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Search Results: 1 - 10 of 310625 matches for " Andrew J. Parker "
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A micro-pool model for decision-related signals in visual cortical areas
Andrew J. Parker
Frontiers in Computational Neuroscience , 2013, DOI: 10.3389/fncom.2013.00115
Abstract: The study of sensory signaling in the visual cortex has been greatly advanced by the recording of neural activity simultaneously with the performance of a specific psychophysical task. Individual nerve cells may also increase their firing leading up to the particular choice or decision made on a single psychophysical trial. Understanding these signals is important because they have been taken as evidence that a particular nerve cell or group of nerve cells in the cortex is involved in the formation of the perceptual decision ultimately signaled by the organism. However, recent analyses show that the size of a decision-related change in firing in a particular neuron is not a secure basis for concluding anything about the contribution of a single neuron to the formation of a decision: rather the size of the decision-related firing is expected to be dominated by the extent to which the activation of a single neuron is correlated with the firing of the pool of neurons. The critical question becomes what defines membership of a population of neurons. This article presents the proposal that groups of neurons are naturally linked together by their connectivity, which in turn reflects the previous history of sensory stimulations. When a new psychophysical task is performed, a group of neurons relevant to the judgment becomes involved because the firing of some neurons in that group is strongly relevant to the task. This group of neurons is called a micro-pool. This article examines the consequences of such a proposal within the visual nervous system. The main focus is on the signals available from single neurons, but it argued that models of choice-related signals must scale up to larger numbers of neurons because MRI and MEG studies also show evidence of similar choice signals.
Simple tools for assembling and searching high-density picolitre pyrophosphate sequence data
Nicolas J Parker, Andrew G Parker
Source Code for Biology and Medicine , 2008, DOI: 10.1186/1751-0473-3-5
Abstract: A set of tools is provided to search a large data set of pyrophosphate sequence reads under a "live" CD version of Linux on a standard PC that can be used by anyone without prior knowledge of Linux and without having to install a Linux setup on the computer. The tools permit short lengths of de novo assembly, checking of existing assembled sequences, selection and display of reads from the data set and gathering counts of sequences in the reads.Demonstrations are given of the use of the tools to help with checking an assembly against the fragment data set; investigating homopolymer lengths, repeat regions and polymorphisms; and resolving inserted bases caused by incomplete chain extension.The additional information contained in a pyrophosphate sequencing data set beyond a basic assembly is difficult to access due to a lack of tools. The set of simple tools presented here would allow anyone with basic computer skills and a standard PC to access this information.The introduction of micro-fabricated high-density picolitre reactor pyrophosphate sequencing [1,2] by the company 454 Life Sciences (454 Life Sciences Corp., 20 Commercial Street, Branford, Connecticut 06405, USA; hereafter referred to as 454 sequencing) makes available for the first time large quantities of sequence data at reasonable cost. The continual reduction in sequencing cost will encourage sequencing by small groups or individual researchers with modest computer resources and limited experience of bioinformatics tools.The nature of the data from pyrophosphate sequencing is however both qualitatively and quantitatively different from that generated by Sanger sequencing [3] using fluorescent chain-terminating nucleotide analogues [4]. Instead of receiving a single consensus sequence with associated chromatogram (scf) file, this form of pyrophosphate sequencing generated for us 300 000 short sequence reads, around 100 bases long [5], assembled into several hundred contigs. However the normal system of ch
Human Cortical Activity Evoked by the Assignment of Authenticity when Viewing Works of Art
Mengfei Huang,Holly Bridge,Andrew J. Parker
Frontiers in Human Neuroscience , 2011, DOI: 10.3389/fnhum.2011.00134
Abstract: The expertise of others is a major social influence on our everyday decisions and actions. Many viewers of art, whether expert or na?ve, are convinced that the full esthetic appreciation of an artwork depends upon the assurance that the work is genuine rather than fake. Rembrandt portraits provide an interesting image set for testing this idea, as there is a large number of them and recent scholarship has determined that quite a few fakes and copies exist. Use of this image set allowed us to separate the brain’s response to images of genuine and fake pictures from the brain’s response to external advice about the authenticity of the paintings. Using functional magnetic resonance imaging, viewing of artworks assigned as “copy,” rather than “authentic,” evoked stronger responses in frontopolar cortex (FPC), and right precuneus, regardless of whether the portrait was actually genuine. Advice about authenticity had no direct effect on the cortical visual areas responsive to the paintings, but there was a significant psycho-physiological interaction between the FPC and the lateral occipital area, which suggests that these visual areas may be modulated by FPC. We propose that the activation of brain networks rather than a single cortical area in this paradigm supports the art scholars’ view that esthetic judgments are multi-faceted and multi-dimensional in nature.
Toll-like receptors and NOD-like receptors in rheumatic diseases
William J McCormack, Andrew E Parker, Luke A O'Neill
Arthritis Research & Therapy , 2009, DOI: 10.1186/ar2729
Abstract: Proinflammatory cytokines such as TNF, IL-6 and IL-1 have proven to be excellent therapeutic targets for diseases such as rheumatoid arthritis (RA). More recently, however, attention has focused on the mechanisms whereby these cytokines are induced. In this regard there has been remarkable progress in the elucidation of receptors that drive their production as well as other inflammatory mediators. This progress has led to a renaissance of interest in innate immunity among immunologists, since these receptors also sense microbial products to drive host defense.Two particular classes - the Toll-like receptors (TLRs) and NOD-like receptors (NLRs), which are pattern recognition receptors (PRRs) - have been most extensively studied. Certain TLRs (for example, TLR2, TLR4 and TLR9) and certain NLRs (for example, Nalp3) have been implicated in various inflammatory arthopathies. More recently evidence has been presented that these TLRs and NLRs might also be activated by noninfectious endogenous signals, making them even more attractive as important drivers of cytokines in diseases with no obvious infection.In the present review we will summarise the current state of knowledge in TLRs and NLRs, and also speculate on their roles in the pathogenesis of autoinflammatory joint diseases.The past 10 years have seen over 11,000 papers published on TLRs, which is a testament to the importance placed upon them by inflammation biologists and immunologists. Ten TLRs occur in humans, and the roles of nine of them (TLR1 to TLR9) have been determined [1].TLR2 senses lipopeptides from bacteria, with TLR1/2 dimers sensing triacylated lipopeptides and TLR2/6 dimers sensing diacylated lipopeptides. In addition, TLR2 also senses zymosan from fungi. The structure of the TLR1/2 dimer has been solved [2], as has the structure of TLR4 in complex with its ligand lipopolysacharide from Gram-negative bacteria that are presented to TLR4 by MD2 [3]. TLR4 can also sense F protein from respiratory syncyt
Effects of Spatial and Feature Attention on Disparity-Rendered Structure-From-Motion Stimuli in the Human Visual Cortex
Ifan Betina Ip, Holly Bridge, Andrew J. Parker
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0100074
Abstract: An important advance in the study of visual attention has been the identification of a non-spatial component of attention that enhances the response to similar features or objects across the visual field. Here we test whether this non-spatial component can co-select individual features that are perceptually bound into a coherent object. We combined human psychophysics and functional magnetic resonance imaging (fMRI) to demonstrate the ability to co-select individual features from perceptually coherent objects. Our study used binocular disparity and visual motion to define disparity structure-from-motion (dSFM) stimuli. Although the spatial attention system induced strong modulations of the fMRI response in visual regions, the non-spatial system’s ability to co-select features of the dSFM stimulus was less pronounced and variable across subjects. Our results demonstrate that feature and global feature attention effects are variable across participants, suggesting that the feature attention system may be limited in its ability to automatically select features within the attended object. Careful comparison of the task design suggests that even minor differences in the perceptual task may be critical in revealing the presence of global feature attention.
Benefits of Carrier Pocket Anisotropy to Thermoelectric Performance: The case of $p$-type AgBiSe$_2$
David Parker,Andrew F. May,David J. Singh
Physics , 2015,
Abstract: We study theoretically the effects of anisotropy on the thermoelectric performance of $p$-type AgBiSe$_2$. We present an apparent realization of the thermoelectric benefits of one-dimensional "plate-like" carrier pocket anisotropy in the valence band of this material. Based on first principles calculations we find a substantial anisotropy in the electronic structure, likely favorable for thermoelectric performance, in the valence bands of the hexagonal phase of the silver chalcogenide thermoelectric AgBiSe$_2$, while the conduction bands are more isotropic, and in our experiments do not attain high performance. AgBiSe$_2$ has already exhibited a $ZT$ value of 1.5 in a high-temperature disordered fcc phase, but room-temperature performance has not been demonstrated. We develop a theory for the ability of anisotropy to decouple the density-of-states and conductivity effective masses, pointing out the influence of this effect in the high performance thermoelectrics Bi$_2$Te$_3$ and PbTe. From our first principles and Boltzmann transport calculations we estimate the performance of $p$-type AgBiSe$_{2}$.
Tsetse Salivary Gland Hypertrophy Virus: Hope or Hindrance for Tsetse Control?
Adly M. M. Abd-Alla ,Andrew G. Parker,Marc J. B. Vreysen,Max Bergoin
PLOS Neglected Tropical Diseases , 2011, DOI: 10.1371/journal.pntd.0001220
Abstract: Many species of tsetse flies (Diptera: Glossinidae) are infected with a virus that causes salivary gland hypertrophy (SGH), and flies with SGH symptoms have a reduced fecundity and fertility. The prevalence of SGH in wild tsetse populations is usually very low (0.2%–5%), but higher prevalence rates (15.2%) have been observed occasionally. The successful eradication of a Glossina austeni population from Unguja Island (Zanzibar) using an area-wide integrated pest management approach with a sterile insect technique (SIT) component (1994–1997) encouraged several African countries, including Ethiopia, to incorporate the SIT in their national tsetse control programs. A large facility to produce tsetse flies for SIT application in Ethiopia was inaugurated in 2007. To support this project, a Glossina pallidipes colony originating from Ethiopia was successfully established in 1996, but later up to 85% of adult flies displayed symptoms of SGH. As a result, the colony declined and became extinct by 2002. The difficulties experienced with the rearing of G. pallidipes, epitomized by the collapse of the G. pallidipes colony originating from Ethiopia, prompted the urgent need to develop management strategies for the salivary gland hypertrophy virus (SGHV) for this species. As a first step to identify suitable management strategies, the virus isolated from G. pallidipes (GpSGHV) was recently sequenced and research was initiated on virus transmission and pathology. Different approaches to prevent virus replication and its horizontal transmission during blood feeding have been proposed. These include the use of antiviral drugs such as acyclovir and valacyclovir added to the blood for feeding or the use of antibodies against SGHV virion proteins. In addition, preliminary attempts to silence the expression of an essential viral protein using RNA interference will be discussed.
Repeat Prostate Biopsy Strategies after Initial Negative Biopsy: Meta-Regression Comparing Cancer Detection of Transperineal, Transrectal Saturation and MRI Guided Biopsy
Adam W. Nelson, Rebecca C. Harvey, Richard A. Parker, Christof Kastner, Andrew Doble, Vincent J. Gnanapragasam
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0057480
Abstract: Introduction There is no consensus on how to investigate men with negative transrectal ultrasound guided prostate biopsy (TRUS-B) but ongoing suspicion of cancer. Three strategies used are transperineal (TP-B), transrectal saturation (TS-B) and MRI-guided biopsy (MRI-B). We compared cancer yields of these strategies. Methods Papers were identified by search of Pubmed, Embase and Ovid Medline. Included studies investigated biopsy diagnostic yield in men with at least one negative TRUS-B and ongoing suspicion of prostate cancer. Data including age, PSA, number of previous biopsy episodes, number of cores at re-biopsy, cancer yield, and Gleason score of detected cancers were extracted. Meta-regression analyses were used to analyse the data. Results Forty-six studies were included; 12 of TS-B, 14 of TP-B, and 20 of MRI-B, representing 4,657 patients. Mean patient age, PSA and number of previous biopsy episodes were similar between the strategies. The mean number of biopsy cores obtained by TP-B and TS-B were greater than MRI-B. Cancer detection rates were 30·0%, 36·8%, and 37·6% for TS-B, TP-B, and MRI-B respectively. Meta-regression analysis showed that MRI-B had significantly higher cancer detection than TS-B. There were no significant differences however between MRI-B and TP-B, or TP-B and TS-B. In a sensitivity analysis incorporating number of previous biopsy episodes (36 studies) the difference between MRI-B and TP-B was not maintained resulting in no significant difference in cancer detection between the groups. There were no significant differences in median Gleason scores detected comparing the three strategies. Conclusions In the re-biopsy setting, it is unclear which strategy offers the highest cancer detection rate. MRI-B may potentially detect more prostate cancers than other modalities and can achieve this with fewer biopsy cores. However, well–designed prospective studies with standardised outcome measures are needed to accurately compare modalities and define an optimum re-biopsy approach.
Localization of MEG human brain responses to retinotopic visual stimuli with contrasting source reconstruction approaches
Nela Cicmil,Holly Bridge,Andrew J. Parker,Mark W. Woolrich,Kristine Krug
Frontiers in Neuroscience , 2014, DOI: 10.3389/fnins.2014.00127
Abstract: Magnetoencephalography (MEG) allows the physiological recording of human brain activity at high temporal resolution. However, spatial localization of the source of the MEG signal is an ill-posed problem as the signal alone cannot constrain a unique solution and additional prior assumptions must be enforced. An adequate source reconstruction method for investigating the human visual system should place the sources of early visual activity in known locations in the occipital cortex. We localized sources of retinotopic MEG signals from the human brain with contrasting reconstruction approaches (minimum norm, multiple sparse priors, and beamformer) and compared these to the visual retinotopic map obtained with fMRI in the same individuals. When reconstructing brain responses to visual stimuli that differed by angular position, we found reliable localization to the appropriate retinotopic visual field quadrant by a minimum norm approach and by beamforming. Retinotopic map eccentricity in accordance with the fMRI map could not consistently be localized using an annular stimulus with any reconstruction method, but confining eccentricity stimuli to one visual field quadrant resulted in significant improvement with the minimum norm. These results inform the application of source analysis approaches for future MEG studies of the visual system, and indicate some current limits on localization accuracy of MEG signals.
An Online Environment for Democratic Deliberation: Motivations, Principles, and Design
Todd Davies,Brendan O'Connor,Alex Cochran,Jonathan J. Effrat,Andrew Parker,Benjamin Newman,Aaron Tam
Computer Science , 2013,
Abstract: We have created a platform for online deliberation called Deme (which rhymes with 'team'). Deme is designed to allow groups of people to engage in collaborative drafting, focused discussion, and decision making using the Internet. The Deme project has evolved greatly from its beginning in 2003. This chapter outlines the thinking behind Deme's initial design: our motivations for creating it, the principles that guided its construction, and its most important design features. The version of Deme described here was written in PHP and was deployed in 2004 and used by several groups (including organizers of the 2005 Online Deliberation Conference). Other papers describe later developments in the Deme project (see Davies et al. 2005, 2008; Davies and Mintz 2009).
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