomavirus (HPV) infection, but a lack of decline in death rates was still evident. Routine mortality statistics based on underlying cause of death underestimate OCPC deaths but demonstrate trends in OCPC death rates that require continued surveillance in view of increasing incidence rates for HPV-related OCPC. Copyright © 2014 Elsevier Ltd. All rights reserved.

Temporally structured replay of neural activity in a model of entorhinal cortex, hippocampus and postsubiculum

PubMed Central

Hasselmo, Michael E.

2008-01-01

The spiking activity of hippocampal neurons during REM sleep exhibits temporally structured replay of spiking occurring during previously experienced trajectories (Louie and Wilson, 2001). Here, temporally structured replay of place cell activity during REM sleep is modeled in a large-scale network simulation of grid cells, place cells and head direction cells. During simulated waking behavior, the movement of the simulated rat drives activity of a population of head direction cells that updates the activity of a population of entorhinal grid cells. The population of grid cells drives the activity of place cells coding individual locations. Associations between location and movement direction are encoded by modification of excitatory synaptic connections from place cells to speed modulated head direction cells. During simulated REM sleep, the population of place cells coding an experienced location activates the head direction cells coding the associated movement direction. Spiking of head direction cells then causes frequency shifts within the population of entorhinal grid cells to update a phase representation of location. Spiking grid cells then activate new place cells that drive new head direction activity. In contrast to models that perform temporally compressed sequence retrieval similar to sharp wave activity, this model can simulate data on temporally structured replay of hippocampal place cell activity during REM sleep at time scales similar to those observed during waking. These mechanisms could be important for episodic memory of trajectories. PMID:18973557

Older fathers' children have lower evolutionary fitness across four centuries and in four populations

PubMed Central

Willführ, Kai P.; Frans, Emma M.; Verweij, Karin J. H.; Bürkner, Paul-Christian; Myrskylä, Mikko; Voland, Eckart; Zietsch, Brendan P.; Penke, Lars

2017-01-01

Higher paternal age at offspring conception increases de novo genetic mutations. Based on evolutionary genetic theory we predicted older fathers' children, all else equal, would be less likely to survive and reproduce, i.e. have lower fitness. In sibling control studies, we find support for negative paternal age effects on offspring survival and reproductive success across four large populations with an aggregate N > 1.4 million. Three populations were pre-industrial (1670–1850) Western populations and showed negative paternal age effects on infant survival and offspring reproductive success. In twentieth-century Sweden, we found minuscule paternal age effects on survival, but found negative effects on reproductive success. Effects survived tests for key competing explanations, including maternal age and parental loss, but effects varied widely over different plausible model specifications and some competing explanations such as diminishing paternal investment and epigenetic mutations could not be tested. We can use our findings to aid in predicting the effect increasingly older parents in today's society will have on their children's survival and reproductive success. To the extent that we succeeded in isolating a mutation-driven effect of paternal age, our results can be understood to show that de novo mutations reduce offspring fitness across populations and time periods. PMID:28904145

Biologically Plausible, Human-scale Knowledge Representation

ERIC Educational Resources Information Center

Crawford, Eric; Gingerich, Matthew; Eliasmith, Chris

2016-01-01

Several approaches to implementing symbol-like representations in neurally plausible models have been proposed. These approaches include binding through synchrony (Shastri & Ajjanagadde, 1993), "mesh" binding (van der Velde & de Kamps, 2006), and conjunctive binding (Smolensky, 1990). Recent theoretical work has suggested that…

Differences in reported sepsis incidence according to study design: a literature review.

PubMed

Mariansdatter, Saga Elise; Eiset, Andreas Halgreen; Søgaard, Kirstine Kobberøe; Christiansen, Christian Fynbo

2016-10-12

Sepsis and severe sepsis are common conditions in hospital settings, and are associated with high rates of morbidity and mortality, but reported incidences vary considerably. In this literature review, we describe the variation in reported population-based incidences of sepsis and severe sepsis. We also examine methodological and demographic differences between studies that may explain this variation. We carried out a literature review searching three major databases and reference lists of relevant articles, to identify all original studies reporting the incidence of sepsis or severe sepsis in the general population. Two authors independently assessed all articles, and the final decision to exclude an article was reached by consensus. We extracted data according to predetermined variables, including study country, sepsis definition, and data source. We then calculated descriptive statistics for the reported incidences of sepsis and severe sepsis. The studies were classified according to the method used to identify cases of sepsis or severe sepsis: chart-based (i.e. review of patient charts) or code-based (i.e. predetermined International Classification of Diseases [ICD] codes). Among 482 articles initially screened, we identified 23 primary publications reporting incidence of sepsis and/or severe sepsis in the general population. The reported incidences ranged from 74 to 1180 per 100,000 person-years and 3 to 1074 per 100,000 person-years for sepsis and severe sepsis, respectively. Most chart-based studies used the Bone criteria (or a modification hereof) and Protein C Worldwide Evaluation in Severe Sepsis (PROWESS) study criteria to identify cases of sepsis and severe sepsis. Most code-based studies used ICD-9 codes, but the number of codes used ranged from 1 to more than 1200. We found that the incidence varied according to how sepsis was identified (chart-based vs. code-based), calendar year, data source, and world region. The reported incidences of sepsis and severe sepsis in the general population varied greatly between studies. Such differences may be attributable to differences in the methods used to collect the data, the study period, or the world region where the study was undertaken. This finding highlights the importance of standardised definitions and acquisition of data regarding sepsis and severe sepsis.

Isotherm ranking and selection using thirteen literature datasets involving hydrophobic organic compounds.

PubMed

Matott, L Shawn; Jiang, Zhengzheng; Rabideau, Alan J; Allen-King, Richelle M

2015-01-01

Numerous isotherm expressions have been developed for describing sorption of hydrophobic organic compounds (HOCs), including "dual-mode" approaches that combine nonlinear behavior with a linear partitioning component. Choosing among these alternative expressions for describing a given dataset is an important task that can significantly influence subsequent transport modeling and/or mechanistic interpretation. In this study, a series of numerical experiments were undertaken to identify "best-in-class" isotherms by refitting 10 alternative models to a suite of 13 previously published literature datasets. The corrected Akaike Information Criterion (AICc) was used for ranking these alternative fits and distinguishing between plausible and implausible isotherms for each dataset. The occurrence of multiple plausible isotherms was inversely correlated with dataset "richness", such that datasets with fewer observations and/or a narrow range of aqueous concentrations resulted in a greater number of plausible isotherms. Overall, only the Polanyi-partition dual-mode isotherm was classified as "plausible" across all 13 of the considered datasets, indicating substantial statistical support consistent with current advances in sorption theory. However, these findings are predicated on the use of the AICc measure as an unbiased ranking metric and the adoption of a subjective, but defensible, threshold for separating plausible and implausible isotherms. Copyright © 2015 Elsevier B.V. All rights reserved.

Is knowing believing? The role of event plausibility and background knowledge in planting false beliefs about the personal past.

PubMed

Pezdek, Kathy; Blandon-Gitlin, Iris; Lam, Shirley; Hart, Rhiannon Ellis; Schooler, Jonathan W

2006-12-01

False memories are more likely to be planted for plausible than for implausible events, but does just knowing about an implausible event make individuals more likely to think that the event happened to them? Two experiments assessed the independent contributions o f plausibility a nd background knowledge to planting false beliefs. In Experiment 1, subjects rated 20 childhood events as to the likelihood of each event having happened to them. The list included the implausible target event "received an enema," a critical target event of Pezdek, Finger, and Hodge (1997). Two weeks later, subjects were presented with (1) information regarding the high prevalence rate of enemas; (2) background information on how to administer an enema; (3) neither type of information; or (4) both. Immediately or 2 weeks later, they rated the 20 childhood events again. Only plausibility significantly increased occurrence ratings. In Experiment 2, the target event was changed from "barium enema administered in a hospital" to "home enema for constipation"; significant effects of both plausibility and background knowledge resulted. The results suggest that providing background knowledge can increase beliefs about personal events, but that its impact is limited by the extent of the individual's familiarity with the context of the suggested target event.

Proposed new industry code on unhealthy food marketing to children and young people: will it make a difference?

PubMed

Swinburn, Boyd; Vandevijvere, Stefanie; Woodward, Alistair; Hornblow, Andrew; Richardson, Ann; Burlingame, Barbara; Borman, Barry; Taylor, Barry; Breier, Bernhard; Arroll, Bruce; Drummond, Bernadette; Grant, Cameron; Bullen, Chris; Wall, Clare; Mhurchu, Cliona Ni; Cameron-Smith, David; Menkes, David; Murdoch, David; Mangin, Dee; Lennon, Diana; Sarfati, Diana; Sellman, Doug; Rush, Elaine; Sopoaga, Faafetai; Thomson, George; Devlin, Gerry; Abel, Gillian; White, Harvey; Coad, Jane; Hoek, Janet; Connor, Jennie; Krebs, Jeremy; Douwes, Jeroen; Mann, Jim; McCall, John; Broughton, John; Potter, John D; Toop, Les; McCowan, Lesley; Signal, Louise; Beckert, Lutz; Elwood, Mark; Kruger, Marlena; Farella, Mauro; Baker, Michael; Keall, Michael; Skeaff, Murray; Thomson, Murray; Wilson, Nick; Chandler, Nicholas; Reid, Papaarangi; Priest, Patricia; Brunton, Paul; Crampton, Peter; Davis, Peter; Gendall, Philip; Howden-Chapman, Philippa; Taylor, Rachael; Edwards, Richard; Beaglehole, Robert; Doughty, Robert; Scragg, Robert; Gauld, Robin; McGee, Robert; Jackson, Rod; Hughes, Roger; Mulder, Roger; Bonita, Ruth; Kruger, Rozanne; Casswell, Sally; Derrett, Sarah; Ameratunga, Shanthi; Denny, Simon; Hales, Simon; Pullon, Sue; Wells, Susan; Cundy, Tim; Blakely, Tony

2017-02-17

Reducing the exposure of children and young people to the marketing of unhealthy foods is a core strategy for reducing the high overweight and obesity prevalence in this population. The Advertising Standards Authority (ASA) has recently reviewed its self-regulatory codes and proposed a revised single code on advertising to children. This article evaluates the proposed code against eight criteria for an effective code, which were included in a submission to the ASA review process from over 70 New Zealand health professors. The evaluation found that the proposed code largely represents no change or uncertain change from the existing codes, and cannot be expected to provide substantial protection for children and young people from the marketing of unhealthy foods. Government regulations will be needed to achieve this important outcome.

Optimal control of Atlantic population Canada geese

USGS Publications Warehouse

Hauser, C.E.; Runge, M.C.; Cooch, E.G.; Johnson, F.A.; Harvey, W.F.

2007-01-01

Management of Canada geese (Branta canadensis) can be a balance between providing sustained harvest opportunity while not allowing populations to become overabundant and cause damage. In this paper, we focus on the Atlantic population of Canada geese and use stochastic dynamic programming to determine the optimal harvest strategy over a range of plausible models for population dynamics. There is evidence to suggest that the population exhibits significant age structure, and it is possible to reconstruct age structure from surveys. Consequently the harvest strategy is a function of the age composition, as well as the abundance, of the population. The objective is to maximize harvest while maintaining the number of breeding adults in the population between specified upper and lower limits. In addition, the total harvest capacity is limited and there is uncertainty about the strength of density-dependence. We find that under a density-independent model, harvest is maximized by maintaining the breeding population at the highest acceptable abundance. However if harvest capacity is limited, then the optimal long-term breeding population size is lower than the highest acceptable level, to reduce the risk of the population growing to an unacceptably large size. Under the proposed density-dependent model, harvest is maximized by maintaining the breeding population at an intermediate level between the bounds on acceptable population size; limits to harvest capacity have little effect on the optimal long-term population size. It is clear that the strength of density-dependence and constraints on harvest significantly affect the optimal harvest strategy for this population. Model discrimination might be achieved in the long term, while continuing to meet management goals, by adopting an adaptive management strategy.

Naturalness and Animal Welfare.

PubMed

Yeates, James

2018-04-05

Naturalness is considered important for animals, and is one criterion for assessing how we care for them. However, it is a vague and ambiguous term, which needs definition and assessments suitable for scientific and ethical questions. This paper makes a start on that aim. This paper differentiates the term from other related concepts, such as species-typical behaviour and wellbeing. It identifies contingent ways in which naturalness might be used, as: (i) prompts for further welfare assessment; (ii) a plausible hypothesis for what safeguards wellbeing; (iii) a threshold for what is acceptable; (iv) constraints on what improvements are unacceptable; and (v) demarcating what is not morally wrong, because of a lack of human agency. It then suggests an approach to evaluating animals' behaviour that is quantitative, is based on reality, and which assesses naturalness by degrees. It proposes classing unaffected wild populations as natural by definition. Where animals might have been affected by humans, they should be compared to the closest population(s) of unaffected animals. This approach could allow us both to assess naturalness scientifically, and to make practical decisions about the behaviour of domestic animals.

The Evolution of Globular Cluster Systems In Early-Type Galaxies

NASA Astrophysics Data System (ADS)

Grillmair, Carl

1999-07-01

We will measure structural parameters {core radii and concentrations} of globular clusters in three early-type galaxies using deep, four-point dithered observations. We have chosen globular cluster systems which have young, medium-age and old cluster populations, as indicated by cluster colors and luminosities. Our primary goal is to test the hypothesis that globular cluster luminosity functions evolve towards a ``universal'' form. Previous observations have shown that young cluster systems have exponential luminosity functions rather than the characteristic log-normal luminosity function of old cluster systems. We will test to see whether such young system exhibits a wider range of structural parameters than an old systems, and whether and at what rate plausible disruption mechanisms will cause the luminosity function to evolve towards a log-normal form. A simple observational comparison of structural parameters between different age cluster populations and between diff er ent sub-populations within the same galaxy will also provide clues concerning both the formation and destruction mechanisms of star clusters, the distinction between open and globular clusters, and the advisability of using globular cluster luminosity functions as distance indicators.

Effect of diseases on symbiotic systems.

PubMed

Tiwari, Pankaj Kumar; Sasmal, Sourav Kumar; Sha, Amar; Venturino, Ezio; Chattopadhyay, Joydev

2017-09-01

There are many species living in symbiotic communities. In this study, we analyzed models in which populations are in the mutualism symbiotic relations subject to a disease spreading among one of the species. The main goal is the characterization of symbiotic relations of coexisting species through their mutual influences on their respective carrying capacities, taking into account that this influence can be quite strong. The functional dependence of the carrying capacities reflects the fact that the correlations between populations cannot be realized merely through direct interactions, as in the usual predator-prey Lotka-Volterra model, but also through the influence of each species on the carrying capacities of the other one. Equilibria are analyzed for feasibility and stability, substantiated via numerical simulations, and global sensitivity analysis identifies the important parameters having a significant impact on the model dynamics. The infective growth rate and the disease-related mortality rate may alter the stability behavior of the system. Our results show that introducing a symbiotic species is a plausible way to control the disease in the population. Copyright © 2017 Elsevier B.V. All rights reserved.

Meta-Analysis: An Introduction Using Regression Models

ERIC Educational Resources Information Center

Rhodes, William

2012-01-01

Research synthesis of evaluation findings is a multistep process. An investigator identifies a research question, acquires the relevant literature, codes findings from that literature, and analyzes the coded data to estimate the average treatment effect and its distribution in a population of interest. The process of estimating the average…

Motor neuron disease mortality rates in New Zealand 1992-2013.

PubMed

Cao, Maize C; Chancellor, Andrew; Charleston, Alison; Dragunow, Mike; Scotter, Emma L

2018-05-01

We determined the mortality rates of motor neuron disease (MND) in New Zealand over 22 years from 1992 to 2013. Previous studies have found an unusually high and/or increasing incidence of MND in certain regions of New Zealand; however, no studies have examined MND rates nationwide to corroborate this. Death certificate data coded G12.2 by International Classification of Diseases (ICD)-10 coding, or 335.2 by ICD-9 coding were obtained. These codes specify amyotrophic lateral sclerosis, progressive bulbar palsy, or other motor neuron diseases as the underlying cause of death. Mortality rates for MND deaths in New Zealand were age-standardized to the European Standard Population and compared with rates from international studies that also examined death certificate data and were age-standardized to the same standard population. The age-standardized mortality from MND in New Zealand was 2.3 per 100,000 per year from 1992-2007 and 2.8 per 100,000 per year from 2008-2013. These rates were 3.3 and 4.0 per 100,000 per year, respectively, for the population 20 years and older. The increase in rate between these two time periods was likely due to changes in MND death coding from 2008. Contrary to a previous regional study of MND incidence, nationwide mortality rates did not increase steadily over this time period once aging was accounted for. However, New Zealand MND mortality rate was higher than comparable studies we examined internationally (mean 1.67 per 100,000 per year), suggesting that further analysis of MND burden in New Zealand is warranted.

The opponent channel population code of sound location is an efficient representation of natural binaural sounds.

PubMed

Młynarski, Wiktor

2015-05-01

In mammalian auditory cortex, sound source position is represented by a population of broadly tuned neurons whose firing is modulated by sounds located at all positions surrounding the animal. Peaks of their tuning curves are concentrated at lateral position, while their slopes are steepest at the interaural midline, allowing for the maximum localization accuracy in that area. These experimental observations contradict initial assumptions that the auditory space is represented as a topographic cortical map. It has been suggested that a "panoramic" code has evolved to match specific demands of the sound localization task. This work provides evidence suggesting that properties of spatial auditory neurons identified experimentally follow from a general design principle- learning a sparse, efficient representation of natural stimuli. Natural binaural sounds were recorded and served as input to a hierarchical sparse-coding model. In the first layer, left and right ear sounds were separately encoded by a population of complex-valued basis functions which separated phase and amplitude. Both parameters are known to carry information relevant for spatial hearing. Monaural input converged in the second layer, which learned a joint representation of amplitude and interaural phase difference. Spatial selectivity of each second-layer unit was measured by exposing the model to natural sound sources recorded at different positions. Obtained tuning curves match well tuning characteristics of neurons in the mammalian auditory cortex. This study connects neuronal coding of the auditory space with natural stimulus statistics and generates new experimental predictions. Moreover, results presented here suggest that cortical regions with seemingly different functions may implement the same computational strategy-efficient coding.

Defining pediatric traumatic brain injury using International Classification of Diseases Version 10 Codes: a systematic review.

PubMed

Chan, Vincy; Thurairajah, Pravheen; Colantonio, Angela

2015-02-04

Although healthcare administrative data are commonly used for traumatic brain injury (TBI) research, there is currently no consensus or consistency on the International Classification of Diseases Version 10 (ICD-10) codes used to define TBI among children and youth internationally. This study systematically reviewed the literature to explore the range of ICD-10 codes that are used to define TBI in this population. The identification of the range of ICD-10 codes to define this population in administrative data is crucial, as it has implications for policy, resource allocation, planning of healthcare services, and prevention strategies. The databases MEDLINE, MEDLINE In-Process, Embase, PsychINFO, CINAHL, SPORTDiscus, and Cochrane Database of Systematic Reviews were systematically searched. Grey literature was searched using Grey Matters and Google. Reference lists of included articles were also searched for relevant studies. Two reviewers independently screened all titles and abstracts using pre-defined inclusion and exclusion criteria. A full text screen was conducted on articles that met the first screen inclusion criteria. All full text articles that met the pre-defined inclusion criteria were included for analysis in this systematic review. A total of 1,326 publications were identified through the predetermined search strategy and 32 articles/reports met all eligibility criteria for inclusion in this review. Five articles specifically examined children and youth aged 19 years or under with TBI. ICD-10 case definitions ranged from the broad injuries to the head codes (ICD-10 S00 to S09) to concussion only (S06.0). There was overwhelming consensus on the inclusion of ICD-10 code S06, intracranial injury, while codes S00 (superficial injury of the head), S03 (dislocation, sprain, and strain of joints and ligaments of head), and S05 (injury of eye and orbit) were only used by articles that examined head injury, none of which specifically examined children and youth. This review provides evidence for discussion on how best to use ICD codes for different goals. This is an important first step in reaching an appropriate definition and can inform future work on reaching consensus on the ICD-10 codes to define TBI for this vulnerable population.

HLA-E regulatory and coding region variability and haplotypes in a Brazilian population sample.

PubMed

Ramalho, Jaqueline; Veiga-Castelli, Luciana C; Donadi, Eduardo A; Mendes-Junior, Celso T; Castelli, Erick C

2017-11-01

The HLA-E gene is characterized by low but wide expression on different tissues. HLA-E is considered a conserved gene, being one of the least polymorphic class I HLA genes. The HLA-E molecule interacts with Natural Killer cell receptors and T lymphocytes receptors, and might activate or inhibit immune responses depending on the peptide associated with HLA-E and with which receptors HLA-E interacts to. Variable sites within the HLA-E regulatory and coding segments may influence the gene function by modifying its expression pattern or encoded molecule, thus, influencing its interaction with receptors and the peptide. Here we propose an approach to evaluate the gene structure, haplotype pattern and the complete HLA-E variability, including regulatory (promoter and 3'UTR) and coding segments (with introns), by using massively parallel sequencing. We investigated the variability of 420 samples from a very admixed population such as Brazilians by using this approach. Considering a segment of about 7kb, 63 variable sites were detected, arranged into 75 extended haplotypes. We detected 37 different promoter sequences (but few frequent ones), 27 different coding sequences (15 representing new HLA-E alleles) and 12 haplotypes at the 3'UTR segment, two of them presenting a summed frequency of 90%. Despite the number of coding alleles, they encode mainly two different full-length molecules, known as E*01:01 and E*01:03, which corresponds to about 90% of all. In addition, differently from what has been previously observed for other non classical HLA genes, the relationship among the HLA-E promoter, coding and 3'UTR haplotypes is not straightforward because the same promoter and 3'UTR haplotypes were many times associated with different HLA-E coding haplotypes. This data reinforces the presence of only two main full-length HLA-E molecules encoded by the many HLA-E alleles detected in our population sample. In addition, this data does indicate that the distal HLA-E promoter is by far the most variable segment. Further analyses involving the binding of transcription factors and non-coding RNAs, as well as the HLA-E expression in different tissues, are necessary to evaluate whether these variable sites at regulatory segments (or even at the coding sequence) may influence the gene expression profile. Copyright © 2017 Elsevier Ltd. All rights reserved.

A phase code for memory could arise from circuit mechanisms in entorhinal cortex

PubMed Central

Hasselmo, Michael E.; Brandon, Mark P.; Yoshida, Motoharu; Giocomo, Lisa M.; Heys, James G.; Fransen, Erik; Newman, Ehren L.; Zilli, Eric A.

2009-01-01

Neurophysiological data reveals intrinsic cellular properties that suggest how entorhinal cortical neurons could code memory by the phase of their firing. Potential cellular mechanisms for this phase coding in models of entorhinal function are reviewed. This mechanism for phase coding provides a substrate for modeling the responses of entorhinal grid cells, as well as the replay of neural spiking activity during waking and sleep. Efforts to implement these abstract models in more detailed biophysical compartmental simulations raise specific issues that could be addressed in larger scale population models incorporating mechanisms of inhibition. PMID:19656654

Promoting Scientific Thinking and Conceptual Change about Alternative Explanations of Climate Change and Other Controversial Socio-scientific Topics

NASA Astrophysics Data System (ADS)

Lombardi, D.; Sinatra, G. M.

2013-12-01

Critical evaluation and plausibility reappraisal of scientific explanations have been underemphasized in many science classrooms (NRC, 2012). Deep science learning demands that students increase their ability to critically evaluate the quality of scientific knowledge, weigh alternative explanations, and explicitly reappraise their plausibility judgments. Therefore, this lack of instruction about critical evaluation and plausibility reappraisal has, in part, contributed to diminished understanding about complex and controversial topics, such as global climate change. The Model-Evidence Link (MEL) diagram (originally developed by researchers at Rutgers University under an NSF-supported project; Chinn & Buckland, 2012) is an instructional scaffold that promotes students to critically evaluate alternative explanations. We recently developed a climate change MEL and found that the students who used the MEL experienced a significant shift in their plausibility judgments toward the scientifically accepted model of human-induced climate change. Using the MEL for instruction also resulted in conceptual change about the causes of global warming that reflected greater understanding of fundamental scientific principles. Furthermore, students sustained this conceptual change six months after MEL instruction (Lombardi, Sinatra, & Nussbaum, 2013). This presentation will discuss recent educational research that supports use of the MEL to promote critical evaluation, plausibility reappraisal, and conceptual change, and also, how the MEL may be particularly effective for learning about global climate change and other socio-scientific topics. Such instruction to develop these fundamental thinking skills (e.g., critical evaluation and plausibility reappraisal) is demanded by both the Next Generation Science Standards (Achieve, 2013) and the Common Core State Standards for English Language Arts and Mathematics (CCSS Initiative-ELA, 2010; CCSS Initiative-Math, 2010), as well as a society that is equipped to deal with challenges in a way that is beneficial to our national and global community.

Waterfowl populations of conservation concern: learning from diverse challenges, models, and conservation strategies

USGS Publications Warehouse

Austin, Jane E.; Slattery, Stuart; Clark, Robert G.

2014-01-01

There are 30 threatened or endangered species of waterfowl worldwide, and several sub-populations are also threatened. Some of these species occur in North America, and others there are also of conservation concern due to declining population trends and their importance to hunters. Here we review conservation initiatives being undertaken for several of these latter species, along with conservation measures in place in Europe, to seek common themes and approaches that could be useful in developing broad conservation guidelines. While focal species may vary in their life histories, population threats and geopolitical context, most conservation efforts have used a systematic approach to understand factors limiting populations and o identify possible management or policy actions. This approach generally includes a priori identification of plausible hypotheses about population declines or status, incorporation of hypotheses into conceptual or quantitative planning models, and the use of some form of structured decision making and adaptive management to develop and implement conservation actions in the face of many uncertainties. A climate of collaboration among jurisdictions sharing these birds is important to the success of a conservation or management programme. The structured conservation approach exemplified herein provides an opportunity to involve stakeholders at all planning stages, allows for all views to be examined and incorporated into model structures, and yields a format for improved communication, cooperation and learning, which may ultimately be one of the greatest benefits of this strategy.

Ion absorption of the high harmonic fast wave in the National Spherical Torus Experiment

NASA Astrophysics Data System (ADS)

Rosenberg, Adam Lewis

Ion absorption of the high harmonic fast wave in a spherical torus is of critical importance to assessing the viability of the wave as a means of heating and driving current. Analysis of recent NSTX shots has revealed that under some conditions when neutral beam and RF power are injected into the plasma simultaneously, a fast ion population with energy above the beam injection energy is sustained by the wave. In agreement with modeling, these experiments find the RF-induced fast ion tail strength and neutron rate at lower B-fields to be less enhanced, likely due to a larger β profile, which promotes greater off-axis absorption where the fast ion population is small. Ion loss codes find the increased loss fraction with decreased B insufficient to account for the changes in tail strength, providing further evidence that this is an RF interaction effect. Though greater ion absorption is predicted with lower k∥, surprisingly little variation in the tail was observed, along with a neutron rate enhancement with higher k∥. Data from the neutral particle analyzer, neutron detectors, x-ray crystal spectrometer, and Thomson scattering is presented, along with results from the TRANSP transport analysis code, ray-tracing codes HPRT and CURRAY, full-wave code and AORSA, quasilinear code CQL3D, and ion loss codes EIGOL and CONBEAM.

A distributed code for color in natural scenes derived from center-surround filtered cone signals

PubMed Central

Kellner, Christian J.; Wachtler, Thomas

2013-01-01

In the retina of trichromatic primates, chromatic information is encoded in an opponent fashion and transmitted to the lateral geniculate nucleus (LGN) and visual cortex via parallel pathways. Chromatic selectivities of neurons in the LGN form two separate clusters, corresponding to two classes of cone opponency. In the visual cortex, however, the chromatic selectivities are more distributed, which is in accordance with a population code for color. Previous studies of cone signals in natural scenes typically found opponent codes with chromatic selectivities corresponding to two directions in color space. Here we investigated how the non-linear spatio-chromatic filtering in the retina influences the encoding of color signals. Cone signals were derived from hyper-spectral images of natural scenes and preprocessed by center-surround filtering and rectification, resulting in parallel ON and OFF channels. Independent Component Analysis (ICA) on these signals yielded a highly sparse code with basis functions that showed spatio-chromatic selectivities. In contrast to previous analyses of linear transformations of cone signals, chromatic selectivities were not restricted to two main chromatic axes, but were more continuously distributed in color space, similar to the population code of color in the early visual cortex. Our results indicate that spatio-chromatic processing in the retina leads to a more distributed and more efficient code for natural scenes. PMID:24098289

HERC1 polymorphisms: population-specific variations in haplotype composition.

PubMed

Yuasa, Isao; Umetsu, Kazuo; Nishimukai, Hiroaki; Fukumori, Yasuo; Harihara, Shinji; Saitou, Naruya; Jin, Feng; Chattopadhyay, Prasanta K; Henke, Lotte; Henke, Jürgen

2009-08-01

Human HERC1 is one of six HERC proteins and may play an important role in intracellular membrane trafficking. The human HERC1 gene is suggested to have been affected by local positive selection. To assess the global frequency distributions of coding and non-coding single nucleotide polymorphisms (SNPs) in the HERC1 gene, we developed a new simultaneous genotyping method for four SNPs, and applied this method to investigate 1213 individuals from 12 global populations. The results confirmed remarked differences in the allele and haplotype frequencies between East Asian and non-East Asian populations. One of the three common haplotypes observed was found to be characteristic of East Asians, who showed a relatively uniform distribution of haplotypes. Information on haplotypes would be useful for testing the function of polymorphisms in the HERC1 gene. This is the first study to investigate the distribution of HERC1 polymorphisms in various populations. (c) 2009 John Wiley & Sons, Ltd.

PRESTO-II: a low-level waste environmental transport and risk assessment code

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

Fields, D.E.; Emerson, C.J.; Chester, R.O.

PRESTO-II (Prediction of Radiation Effects from Shallow Trench Operations) is a computer code designed for the evaluation of possible health effects from shallow-land and, waste-disposal trenches. The model is intended to serve as a non-site-specific screening model for assessing radionuclide transport, ensuing exposure, and health impacts to a static local population for a 1000-year period following the end of disposal operations. Human exposure scenarios considered include normal releases (including leaching and operational spillage), human intrusion, and limited site farming or reclamation. Pathways and processes of transit from the trench to an individual or population include ground-water transport, overland flow, erosion,more » surface water dilution, suspension, atmospheric transport, deposition, inhalation, external exposure, and ingestion of contaminated beef, milk, crops, and water. Both population doses and individual doses, as well as doses to the intruder and farmer, may be calculated. Cumulative health effects in terms of cancer deaths are calculated for the population over the 1000-year period using a life-table approach. Data are included for three example sites: Barnwell, South Carolina; Beatty, Nevada; and West Valley, New York. A code listing and example input for each of the three sites are included in the appendices to this report.« less

Flood hydrology for Dry Creek, Lake County, Northwestern Montana

USGS Publications Warehouse

Parrett, C.; Jarrett, R.D.

2004-01-01

Dry Creek drains about 22.6 square kilometers of rugged mountainous terrain upstream from Tabor Dam in the Mission Range near St. Ignatius, Montana. Because of uncertainty about plausible peak discharges and concerns regarding the ability of the Tabor Dam spillway to safely convey these discharges, the flood hydrology for Dry Creek was evaluated on the basis of three hydrologic and geologic methods. The first method involved determining an envelope line relating flood discharge to drainage area on the basis of regional historical data and calculating a 500-year flood for Dry Creek using a regression equation. The second method involved paleoflood methods to estimate the maximum plausible discharge for 35 sites in the study area. The third method involved rainfall-runoff modeling for the Dry Creek basin in conjunction with regional precipitation information to determine plausible peak discharges. All of these methods resulted in estimates of plausible peak discharges that are substantially less than those predicted by the more generally applied probable maximum flood technique. Copyright ASCE 2004.

A linear programming model for preserving privacy when disclosing patient spatial information for secondary purposes.

PubMed

Jung, Ho-Won; El Emam, Khaled

2014-05-29

A linear programming (LP) model was proposed to create de-identified data sets that maximally include spatial detail (e.g., geocodes such as ZIP or postal codes, census blocks, and locations on maps) while complying with the HIPAA Privacy Rule's Expert Determination method, i.e., ensuring that the risk of re-identification is very small. The LP model determines the transition probability from an original location of a patient to a new randomized location. However, it has a limitation for the cases of areas with a small population (e.g., median of 10 people in a ZIP code). We extend the previous LP model to accommodate the cases of a smaller population in some locations, while creating de-identified patient spatial data sets which ensure the risk of re-identification is very small. Our LP model was applied to a data set of 11,740 postal codes in the City of Ottawa, Canada. On this data set we demonstrated the limitations of the previous LP model, in that it produces improbable results, and showed how our extensions to deal with small areas allows the de-identification of the whole data set. The LP model described in this study can be used to de-identify geospatial information for areas with small populations with minimal distortion to postal codes. Our LP model can be extended to include other information, such as age and gender.

On the use of log-transformation vs. nonlinear regression for analyzing biological power laws.

PubMed

Xiao, Xiao; White, Ethan P; Hooten, Mevin B; Durham, Susan L

2011-10-01

Power-law relationships are among the most well-studied functional relationships in biology. Recently the common practice of fitting power laws using linear regression (LR) on log-transformed data has been criticized, calling into question the conclusions of hundreds of studies. It has been suggested that nonlinear regression (NLR) is preferable, but no rigorous comparison of these two methods has been conducted. Using Monte Carlo simulations, we demonstrate that the error distribution determines which method performs better, with NLR better characterizing data with additive, homoscedastic, normal error and LR better characterizing data with multiplicative, heteroscedastic, lognormal error. Analysis of 471 biological power laws shows that both forms of error occur in nature. While previous analyses based on log-transformation appear to be generally valid, future analyses should choose methods based on a combination of biological plausibility and analysis of the error distribution. We provide detailed guidelines and associated computer code for doing so, including a model averaging approach for cases where the error structure is uncertain.

Origin of microbial life: Nano- and molecular events, thermodynamics/entropy, quantum mechanisms and genetic instructions.

PubMed

Trevors, J T

2011-03-01

Currently, there are no agreed upon mechanisms and supporting evidence for the origin of the first microbial cells on the Earth. However, some hypotheses have been proposed with minimal supporting evidence and experimentation/observations. The approach taken in this article is that life originated at the nano- and molecular levels of biological organization, using quantum mechanic principles that became manifested as classical microbial cell(s), allowing the origin of microbial life on the Earth with a core or minimal, organic, genetic code containing the correct instructions for cell(s) for growth and division, in a micron dimension environment, with a local entropy range conducive to life (present about 4 billion years ago), and obeying the laws of thermodynamics. An integrated approach that explores all encompassing factors necessary for the origin of life, may bring forth plausible hypotheses (and mechanisms) with much needed supporting experimentation and observations for an origin of life theory. Copyright © 2010 Elsevier B.V. All rights reserved.

Reasons for withdrawing belief in vivid autobiographical memories.

PubMed

Scoboria, Alan; Boucher, Chantal; Mazzoni, Giuliana

2015-01-01

Previous studies have shown that many people hold personal memories for events that they no longer believe occurred. This study examines the reasons that people provide for choosing to reduce autobiographical belief in vividly recollected autobiographical memories. A body of non-believed memories provided by 374 individuals was reviewed to develop a qualitatively derived categorisation system. The final scheme consisted of 8 major categories (in descending order of mention): social feedback, event plausibility, alternative attributions, general memory beliefs, internal event features, consistency with external evidence, views of self/others, personal motivation and numerous sub-categories. Independent raters coded the reports and judged the primary reason that each person provided for withdrawing belief. The nature of each category, frequency of category endorsement, category overlap and phenomenological ratings are presented, following which links to related literature and implications are discussed. This study documents that a wide variety of recollective and non-recollective sources of information influence decision-making about the occurrence of autobiographical events.

Genetic background of extreme violent behavior

PubMed Central

Tiihonen, J; Rautiainen, M-R; Ollila, HM; Repo-Tiihonen, E; Virkkunen, M; Palotie, A; Pietiläinen, O; Kristiansson, K; Joukamaa, M; Lauerma, H; Saarela, J; Tyni, S; Vartiainen, H; Paananen, J; Goldman, D; Paunio, T

2015-01-01

In developed countries, the majority of all violent crime is committed by a small group of antisocial recidivistic offenders, but no genes have been shown to contribute to recidivistic violent offending or severe violent behavior, such as homicide. Our results, from two independent cohorts of Finnish prisoners, revealed that a monoamine oxidase A (MAOA) low-activity genotype (contributing to low dopamine turnover rate) as well as the CDH13 gene (coding for neuronal membrane adhesion protein) are associated with extremely violent behavior (at least 10 committed homicides, attempted homicides or batteries). No substantial signal was observed for either MAOA or CDH13 among non-violent offenders, indicating that findings were specific for violent offending, and not largely attributable to substance abuse or antisocial personality disorder. These results indicate both low monoamine metabolism and neuronal membrane dysfunction as plausible factors in the etiology of extreme criminal violent behavior, and imply that at least about 5–10% of all severe violent crime in Finland is attributable to the aforementioned MAOA and CDH13 genotypes. PMID:25349169

Using Grid Cells for Navigation.

PubMed

Bush, Daniel; Barry, Caswell; Manson, Daniel; Burgess, Neil

2015-08-05

Mammals are able to navigate to hidden goal locations by direct routes that may traverse previously unvisited terrain. Empirical evidence suggests that this "vector navigation" relies on an internal representation of space provided by the hippocampal formation. The periodic spatial firing patterns of grid cells in the hippocampal formation offer a compact combinatorial code for location within large-scale space. Here, we consider the computational problem of how to determine the vector between start and goal locations encoded by the firing of grid cells when this vector may be much longer than the largest grid scale. First, we present an algorithmic solution to the problem, inspired by the Fourier shift theorem. Second, we describe several potential neural network implementations of this solution that combine efficiency of search and biological plausibility. Finally, we discuss the empirical predictions of these implementations and their relationship to the anatomy and electrophysiology of the hippocampal formation. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Neural network system for purposeful behavior based on foveal visual preprocessor

NASA Astrophysics Data System (ADS)

Golovan, Alexander V.; Shevtsova, Natalia A.; Klepatch, Arkadi A.

1996-10-01

Biologically plausible model of the system with an adaptive behavior in a priori environment and resistant to impairment has been developed. The system consists of input, learning, and output subsystems. The first subsystems classifies input patterns presented as n-dimensional vectors in accordance with some associative rule. The second one being a neural network determines adaptive responses of the system to input patterns. Arranged neural groups coding possible input patterns and appropriate output responses are formed during learning by means of negative reinforcement. Output subsystem maps a neural network activity into the system behavior in the environment. The system developed has been studied by computer simulation imitating a collision-free motion of a mobile robot. After some learning period the system 'moves' along a road without collisions. It is shown that in spite of impairment of some neural network elements the system functions reliably after relearning. Foveal visual preprocessor model developed earlier has been tested to form a kind of visual input to the system.

A Simple Principled Approach for Modeling and Understanding Uniform Color Metrics

PubMed Central

Smet, Kevin A.G.; Webster, Michael A.; Whitehead, Lorne A.

2016-01-01

An important goal in characterizing human color vision is to order color percepts in a way that captures their similarities and differences. This has resulted in the continuing evolution of “uniform color spaces,” in which the distances within the space represent the perceptual differences between the stimuli. While these metrics are now very successful in predicting how color percepts are scaled, they do so in largely empirical, ad hoc ways, with limited reference to actual mechanisms of color vision. In this article our aim is to instead begin with general and plausible assumptions about color coding, and then develop a model of color appearance that explicitly incorporates them. We show that many of the features of empirically-defined color order systems (such as those of Munsell, Pantone, NCS, and others) as well as many of the basic phenomena of color perception, emerge naturally from fairly simple principles of color information encoding in the visual system and how it can be optimized for the spectral characteristics of the environment. PMID:26974939

Bayesian analysis of caustic-crossing microlensing events

NASA Astrophysics Data System (ADS)

Cassan, A.; Horne, K.; Kains, N.; Tsapras, Y.; Browne, P.

2010-06-01

Aims: Caustic-crossing binary-lens microlensing events are important anomalous events because they are capable of detecting an extrasolar planet companion orbiting the lens star. Fast and robust modelling methods are thus of prime interest in helping to decide whether a planet is detected by an event. Cassan introduced a new set of parameters to model binary-lens events, which are closely related to properties of the light curve. In this work, we explain how Bayesian priors can be added to this framework, and investigate on interesting options. Methods: We develop a mathematical formulation that allows us to compute analytically the priors on the new parameters, given some previous knowledge about other physical quantities. We explicitly compute the priors for a number of interesting cases, and show how this can be implemented in a fully Bayesian, Markov chain Monte Carlo algorithm. Results: Using Bayesian priors can accelerate microlens fitting codes by reducing the time spent considering physically implausible models, and helps us to discriminate between alternative models based on the physical plausibility of their parameters.

Cannabis in sport: anti-doping perspective.

PubMed

Huestis, Marilyn A; Mazzoni, Irene; Rabin, Olivier

2011-11-01

Since 2004, when the World Anti-Doping Agency assumed the responsibility for establishing and maintaining the list of prohibited substances and methods in sport (i.e. the Prohibited List), cannabinoids have been prohibited in all sports during competition. The basis for this prohibition can be found in the World Anti-Doping Code, which defines the three criteria used to consider banning a substance. In this context, we discuss the potential of cannabis to enhance sports performance, the risk it poses to the athlete's health and its violation of the spirit of sport. Although these compounds are prohibited in-competition only, we explain why the pharmacokinetics of their main psychoactive compound, Δ(9)-tetrahydrocannabinol, may complicate the results management of adverse analytical findings. Passive inhalation does not appear to be a plausible explanation for a positive test. Although the prohibition of cannabinoids in sports is one of the most controversial issues in anti-doping, in this review we stress the reasons behind this prohibition, with strong emphasis on the evolving knowledge of cannabinoid pharmacology.

Genetic background of extreme violent behavior.

PubMed

Tiihonen, J; Rautiainen, M-R; Ollila, H M; Repo-Tiihonen, E; Virkkunen, M; Palotie, A; Pietiläinen, O; Kristiansson, K; Joukamaa, M; Lauerma, H; Saarela, J; Tyni, S; Vartiainen, H; Paananen, J; Goldman, D; Paunio, T

2015-06-01

In developed countries, the majority of all violent crime is committed by a small group of antisocial recidivistic offenders, but no genes have been shown to contribute to recidivistic violent offending or severe violent behavior, such as homicide. Our results, from two independent cohorts of Finnish prisoners, revealed that a monoamine oxidase A (MAOA) low-activity genotype (contributing to low dopamine turnover rate) as well as the CDH13 gene (coding for neuronal membrane adhesion protein) are associated with extremely violent behavior (at least 10 committed homicides, attempted homicides or batteries). No substantial signal was observed for either MAOA or CDH13 among non-violent offenders, indicating that findings were specific for violent offending, and not largely attributable to substance abuse or antisocial personality disorder. These results indicate both low monoamine metabolism and neuronal membrane dysfunction as plausible factors in the etiology of extreme criminal violent behavior, and imply that at least about 5-10% of all severe violent crime in Finland is attributable to the aforementioned MAOA and CDH13 genotypes.

DL-ReSuMe: A Delay Learning-Based Remote Supervised Method for Spiking Neurons.

PubMed

Taherkhani, Aboozar; Belatreche, Ammar; Li, Yuhua; Maguire, Liam P

2015-12-01

Recent research has shown the potential capability of spiking neural networks (SNNs) to model complex information processing in the brain. There is biological evidence to prove the use of the precise timing of spikes for information coding. However, the exact learning mechanism in which the neuron is trained to fire at precise times remains an open problem. The majority of the existing learning methods for SNNs are based on weight adjustment. However, there is also biological evidence that the synaptic delay is not constant. In this paper, a learning method for spiking neurons, called delay learning remote supervised method (DL-ReSuMe), is proposed to merge the delay shift approach and ReSuMe-based weight adjustment to enhance the learning performance. DL-ReSuMe uses more biologically plausible properties, such as delay learning, and needs less weight adjustment than ReSuMe. Simulation results have shown that the proposed DL-ReSuMe approach achieves learning accuracy and learning speed improvements compared with ReSuMe.

Cannabis in Sport

PubMed Central

Huestis, Marilyn A.; Mazzoni, Irene; Rabin, Olivier

2013-01-01

Since 2004, when the World Anti-Doping Agency assumed the responsi-bility for establishing and maintaining the list of prohibited substances and methods in sport (i.e. the Prohibited List), cannabinoids have been prohibited in all sports during competition. The basis for this prohibition can be found in the World Anti-Doping Code, which defines the three criteria used to consider banning a substance. In this context, we discuss the potential of can-nabis to enhance sports performance, the risk it poses to the athlete’s health and its violation of the spirit of sport. Although these compounds are prohibited in-competition only, we explain why the pharmacokinetics of their main psychoactive compound, Δ9-tetrahydrocannabinol, may complicate the results management of adverse analytical findings. Passive inhalation does not appear to be a plausible explanation for a positive test. Although the prohibition of cannabinoids in sports is one of the most controversial issues in anti-doping, in this review we stress the reasons behind this prohibition, with strong emphasis on the evolving knowledge of cannabinoid pharmacology. PMID:21985215

Peak Dose Assessment for Proposed DOE-PPPO Authorized Limits

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

Maldonado, Delis

2012-06-01

The Oak Ridge Institute for Science and Education (ORISE), a U.S. Department of Energy (DOE) prime contractor, was contracted by the DOE Portsmouth/Paducah Project Office (DOE-PPPO) to conduct a peak dose assessment in support of the Authorized Limits Request for Solid Waste Disposal at Landfill C-746-U at the Paducah Gaseous Diffusion Plant (DOE-PPPO 2011a). The peak doses were calculated based on the DOE-PPPO Proposed Single Radionuclides Soil Guidelines and the DOE-PPPO Proposed Authorized Limits (AL) Volumetric Concentrations available in DOE-PPPO 2011a. This work is provided as an appendix to the Dose Modeling Evaluations and Technical Support Document for the Authorizedmore » Limits Request for the C-746-U Landfill at the Paducah Gaseous Diffusion Plant, Paducah, Kentucky (ORISE 2012). The receptors evaluated in ORISE 2012 were selected by the DOE-PPPO for the additional peak dose evaluations. These receptors included a Landfill Worker, Trespasser, Resident Farmer (onsite), Resident Gardener, Recreational User, Outdoor Worker and an Offsite Resident Farmer. The RESRAD (Version 6.5) and RESRAD-OFFSITE (Version 2.5) computer codes were used for the peak dose assessments. Deterministic peak dose assessments were performed for all the receptors and a probabilistic dose assessment was performed only for the Offsite Resident Farmer at the request of the DOE-PPPO. In a deterministic analysis, a single input value results in a single output value. In other words, a deterministic analysis uses single parameter values for every variable in the code. By contrast, a probabilistic approach assigns parameter ranges to certain variables, and the code randomly selects the values for each variable from the parameter range each time it calculates the dose (NRC 2006). The receptor scenarios, computer codes and parameter input files were previously used in ORISE 2012. A few modifications were made to the parameter input files as appropriate for this effort. Some of these changes included increasing the time horizon beyond 1,050 years (yr), and using the radionuclide concentrations provided by the DOE-PPPO as inputs into the codes. The deterministic peak doses were evaluated within time horizons of 70 yr (for the Landfill Worker and Trespasser), 1,050 yr, 10,000 yr and 100,000 yr (for the Resident Farmer [onsite], Resident Gardener, Recreational User, Outdoor Worker and Offsite Resident Farmer) at the request of the DOE-PPPO. The time horizons of 10,000 yr and 100,000 yr were used at the request of the DOE-PPPO for informational purposes only. The probabilistic peak of the mean dose assessment was performed for the Offsite Resident Farmer using Technetium-99 (Tc-99) and a time horizon of 1,050 yr. The results of the deterministic analyses indicate that among all receptors and time horizons evaluated, the highest projected dose, 2,700 mrem/yr, occurred for the Resident Farmer (onsite) at 12,773 yr. The exposure pathways contributing to the peak dose are ingestion of plants, external gamma, and ingestion of milk, meat and soil. However, this receptor is considered an implausible receptor. The only receptors considered plausible are the Landfill Worker, Recreational User, Outdoor Worker and the Offsite Resident Farmer. The maximum projected dose among the plausible receptors is 220 mrem/yr for the Outdoor Worker and it occurs at 19,045 yr. The exposure pathways contributing to the dose for this receptor are external gamma and soil ingestion. The results of the probabilistic peak of the mean dose analysis for the Offsite Resident Farmer indicate that the average (arithmetic mean) of the peak of the mean doses for this receptor is 0.98 mrem/yr and it occurs at 1,050 yr. This dose corresponds to Tc-99 within the time horizon of 1,050 yr.« less

Temporal trends in prevalence, incidence, and mortality for rheumatoid arthritis in Quebec, Canada: a population-based study.

PubMed

Jean, Sonia; Hudson, Marie; Gamache, Philippe; Bessette, Louis; Fortin, Paul R; Boire, Gilles; Bernatsky, Sasha

2017-12-01

Health administrative data are a potentially efficient resource to conduct population-based research and surveillance, including trends in incidence and mortality over time. Our objective was to explore time trends in incidence and mortality for rheumatoid arthritis (RA), as well as estimating period prevalence. Our RA case definition was based on one or more hospitalizations with a RA diagnosis code, or three or more RA physician-billing codes, over 2 years, with at least one RA billing code by a rheumatologist, orthopedic surgeon, or internist. To identify incident cases, a "run-in" period of 5 years (1996-2000) was used to exclude prevalent cases. Crude age and sex-specific incidence rates were calculated (using data from 2001 to 2015), and sex-specific incidence rates were also standardized to the 2001 age structure of the Quebec population. We linked the RA cohort (both prevalent and incident patients) to the vital statistics registry, and standardized mortality rate ratios were generated. Negative binomial regression was used to test for linear change in standardized incidence rates and mortality ratios. The linear trends in standardized incidence rates did not show significant change over the study period. Mortality in RA was significantly higher than the general population and this remained true throughout the study period. Our prevalence estimate suggested 0.8% of the Quebec population may be affected by RA. RA incidence appeared relatively stable, and mortality was substantially higher in RA versus the general population and remained so over the study period. This suggests the need to optimize long-term RA outcomes.

Population-based evaluation of a suggested anatomic and clinical classification of congenital heart defects based on the International Paediatric and Congenital Cardiac Code.

PubMed

Houyel, Lucile; Khoshnood, Babak; Anderson, Robert H; Lelong, Nathalie; Thieulin, Anne-Claire; Goffinet, François; Bonnet, Damien

2011-10-03

Classification of the overall spectrum of congenital heart defects (CHD) has always been challenging, in part because of the diversity of the cardiac phenotypes, but also because of the oft-complex associations. The purpose of our study was to establish a comprehensive and easy-to-use classification of CHD for clinical and epidemiological studies based on the long list of the International Paediatric and Congenital Cardiac Code (IPCCC). We coded each individual malformation using six-digit codes from the long list of IPCCC. We then regrouped all lesions into 10 categories and 23 subcategories according to a multi-dimensional approach encompassing anatomic, diagnostic and therapeutic criteria. This anatomic and clinical classification of congenital heart disease (ACC-CHD) was then applied to data acquired from a population-based cohort of patients with CHD in France, made up of 2867 cases (82% live births, 1.8% stillbirths and 16.2% pregnancy terminations). The majority of cases (79.5%) could be identified with a single IPCCC code. The category "Heterotaxy, including isomerism and mirror-imagery" was the only one that typically required more than one code for identification of cases. The two largest categories were "ventricular septal defects" (52%) and "anomalies of the outflow tracts and arterial valves" (20% of cases). Our proposed classification is not new, but rather a regrouping of the known spectrum of CHD into a manageable number of categories based on anatomic and clinical criteria. The classification is designed to use the code numbers of the long list of IPCCC but can accommodate ICD-10 codes. Its exhaustiveness, simplicity, and anatomic basis make it useful for clinical and epidemiologic studies, including those aimed at assessment of risk factors and outcomes.

Heuristic Elements of Plausible Reasoning.

ERIC Educational Resources Information Center

Dudczak, Craig A.

At least some of the reasoning processes involved in argumentation rely on inferences which do not fit within the traditional categories of inductive or deductive reasoning. The reasoning processes involved in plausibility judgments have neither the formal certainty of deduction nor the imputed statistical probability of induction. When utilizing…

Impaired associative learning in schizophrenia: behavioral and computational studies

PubMed Central

Diwadkar, Vaibhav A.; Flaugher, Brad; Jones, Trevor; Zalányi, László; Ujfalussy, Balázs; Keshavan, Matcheri S.

2008-01-01

Associative learning is a central building block of human cognition and in large part depends on mechanisms of synaptic plasticity, memory capacity and fronto–hippocampal interactions. A disorder like schizophrenia is thought to be characterized by altered plasticity, and impaired frontal and hippocampal function. Understanding the expression of this dysfunction through appropriate experimental studies, and understanding the processes that may give rise to impaired behavior through biologically plausible computational models will help clarify the nature of these deficits. We present a preliminary computational model designed to capture learning dynamics in healthy control and schizophrenia subjects. Experimental data was collected on a spatial-object paired-associate learning task. The task evinces classic patterns of negatively accelerated learning in both healthy control subjects and patients, with patients demonstrating lower rates of learning than controls. Our rudimentary computational model of the task was based on biologically plausible assumptions, including the separation of dorsal/spatial and ventral/object visual streams, implementation of rules of learning, the explicit parameterization of learning rates (a plausible surrogate for synaptic plasticity), and learning capacity (a plausible surrogate for memory capacity). Reductions in learning dynamics in schizophrenia were well-modeled by reductions in learning rate and learning capacity. The synergy between experimental research and a detailed computational model of performance provides a framework within which to infer plausible biological bases of impaired learning dynamics in schizophrenia. PMID:19003486

Signatures of criticality arise from random subsampling in simple population models.

PubMed

Nonnenmacher, Marcel; Behrens, Christian; Berens, Philipp; Bethge, Matthias; Macke, Jakob H

2017-10-01

The rise of large-scale recordings of neuronal activity has fueled the hope to gain new insights into the collective activity of neural ensembles. How can one link the statistics of neural population activity to underlying principles and theories? One attempt to interpret such data builds upon analogies to the behaviour of collective systems in statistical physics. Divergence of the specific heat-a measure of population statistics derived from thermodynamics-has been used to suggest that neural populations are optimized to operate at a "critical point". However, these findings have been challenged by theoretical studies which have shown that common inputs can lead to diverging specific heat. Here, we connect "signatures of criticality", and in particular the divergence of specific heat, back to statistics of neural population activity commonly studied in neural coding: firing rates and pairwise correlations. We show that the specific heat diverges whenever the average correlation strength does not depend on population size. This is necessarily true when data with correlations is randomly subsampled during the analysis process, irrespective of the detailed structure or origin of correlations. We also show how the characteristic shape of specific heat capacity curves depends on firing rates and correlations, using both analytically tractable models and numerical simulations of a canonical feed-forward population model. To analyze these simulations, we develop efficient methods for characterizing large-scale neural population activity with maximum entropy models. We find that, consistent with experimental findings, increases in firing rates and correlation directly lead to more pronounced signatures. Thus, previous reports of thermodynamical criticality in neural populations based on the analysis of specific heat can be explained by average firing rates and correlations, and are not indicative of an optimized coding strategy. We conclude that a reliable interpretation of statistical tests for theories of neural coding is possible only in reference to relevant ground-truth models.

Multicultural and Diversity Considerations in the New "Code of Professional Ethics for Rehabilitation Counselors"

ERIC Educational Resources Information Center

Cartwright, Brenda Y.; Fleming, Christine L.

2010-01-01

As the demographic transformation of the U.S. population continues, the challenges of multicultural and diversity-based considerations remain a central focus, as does the need to incorporate cultural competencies into the practice of rehabilitation. The Commission on Rehabilitation Counselor Certification's 2010 "Code of Professional Ethics for…

Locomotor performance of cane toads differs between native-range and invasive populations.

PubMed

Kosmala, Georgia; Christian, Keith; Brown, Gregory; Shine, Richard

2017-07-01

Invasive species provide a robust opportunity to evaluate how animals deal with novel environmental challenges. Shifts in locomotor performance-and thus the ability to disperse-(and especially, the degree to which it is constrained by thermal and hydric extremes) are of special importance, because they might affect the rate that an invader can spread. We studied cane toads ( Rhinella marina ) across a broad geographical range: two populations within the species' native range in Brazil, two invasive populations on the island of Hawai'i and eight invasive populations encompassing the eastern, western and southern limits of the toad invasion in Australia. A toad's locomotor performance on a circular raceway was strongly affected by both its temperature and its hydration state, but the nature and magnitude of those constraints differed across populations. In their native range, cane toads exhibited relatively low performance (even under optimal test conditions) and a rapid decrease in performance at lower temperatures and hydration levels. At the other extreme, performance was high in toads from southern Australia, and virtually unaffected by desiccation. Hawai'ian toads broadly resembled their Brazilian conspecifics, plausibly reflecting similar climatic conditions. The invasion of Australia has been accompanied by a dramatic enhancement in the toads' locomotor abilities, and (in some populations) by an ability to maintain locomotor performance even when the animal is cold and/or dehydrated. The geographical divergences in performance among cane toad populations graphically attest to the adaptability of invasive species in the face of novel abiotic challenges.

Representation of memories in the cortical-hippocampal system: Results from the application of population similarity analyses

PubMed Central

McKenzie, Sam; Keene, Chris; Farovik, Anja; Blandon, John; Place, Ryan; Komorowski, Robert; Eichenbaum, Howard

2016-01-01

Here we consider the value of neural population analysis as an approach to understanding how information is represented in the hippocampus and cortical areas and how these areas might interact as a brain system to support memory. We argue that models based on sparse coding of different individual features by single neurons in these areas (e.g., place cells, grid cells) are inadequate to capture the complexity of experience represented within this system. By contrast, population analyses of neurons with denser coding and mixed selectivity reveal new and important insights into the organization of memories. Furthermore, comparisons of the organization of information in interconnected areas suggest a model of hippocampal-cortical interactions that mediates the fundamental features of memory. PMID:26748022

Targeting obesity-related adipose tissue dysfunction to prevent cancer development and progression

PubMed Central

Gucalp, Ayca; Iyengar, Neil M.; Hudis, Clifford A.; Dannenberg, Andrew J.

2016-01-01

The incidence of obesity, a leading modifiable risk factor for common solid tumors, is increasing. Effective interventions are needed to minimize the public health implications of obesity. Although the mechanisms linking increased adiposity to malignancy are incompletely understood, growing evidence points to complex interactions among multiple systemic and tissue-specific pathways including inflamed white adipose tissue. The metabolic and inflammatory consequences of white adipose tissue dysfunction collectively provide a plausible explanation for the link between overweight/obesity and carcinogenesis. Gaining a better understanding of these underlying molecular pathways and developing risk assessment tools that identify at-risk populations will be critical in implementing effective and novel cancer prevention and management strategies. PMID:26970134

Modelling the spread of innovation in wild birds.

PubMed

Shultz, Thomas R; Montrey, Marcel; Aplin, Lucy M

2017-06-01

We apply three plausible algorithms in agent-based computer simulations to recent experiments on social learning in wild birds. Although some of the phenomena are simulated by all three learning algorithms, several manifestations of social conformity bias are simulated by only the approximate majority (AM) algorithm, which has roots in chemistry, molecular biology and theoretical computer science. The simulations generate testable predictions and provide several explanatory insights into the diffusion of innovation through a population. The AM algorithm's success raises the possibility of its usefulness in studying group dynamics more generally, in several different scientific domains. Our differential-equation model matches simulation results and provides mathematical insights into the dynamics of these algorithms. © 2017 The Author(s).

Scale-Free Distribution of Avian Influenza Outbreaks

NASA Astrophysics Data System (ADS)

Small, Michael; Walker, David M.; Tse, Chi Kong

2007-11-01

Using global case data for the period from 25 November 2003 to 10 March 2007, we construct a network of plausible transmission pathways for the spread of avian influenza among domestic and wild birds. The network structure we obtain is complex and exhibits scale-free (although not necessarily small-world) properties. Communities within this network are connected with a distribution of links with infinite variance. Hence, the disease transmission model does not exhibit a threshold and so the infection will continue to propagate even with very low transmissibility. Consequentially, eradication with methods applicable to locally homogeneous populations is not possible. Any control measure needs to focus explicitly on the hubs within this network structure.

The P Value Problem in Otolaryngology: Shifting to Effect Sizes and Confidence Intervals.

PubMed

Vila, Peter M; Townsend, Melanie Elizabeth; Bhatt, Neel K; Kao, W Katherine; Sinha, Parul; Neely, J Gail

2017-06-01

There is a lack of reporting effect sizes and confidence intervals in the current biomedical literature. The objective of this article is to present a discussion of the recent paradigm shift encouraging the use of reporting effect sizes and confidence intervals. Although P values help to inform us about whether an effect exists due to chance, effect sizes inform us about the magnitude of the effect (clinical significance), and confidence intervals inform us about the range of plausible estimates for the general population mean (precision). Reporting effect sizes and confidence intervals is a necessary addition to the biomedical literature, and these concepts are reviewed in this article.

Comparison of ICD code-based diagnosis of obesity with measured obesity in children and the implications for health care cost estimates.

PubMed

Kuhle, Stefan; Kirk, Sara F L; Ohinmaa, Arto; Veugelers, Paul J

2011-12-21

Administrative health databases are a valuable research tool to assess health care utilization at the population level. However, their use in obesity research limited due to the lack of data on body weight. A potential workaround is to use the ICD code of obesity to identify obese individuals. The objective of the current study was to investigate the sensitivity and specificity of an ICD code-based diagnosis of obesity from administrative health data relative to the gold standard measured BMI. Linkage of a population-based survey with anthropometric measures in elementary school children in 2003 with longitudinal administrative health data (physician visits and hospital discharges 1992-2006) from the Canadian province of Nova Scotia. Measured obesity was defined based on the CDC cut-offs applied to the measured BMI. An ICD code-based diagnosis obesity was defined as one or more ICD-9 (278) or ICD-10 code (E66-E68) of obesity from a physician visit or a hospital stay. Sensitivity and specificity were calculated and health care cost estimates based on measured obesity and ICD-based obesity were compared. The sensitivity of an ICD code-based obesity diagnosis was 7.4% using ICD codes between 2002 and 2004. Those correctly identified had a higher BMI and had higher health care utilization and costs. An ICD diagnosis of obesity in Canadian administrative health data grossly underestimates the true prevalence of childhood obesity and overestimates the health care cost differential between obese and non-obese children.

The Utility of Cognitive Plausibility in Language Acquisition Modeling: Evidence from Word Segmentation

ERIC Educational Resources Information Center

Phillips, Lawrence; Pearl, Lisa

2015-01-01

The informativity of a computational model of language acquisition is directly related to how closely it approximates the actual acquisition task, sometimes referred to as the model's "cognitive plausibility." We suggest that though every computational model necessarily idealizes the modeled task, an informative language acquisition…

Spectral fitting, shock layer modeling, and production of nitrogen oxides and excited nitrogen

NASA Technical Reports Server (NTRS)

Blackwell, H. E.

1991-01-01

An analysis was made of N2 emission from 8.72 MJ/kg shock layer at 2.54, 1.91, and 1.27 cm positions and vibrational state distributions, temperatures, and relative electronic state populations was obtained from data sets. Other recorded arc jet N2 and air spectral data were reviewed and NO emission characteristics were studied. A review of operational procedures of the DSMC code was made. Information on other appropriate codes and modifications, including ionization, were made as well as a determination of the applicability of codes reviewed to task requirement. A review was also made of computational procedures used in CFD codes of Li and other codes on JSC computers. An analysis was made of problems associated with integration of specific chemical kinetics applicable to task into CFD codes.

Python Radiative Transfer Emission code (PyRaTE): non-LTE spectral lines simulations

NASA Astrophysics Data System (ADS)

Tritsis, A.; Yorke, H.; Tassis, K.

2018-05-01

We describe PyRaTE, a new, non-local thermodynamic equilibrium (non-LTE) line radiative transfer code developed specifically for post-processing astrochemical simulations. Population densities are estimated using the escape probability method. When computing the escape probability, the optical depth is calculated towards all directions with density, molecular abundance, temperature and velocity variations all taken into account. A very easy-to-use interface, capable of importing data from simulations outputs performed with all major astrophysical codes, is also developed. The code is written in PYTHON using an "embarrassingly parallel" strategy and can handle all geometries and projection angles. We benchmark the code by comparing our results with those from RADEX (van der Tak et al. 2007) and against analytical solutions and present case studies using hydrochemical simulations. The code will be released for public use.

Why patients visit their doctors: assessing the most prevalent conditions in a defined American population.

PubMed

St Sauver, Jennifer L; Warner, David O; Yawn, Barbara P; Jacobson, Debra J; McGree, Michaela E; Pankratz, Joshua J; Melton, L Joseph; Roger, Véronique L; Ebbert, Jon O; Rocca, Walter A

2013-01-01

To describe the prevalence of nonacute conditions among patients seeking health care in a defined US population, emphasizing age, sex, and ethnic differences. The Rochester Epidemiology Project (REP) medical records linkage system was used to identify all residents of Olmsted County, Minnesota, on April 1, 2009, who had consented to review of their medical records for research (142,377 patients). We then electronically extracted all International Classification of Diseases, Ninth Revision codes noted in the records of these patients by any health care institution between January 1, 2005, and December 31, 2009. We grouped International Classification of Diseases, Ninth Revision codes into clinical classification codes and then into 47 broader disease groups associated with health-related quality of life. Age- and sex-specific prevalence was estimated by dividing the number of individuals within each group by the corresponding age- and sex-specific population. Patients within a group who had multiple codes were counted only once. We included a total of 142,377 patients, 75,512 (53%) of whom were female. Skin disorders (42.7%), osteoarthritis and joint disorders (33.6%), back problems (23.9%), disorders of lipid metabolism (22.4%), and upper respiratory tract disease (22.1%, excluding asthma) were the most prevalent disease groups in this population. Ten of the 15 most prevalent disease groups were more common in women in almost all age groups, whereas disorders of lipid metabolism, hypertension, and diabetes were more common in men. Additionally, the prevalence of 7 of the 10 most common groups increased with advancing age. Prevalence also varied across ethnic groups (whites, blacks, and Asians). Our findings suggest areas for focused research that may lead to better health care delivery and improved population health. Copyright © 2013 Mayo Foundation for Medical Education and Research. Published by Elsevier Inc. All rights reserved.

A new stellar spectrum interpolation algorithm and its application to Yunnan-III evolutionary population synthesis models

NASA Astrophysics Data System (ADS)

Cheng, Liantao; Zhang, Fenghui; Kang, Xiaoyu; Wang, Lang

2018-05-01

In evolutionary population synthesis (EPS) models, we need to convert stellar evolutionary parameters into spectra via interpolation in a stellar spectral library. For theoretical stellar spectral libraries, the spectrum grid is homogeneous on the effective-temperature and gravity plane for a given metallicity. It is relatively easy to derive stellar spectra. For empirical stellar spectral libraries, stellar parameters are irregularly distributed and the interpolation algorithm is relatively complicated. In those EPS models that use empirical stellar spectral libraries, different algorithms are used and the codes are often not released. Moreover, these algorithms are often complicated. In this work, based on a radial basis function (RBF) network, we present a new spectrum interpolation algorithm and its code. Compared with the other interpolation algorithms that are used in EPS models, it can be easily understood and is highly efficient in terms of computation. The code is written in MATLAB scripts and can be used on any computer system. Using it, we can obtain the interpolated spectra from a library or a combination of libraries. We apply this algorithm to several stellar spectral libraries (such as MILES, ELODIE-3.1 and STELIB-3.2) and give the integrated spectral energy distributions (ISEDs) of stellar populations (with ages from 1 Myr to 14 Gyr) by combining them with Yunnan-III isochrones. Our results show that the differences caused by the adoption of different EPS model components are less than 0.2 dex. All data about the stellar population ISEDs in this work and the RBF spectrum interpolation code can be obtained by request from the first author or downloaded from http://www1.ynao.ac.cn/˜zhangfh.

Code-based Diagnostic Algorithms for Idiopathic Pulmonary Fibrosis. Case Validation and Improvement.

PubMed

Ley, Brett; Urbania, Thomas; Husson, Gail; Vittinghoff, Eric; Brush, David R; Eisner, Mark D; Iribarren, Carlos; Collard, Harold R

2017-06-01

Population-based studies of idiopathic pulmonary fibrosis (IPF) in the United States have been limited by reliance on diagnostic code-based algorithms that lack clinical validation. To validate a well-accepted International Classification of Diseases, Ninth Revision, code-based algorithm for IPF using patient-level information and to develop a modified algorithm for IPF with enhanced predictive value. The traditional IPF algorithm was used to identify potential cases of IPF in the Kaiser Permanente Northern California adult population from 2000 to 2014. Incidence and prevalence were determined overall and by age, sex, and race/ethnicity. A validation subset of cases (n = 150) underwent expert medical record and chest computed tomography review. A modified IPF algorithm was then derived and validated to optimize positive predictive value. From 2000 to 2014, the traditional IPF algorithm identified 2,608 cases among 5,389,627 at-risk adults in the Kaiser Permanente Northern California population. Annual incidence was 6.8/100,000 person-years (95% confidence interval [CI], 6.1-7.7) and was higher in patients with older age, male sex, and white race. The positive predictive value of the IPF algorithm was only 42.2% (95% CI, 30.6 to 54.6%); sensitivity was 55.6% (95% CI, 21.2 to 86.3%). The corrected incidence was estimated at 5.6/100,000 person-years (95% CI, 2.6-10.3). A modified IPF algorithm had improved positive predictive value but reduced sensitivity compared with the traditional algorithm. A well-accepted International Classification of Diseases, Ninth Revision, code-based IPF algorithm performs poorly, falsely classifying many non-IPF cases as IPF and missing a substantial proportion of IPF cases. A modification of the IPF algorithm may be useful for future population-based studies of IPF.

Estimating the Potential Impact of Canine Distemper Virus on the Amur Tiger Population (Panthera tigris altaica) in Russia

PubMed Central

Gilbert, Martin; Miquelle, Dale G.; Goodrich, John M.; Reeve, Richard; Cleaveland, Sarah; Matthews, Louise; Joly, Damien O.

2014-01-01

Lethal infections with canine distemper virus (CDV) have recently been diagnosed in Amur tigers (Panthera tigris altaica), but long-term implications for the population are unknown. This study evaluates the potential impact of CDV on a key tiger population in Sikhote-Alin Biosphere Zapovednik (SABZ), and assesses how CDV might influence the extinction potential of other tiger populations of varying sizes. An individual-based stochastic, SIRD (susceptible-infected-recovered/dead) model was used to simulate infection through predation of infected domestic dogs, and/or wild carnivores, and direct tiger-to-tiger transmission. CDV prevalence and effective contact based on published and observed data was used to define plausible low- and high-risk infection scenarios. CDV infection increased the 50-year extinction probability of tigers in SABZ by 6.3% to 55.8% compared to a control population, depending on risk scenario. The most significant factors influencing model outcome were virus prevalence in the reservoir population(s) and its effective contact rate with tigers. Adjustment of the mortality rate had a proportional impact, while inclusion of epizootic infection waves had negligible additional impact. Small populations were found to be disproportionately vulnerable to extinction through CDV infection. The 50-year extinction risk in populations consisting of 25 individuals was 1.65 times greater when CDV was present than that of control populations. The effects of density dependence do not protect an endangered population from the impacts of a multi-host pathogen, such as CDV, where they coexist with an abundant reservoir presenting a persistent threat. Awareness of CDV is a critical component of a successful tiger conservation management policy. PMID:25354196

Populations potentially exposed to traffic-related air pollution in seven world cities.

PubMed

Su, Jason G; Apte, Joshua S; Lipsitt, Jonah; Garcia-Gonzales, Diane A; Beckerman, Bernardo S; de Nazelle, Audrey; Texcalac-Sangrador, José Luis; Jerrett, Michael

2015-05-01

Traffic-related air pollution (TRAP) likely exerts a large burden of disease globally, and in many places, traffic is increasing dramatically. The impact, however, of urban form on the portion of population potentially exposed to TRAP remains poorly understood. In this study, we estimate portions of population potentially exposed to TRAP across seven global cities of various urban forms. Data on population distributions and road networks were collected from the best available sources in each city and from remote sensing analysis. Using spatial mapping techniques, we first overlaid road buffers onto population data to estimate the portions of population potentially exposed for four plausible impact zones. Based on a most likely scenario with impacts from highways up to 300meters and major roadways up to 50meters, we identified that the portions of population potentially exposed for the seven cities ranged from 23 to 96%. High-income North American cities had the lowest potential exposure portions, while those in Europe had the highest. Second, we adjusted exposure zone concentration levels based on a literature suggested multiplier for each city using corresponding background concentrations. Though Beijing and Mexico City did not have the highest portion of population exposure, those in their exposure zones had the highest levels of exposure. For all seven cities, the portion of population potentially exposed was positively correlated with roadway density and, to a lesser extent, with population density. These analyses suggest that urban form may influence the portion of population exposed to TRAP and vehicle emissions and other factors may influence the exposure levels. Greater understanding of urban form and other factors influencing potential exposure to TRAP may help inform interventions that protect public health. Copyright © 2014 Elsevier Ltd. All rights reserved.

Estimating the potential impact of canine distemper virus on the Amur tiger population (Panthera tigris altaica) in Russia.

PubMed

Gilbert, Martin; Miquelle, Dale G; Goodrich, John M; Reeve, Richard; Cleaveland, Sarah; Matthews, Louise; Joly, Damien O

2014-01-01

Lethal infections with canine distemper virus (CDV) have recently been diagnosed in Amur tigers (Panthera tigris altaica), but long-term implications for the population are unknown. This study evaluates the potential impact of CDV on a key tiger population in Sikhote-Alin Biosphere Zapovednik (SABZ), and assesses how CDV might influence the extinction potential of other tiger populations of varying sizes. An individual-based stochastic, SIRD (susceptible-infected-recovered/dead) model was used to simulate infection through predation of infected domestic dogs, and/or wild carnivores, and direct tiger-to-tiger transmission. CDV prevalence and effective contact based on published and observed data was used to define plausible low- and high-risk infection scenarios. CDV infection increased the 50-year extinction probability of tigers in SABZ by 6.3% to 55.8% compared to a control population, depending on risk scenario. The most significant factors influencing model outcome were virus prevalence in the reservoir population(s) and its effective contact rate with tigers. Adjustment of the mortality rate had a proportional impact, while inclusion of epizootic infection waves had negligible additional impact. Small populations were found to be disproportionately vulnerable to extinction through CDV infection. The 50-year extinction risk in populations consisting of 25 individuals was 1.65 times greater when CDV was present than that of control populations. The effects of density dependence do not protect an endangered population from the impacts of a multi-host pathogen, such as CDV, where they coexist with an abundant reservoir presenting a persistent threat. Awareness of CDV is a critical component of a successful tiger conservation management policy.

Learning-by-doing, population pressure, and the theory of demographic transition.

PubMed

Strulik, H

1997-01-01

The long-term effects of two interdependent relations between economic growth and population growth are discussed. The empirical work of Boserup (1981) was utilized, which focused on rural, sparsely populated economies with low income per capita. According to the formulation of the population-push hypothesis, learning-by-doing effects in production lead to increasing returns to scale and, therefore, to a positive correlation between economic and population growth. In accordance with the theory of demographic transition, the population growth rate initially increases with rising income levels and then declines. The approach originating from Cigno (1984) modified the economic model, which allowed the establishment of two different stable equilibria. Regarding this relationship, the existence and stability of low-income and high-income equilibrium was shown in a neoclassical growth model. Under plausible conditions a demo-economic transition from the first to the second steady-state took place. The instability of the Malthusian steady-state is also possible when a country develops along a path of economic growth which is compatible with the demographic transition. In this context, learning means the application of new techniques of agrarian production. In developed economies with a stable population the learning-or-doing decision lead to accumulation of human capital and the invention of new technologies and goods. The interdependence of income-determined population growth and learning-by-doing may serve as an explanation for the weak and partly controversial empirical support for an overall correlation between income and population growth. The result yielded a meaningful interpretation of the population-push hypothesis, which is consistent with the empirical findings on the correlation between economic and population growth.

The Opponent Channel Population Code of Sound Location Is an Efficient Representation of Natural Binaural Sounds

PubMed Central

Młynarski, Wiktor

2015-01-01

In mammalian auditory cortex, sound source position is represented by a population of broadly tuned neurons whose firing is modulated by sounds located at all positions surrounding the animal. Peaks of their tuning curves are concentrated at lateral position, while their slopes are steepest at the interaural midline, allowing for the maximum localization accuracy in that area. These experimental observations contradict initial assumptions that the auditory space is represented as a topographic cortical map. It has been suggested that a “panoramic” code has evolved to match specific demands of the sound localization task. This work provides evidence suggesting that properties of spatial auditory neurons identified experimentally follow from a general design principle- learning a sparse, efficient representation of natural stimuli. Natural binaural sounds were recorded and served as input to a hierarchical sparse-coding model. In the first layer, left and right ear sounds were separately encoded by a population of complex-valued basis functions which separated phase and amplitude. Both parameters are known to carry information relevant for spatial hearing. Monaural input converged in the second layer, which learned a joint representation of amplitude and interaural phase difference. Spatial selectivity of each second-layer unit was measured by exposing the model to natural sound sources recorded at different positions. Obtained tuning curves match well tuning characteristics of neurons in the mammalian auditory cortex. This study connects neuronal coding of the auditory space with natural stimulus statistics and generates new experimental predictions. Moreover, results presented here suggest that cortical regions with seemingly different functions may implement the same computational strategy-efficient coding. PMID:25996373

Dual Coding of Frequency Modulation in the Ventral Cochlear Nucleus.

PubMed

Paraouty, Nihaad; Stasiak, Arkadiusz; Lorenzi, Christian; Varnet, Léo; Winter, Ian M

2018-04-25

Frequency modulation (FM) is a common acoustic feature of natural sounds and is known to play a role in robust sound source recognition. Auditory neurons show precise stimulus-synchronized discharge patterns that may be used for the representation of low-rate FM. However, it remains unclear whether this representation is based on synchronization to slow temporal envelope (ENV) cues resulting from cochlear filtering or phase locking to faster temporal fine structure (TFS) cues. To investigate the plausibility of those encoding schemes, single units of the ventral cochlear nucleus of guinea pigs of either sex were recorded in response to sine FM tones centered at the unit's best frequency (BF). The results show that, in contrast to high-BF units, for modulation depths within the receptive field, low-BF units (<4 kHz) demonstrate good phase locking to TFS. For modulation depths extending beyond the receptive field, the discharge patterns follow the ENV and fluctuate at the modulation rate. The receptive field proved to be a good predictor of the ENV responses for most primary-like and chopper units. The current in vivo data also reveal a high level of diversity in responses across unit types. TFS cues are mainly conveyed by low-frequency and primary-like units and ENV cues by chopper and onset units. The diversity of responses exhibited by cochlear nucleus neurons provides a neural basis for a dual-coding scheme of FM in the brainstem based on both ENV and TFS cues. SIGNIFICANCE STATEMENT Natural sounds, including speech, convey informative temporal modulations in frequency. Understanding how the auditory system represents those frequency modulations (FM) has important implications as robust sound source recognition depends crucially on the reception of low-rate FM cues. Here, we recorded 115 single-unit responses from the ventral cochlear nucleus in response to FM and provide the first physiological evidence of a dual-coding mechanism of FM via synchronization to temporal envelope cues and phase locking to temporal fine structure cues. We also demonstrate a diversity of neural responses with different coding specializations. These results support the dual-coding scheme proposed by psychophysicists to account for FM sensitivity in humans and provide new insights on how this might be implemented in the early stages of the auditory pathway. Copyright © 2018 the authors 0270-6474/18/384123-15$15.00/0.

Learning and coding in biological neural networks

NASA Astrophysics Data System (ADS)

Fiete, Ila Rani

How can large groups of neurons that locally modify their activities learn to collectively perform a desired task? Do studies of learning in small networks tell us anything about learning in the fantastically large collection of neurons that make up a vertebrate brain? What factors do neurons optimize by encoding sensory inputs or motor commands in the way they do? In this thesis I present a collection of four theoretical works: each of the projects was motivated by specific constraints and complexities of biological neural networks, as revealed by experimental studies; together, they aim to partially address some of the central questions of neuroscience posed above. We first study the role of sparse neural activity, as seen in the coding of sequential commands in a premotor area responsible for birdsong. We show that the sparse coding of temporal sequences in the songbird brain can, in a network where the feedforward plastic weights must translate the sparse sequential code into a time-varying muscle code, facilitate learning by minimizing synaptic interference. Next, we propose a biologically plausible synaptic plasticity rule that can perform goal-directed learning in recurrent networks of voltage-based spiking neurons that interact through conductances. Learning is based on the correlation of noisy local activity with a global reward signal; we prove that this rule performs stochastic gradient ascent on the reward. Thus, if the reward signal quantifies network performance on some desired task, the plasticity rule provably drives goal-directed learning in the network. To assess the convergence properties of the learning rule, we compare it with a known example of learning in the brain. Song-learning in finches is a clear example of a learned behavior, with detailed available neurophysiological data. With our learning rule, we train an anatomically accurate model birdsong network that drives a sound source to mimic an actual zebrafinch song. Simulation and theoretical results on the scalability of this rule show that learning with stochastic gradient ascent may be adequately fast to explain learning in the bird. Finally, we address the more general issue of the scalability of stochastic gradient learning on quadratic cost surfaces in linear systems, as a function of system size and task characteristics, by deriving analytical expressions for the learning curves.

Reduced adaptability, but no fundamental disruption, of norm-based face coding following early visual deprivation from congenital cataracts.

PubMed

Rhodes, Gillian; Nishimura, Mayu; de Heering, Adelaide; Jeffery, Linda; Maurer, Daphne

2017-05-01

Faces are adaptively coded relative to visual norms that are updated by experience, and this adaptive coding is linked to face recognition ability. Here we investigated whether adaptive coding of faces is disrupted in individuals (adolescents and adults) who experience face recognition difficulties following visual deprivation from congenital cataracts in infancy. We measured adaptive coding using face identity aftereffects, where smaller aftereffects indicate less adaptive updating of face-coding mechanisms by experience. We also examined whether the aftereffects increase with adaptor identity strength, consistent with norm-based coding of identity, as in typical populations, or whether they show a different pattern indicating some more fundamental disruption of face-coding mechanisms. Cataract-reversal patients showed significantly smaller face identity aftereffects than did controls (Experiments 1 and 2). However, their aftereffects increased significantly with adaptor strength, consistent with norm-based coding (Experiment 2). Thus we found reduced adaptability but no fundamental disruption of norm-based face-coding mechanisms in cataract-reversal patients. Our results suggest that early visual experience is important for the normal development of adaptive face-coding mechanisms. © 2016 John Wiley & Sons Ltd.

Variation in geographic access to chemotherapy by definitions of providers and service locations: a population-based observational study.

PubMed

Schroeder, Mary C; Chapman, Cole G; Nattinger, Matthew C; Halfdanarson, Thorvardur R; Abu-Hejleh, Taher; Tien, Yu-Yu; Brooks, John M

2016-07-18

An aging population, with its associated rise in cancer incidence and strain on the oncology workforce, will continue to motivate patients, healthcare providers and policy makers to better understand the existing and growing challenges of access to chemotherapy. Administrative data, and SEER-Medicare data in particular, have been used to assess patterns of healthcare utilization because of its rich information regarding patients, their treatments, and their providers. To create measures of geographic access to chemotherapy, patients and oncologists must first be identified. Others have noted that identifying chemotherapy providers from Medicare claims is not always straightforward, as providers may report multiple or incorrect specialties and/or practice in multiple locations. Although previous studies have found that specialty codes alone fail to identify all oncologists, none have assessed whether various methods of identifying chemotherapy providers and their locations affect estimates of geographic access to care. SEER-Medicare data was used to identify patients, physicians, and chemotherapy use in this population-based observational study. We compared two measures of geographic access to chemotherapy, local area density and distance to nearest provider, across two definitions of chemotherapy provider (identified by specialty codes or billing codes) and two definitions of chemotherapy service location (where chemotherapy services were proven to be or possibly available) using descriptive statistics. Access measures were mapped for three representative registries. In our sample, 57.2 % of physicians who submitted chemotherapy claims reported a specialty of hematology/oncology or medical oncology. These physicians were associated with 91.0 % of the chemotherapy claims. When providers were identified through billing codes instead of specialty codes, an additional 50.0 % of beneficiaries (from 23.8 % to 35.7 %) resided in the same ZIP code as a chemotherapy provider. Beneficiaries were also 1.3 times closer to a provider, in terms of driving time. Our access measures did not differ significantly across definitions of service location. Measures of geographic access to care were sensitive to definitions of chemotherapy providers; far more providers were identified through billing codes than specialty codes. They were not sensitive to definitions of service locations, as providers, regardless of how they are identified, generally provided chemotherapy at each of their practice locations.

The non-coding RNA landscape of human hematopoiesis and leukemia.

PubMed

Schwarzer, Adrian; Emmrich, Stephan; Schmidt, Franziska; Beck, Dominik; Ng, Michelle; Reimer, Christina; Adams, Felix Ferdinand; Grasedieck, Sarah; Witte, Damian; Käbler, Sebastian; Wong, Jason W H; Shah, Anushi; Huang, Yizhou; Jammal, Razan; Maroz, Aliaksandra; Jongen-Lavrencic, Mojca; Schambach, Axel; Kuchenbauer, Florian; Pimanda, John E; Reinhardt, Dirk; Heckl, Dirk; Klusmann, Jan-Henning

2017-08-09

Non-coding RNAs have emerged as crucial regulators of gene expression and cell fate decisions. However, their expression patterns and regulatory functions during normal and malignant human hematopoiesis are incompletely understood. Here we present a comprehensive resource defining the non-coding RNA landscape of the human hematopoietic system. Based on highly specific non-coding RNA expression portraits per blood cell population, we identify unique fingerprint non-coding RNAs-such as LINC00173 in granulocytes-and assign these to critical regulatory circuits involved in blood homeostasis. Following the incorporation of acute myeloid leukemia samples into the landscape, we further uncover prognostically relevant non-coding RNA stem cell signatures shared between acute myeloid leukemia blasts and healthy hematopoietic stem cells. Our findings highlight the importance of the non-coding transcriptome in the formation and maintenance of the human blood hierarchy.While micro-RNAs are known regulators of haematopoiesis and leukemogenesis, the role of long non-coding RNAs is less clear. Here the authors provide a non-coding RNA expression landscape of the human hematopoietic system, highlighting their role in the formation and maintenance of the human blood hierarchy.

Fine-coarse semantic processing in schizophrenia: a reversed pattern of hemispheric dominance.

PubMed

Zeev-Wolf, Maor; Goldstein, Abraham; Levkovitz, Yechiel; Faust, Miriam

2014-04-01

Left lateralization for language processing is a feature of neurotypical brains. In individuals with schizophrenia, lack of left lateralization is associated with the language impairments manifested in this population. Beeman׳s fine-coarse semantic coding model asserts left hemisphere specialization in fine (i.e., conventionalized) semantic coding and right hemisphere specialization in coarse (i.e., non-conventionalized) semantic coding. Applying this model to schizophrenia would suggest that language impairments in this population are a result of greater reliance on coarse semantic coding. We investigated this hypothesis and examined whether a reversed pattern of hemispheric involvement in fine-coarse semantic coding along the time course of activation could be detected in individuals with schizophrenia. Seventeen individuals with schizophrenia and 30 neurotypical participants were presented with two word expressions of four types: literal, conventional metaphoric, unrelated (exemplars of fine semantic coding) and novel metaphoric (an exemplar of coarse semantic coding). Expressions were separated by either a short (250 ms) or long (750 ms) delay. Findings indicate that whereas during novel metaphor processing, controls displayed a left hemisphere advantage at 250 ms delay and right hemisphere advantage at 750 ms, individuals with schizophrenia displayed the opposite. For conventional metaphoric and unrelated expressions, controls showed left hemisphere advantage across times, while individuals with schizophrenia showed a right hemisphere advantage. Furthermore, whereas individuals with schizophrenia were less accurate than control at judging literal, conventional metaphoric and unrelated expressions they were more accurate when judging novel metaphors. Results suggest that individuals with schizophrenia display a reversed pattern of lateralization for semantic coding which causes them to rely more heavily on coarse semantic coding. Thus, for individuals with schizophrenia, speech situation are always non-conventional, compelling them to constantly seek for meanings and prejudicing them toward novel or atypical speech acts. This, in turn, may disadvantage them in conventionalized communication and result in language impairment. Copyright © 2014 Elsevier Ltd. All rights reserved.

A Comparison of Six MMPI Short Forms: Code Type Correspondence and Indices of Psychopathology.

ERIC Educational Resources Information Center

Willcockson, James C.; And Others

1983-01-01

Compared six Minnesota Multiphasic Personality Inventory (MMPI) short forms with the full-length MMPI for ability to identify code-types and indices of psychopathology in renal dialysis patients (N=53) and paranoid schizophrenics (N=58). Results suggested that the accuracy of the short forms fluctuates for different patient populations and…

The Challenges of Inclusion: Perceptions of Superintendents, Principals, and Teachers in Mississippi Alternative Schools

ERIC Educational Resources Information Center

Tune, Gary Lynn

2013-01-01

Alternative schools serve a population of students who have come in conflict with the codes of conduct of their home school district. Students with disabilities are subject to the same codes of conduct and occasionally are referred to alternative schools. These referrals constitute a change in placement mandating alternative schools to provide…

A HYPOTHESIS FOR THE COLOR BIMODALITY OF JUPITER TROJANS

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

Wong, Ian; Brown, Michael E., E-mail: iwong@caltech.edu

One of the most enigmatic and hitherto unexplained properties of Jupiter Trojans is their bimodal color distribution. This bimodality is indicative of two sub-populations within the Trojans, which have distinct size distributions. In this paper, we present a simple, plausible hypothesis for the origin and evolution of the two Trojan color sub-populations. In the framework of dynamical instability models of early solar system evolution, which suggest a common primordial progenitor population for both Trojans and Kuiper Belt objects, we use observational constraints to assert that the color bimodalities evident in both minor body populations developed within the primordial population priormore » to the onset of instability. We show that, beginning with an initial composition of rock and ices, location-dependent volatile loss through sublimation in this primordial population could have led to sharp changes in the surface composition with heliocentric distance. We propose that the depletion or retention of H{sub 2}S ice on the surface of these objects was the key factor in creating an initial color bimodality. Objects that retained H{sub 2}S on their surfaces developed characteristically redder colors upon irradiation than those that did not. After the bodies from the primordial population were scattered and emplaced into their current positions, they preserved this primordial color bimodality to the present day. We explore predictions of the volatile loss model—in particular, the effect of collisions within the Trojan population on the size distributions of the two sub-populations—and propose further experimental and observational tests of our hypothesis.« less

The Birth of a Galaxy: Primordial Metal Enrichment and Stellar Populations

NASA Astrophysics Data System (ADS)

Wise, John H.; Turk, Matthew J.; Norman, Michael L.; Abel, Tom

2012-01-01

By definition, Population III stars are metal-free, and their protostellar collapse is driven by molecular hydrogen cooling in the gas phase, leading to large characteristic masses. Population II stars with lower characteristic masses form when the star-forming gas reaches a critical metallicity of 10-6-10-3.5 Z ⊙. We present an adaptive mesh refinement radiation hydrodynamics simulation that follows the transition from Population III to Population II star formation. The maximum spatial resolution of 1 comoving parsec allows for individual molecular clouds to be well resolved and their stellar associations to be studied in detail. We model stellar radiative feedback with adaptive ray tracing. A top-heavy initial mass function for the Population III stars is considered, resulting in a plausible distribution of pair-instability supernovae and associated metal enrichment. We find that the gas fraction recovers from 5% to nearly the cosmic fraction in halos with merger histories rich in halos above 107 M ⊙. A single pair-instability supernova is sufficient to enrich the host halo to a metallicity floor of 10-3 Z ⊙ and to transition to Population II star formation. This provides a natural explanation for the observed floor on damped Lyα systems metallicities reported in the literature, which is of this order. We find that stellar metallicities do not necessarily trace stellar ages, as mergers of halos with established stellar populations can create superpositions of t-Z evolutionary tracks. A bimodal metallicity distribution is created after a starburst occurs when the halo can cool efficiently through atomic line cooling.

Accurate spin-orbit and spin-other-orbit contributions to the g-tensor for transition metal containing systems.

PubMed

Van Yperen-De Deyne, A; Pauwels, E; Van Speybroeck, V; Waroquier, M

2012-08-14

In this paper an overview is presented of several approximations within Density Functional Theory (DFT) to calculate g-tensors in transition metal containing systems and a new accurate description of the spin-other-orbit contribution for high spin systems is suggested. Various implementations in a broad variety of software packages (ORCA, ADF, Gaussian, CP2K, GIPAW and BAND) are critically assessed on various aspects including (i) non-relativistic versus relativistic Hamiltonians, (ii) spin-orbit coupling contributions and (iii) the gauge. Particular attention is given to the level of accuracy that can be achieved for codes that allow g-tensor calculations under periodic boundary conditions, as these are ideally suited to efficiently describe extended condensed-phase systems containing transition metals. In periodic codes like CP2K and GIPAW, the g-tensor calculation schemes currently suffer from an incorrect treatment of the exchange spin-orbit interaction and a deficient description of the spin-other-orbit term. In this paper a protocol is proposed, making the predictions of the exchange part to the g-tensor shift more plausible. Focus is also put on the influence of the spin-other-orbit interaction which becomes of higher importance for high-spin systems. In a revisited derivation of the various terms arising from the two-electron spin-orbit and spin-other-orbit interaction (SOO), new insight has been obtained revealing amongst other issues new terms for the SOO contribution. The periodic CP2K code has been adapted in view of this new development. One of the objectives of this study is indeed a serious enhancement of the performance of periodic codes in predicting g-tensors in transition metal containing systems at the same level of accuracy as the most advanced but time consuming spin-orbit mean-field approach. The methods are first applied on rhodium carbide but afterwards extended to a broad test set of molecules containing transition metals from the fourth, fifth and sixth row of the periodic table. The set contains doublets as well as high-spin molecules.

Get Real: Effects of Repeated Simulation and Emotion on the Perceived Plausibility of Future Experiences

ERIC Educational Resources Information Center

Szpunar, Karl K.; Schacter, Daniel L.

2013-01-01

People frequently imagine specific interpersonal experiences that might occur in their futures. The present study used a novel experimental paradigm to examine the influence of repeated simulation of future interpersonal experiences on subjective assessments of plausibility for positive, negative, and neutral events. The results demonstrate that…

The Radical Promise of Reformist Zeal: What Makes "Inquiry for Equity" Plausible?

ERIC Educational Resources Information Center

Lashaw, Amanda

2010-01-01

Education reform movements often promise more than they deliver. Why are such promises plausible in light of seemingly perpetual education reform? Drawing on ethnographic fieldwork based in a nonprofit education reform organization, this article explores the appeal of popular notions about "using data to close the racial achievement…

Ambiguity's aftermath: how age differences in resolving lexical ambiguity affect subsequent comprehension.

PubMed

Lee, Chia-lin; Federmeier, Kara D

2012-04-01

When ambiguity resolution is difficult, younger adults recruit selection-related neural resources that older adults do not. To elucidate the nature of those resources and the consequences of their recruitment for subsequent comprehension, we embedded noun/verb homographs and matched unambiguous words in syntactically well-specified but semantically neutral sentences. Target words were followed by a prepositional phrase whose head noun was plausible for only one meaning of the homograph. Replicating past findings, younger but not older adults elicited sustained frontal negativity to homographs compared to unambiguous words. On the subsequent head nouns, younger adults showed plausibility effects in all conditions, attesting to successful meaning selection through suppression. In contrast, older adults showed smaller plausibility effects following ambiguous words and failed to show plausibility effects when the context picked out the homograph's non-dominant meaning (i.e., they did not suppress the contextually-irrelevant dominant meaning). Meaning suppression processes, reflected in the frontal negativity, thus become less available with age, with consequences for subsequent comprehension. Copyright © 2012 Elsevier Ltd. All rights reserved.

Parafoveal preview benefit in sentence reading: Independent effects of plausibility and orthographic relatedness.

PubMed

Veldre, Aaron; Andrews, Sally

2017-04-01

Recent evidence from studies using the gaze-contingent boundary paradigm has suggested that parafoveal preview benefit is contingent on the fit between a preview word and the sentence context. We investigated whether this plausibility preview benefit is modulated by preview-target orthographic relatedness. Participants' eye movements were recorded as they read sentences in which the parafoveal preview of a target word was manipulated. The nonidentical previews were plausible or implausible continuations of the sentence and were either orthographic neighbors of the target or unrelated to the target. All first-pass reading measures showed strong plausibility preview benefits. There was also a benefit from preview-target orthographic relatedness across the reading measures. These two preview effects did not interact for any fixation measure. We also found no evidence that the relatedness effect was caused by misperception of an orthographically similar preview as the target word. These data highlight the existence of two independent mechanisms underlying preview effects: a benefit from the contextual fit of the preview word in the sentence, and a benefit from the sublexical overlap between the preview and target words.

What happened (and what didn’t): Discourse constraints on encoding of plausible alternatives

PubMed Central

Fraundorf, Scott H.; Benjamin, Aaron S.; Watson, Duane G.

2013-01-01

Three experiments investigated how font emphasis influences reading and remembering discourse. Although past work suggests that contrastive pitch contours benefit memory by promoting encoding of salient alternatives, it is unclear both whether this effect generalizes to other forms of linguistic prominence and how the set of alternatives is constrained. Participants read discourses in which some true propositions had salient alternatives (e.g., British scientists found the endangered monkey when the discourse also mentioned French scientists) and completed a recognition memory test. In Experiments 1 and 2, font emphasis in the initial presentation increased participants’ ability to later reject false statements about salient alternatives but not about unmentioned items (e.g., Portuguese scientists). In Experiment 3, font emphasis helped reject false statements about plausible alternatives, but not about less plausible alternatives that were nevertheless established in the discourse. These results suggest readers encode a narrow set of only those alternatives plausible in the particular discourse. They also indicate that multiple manipulations of linguistic prominence, not just prosody, can lead to consideration of alternatives. PMID:24014934