2024-03-29T01:07:47Zhttps://research-repository.st-andrews.ac.uk/oai/requestoai:research-repository.st-andrews.ac.uk:10023/4732019-04-01T10:36:27Zcom_10023_301com_10023_39com_10023_130com_10023_32col_10023_303col_10023_131
Endres, D M
Oram, M W
Schindelin, J.E.
Foldiak, P
Platt, J.C.
Koller, D.
Singer, Y.
Roweis, S.
393-400
2008-05-12T14:33:02Z
2008-05-12T14:33:02Z
2008
Advances in Neural Information Processing Systems 20 393-400 2008
StAndrews.ResExp.Output.OutputID.24452
http://hdl.handle.net/10023/473
http://books.nips.cc/nips20.html
The peristimulus time histogram (PSTH) and its more continuous cousin, the spike density function (SDF) are staples in the analytic toolkit of neurophysiologists. The former is usually obtained by binning spike trains, whereas the standard method for the latter is smoothing with a Gaussian kernel. Selection of a bin width or a kernel size is often done in an relatively arbitrary fashion, even though there have been recent attempts to remedy this situation. We develop an exact Bayesian, generative model approach to estimating PSTHs and demonstate its superiority to competing methods. Further advantages of our scheme include automatic complexity control and error bars on its predictions.
Postprint
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en
MIT Press
Advances in Neural Information Processing Systems 20
Copyright owner Massachusetts Institute of Technology Press
bioinformatics
Neuroscience
Bayesian methods
spiking neurons
Bayesian binning beats approximate alternatives: estimating peri-stimulus time histograms
Journal article
School : Psychology
Published
Peer reviewed
THUMBNAIL
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binsdf_nips2007endres_authorfinalversion.pdf.txt
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oai:research-repository.st-andrews.ac.uk:10023/473
2019-04-01 11:36:27.144
St Andrews Research Repository
Digital-Repository@st-andrews.ac.uk
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oai:research-repository.st-andrews.ac.uk:10023/25552023-04-18T09:44:58Zcom_10023_184com_10023_39com_10023_301com_10023_130com_10023_32com_10023_879com_10023_878col_10023_185col_10023_303col_10023_131col_10023_880
Claidiere, Nicolas
Bowler, Mark Timothy
Whiten, Andrew
The Wellcome Trust
University of St Andrews. School of Psychology and Neuroscience
University of St Andrews. Institute of Behavioural and Neural Sciences
University of St Andrews. ‘Living Links to Human Evolution’ Research Centre
University of St Andrews. Centre for Social Learning & Cognitive Evolution
2012-04-16T11:01:02Z
2012-04-16T11:01:02Z
2012-02-20
Claidiere , N , Bowler , M T & Whiten , A 2012 , ' Evidence for weak or linear conformity but not for hyper-conformity in an everyday social learning context ' , PLoS One , vol. 7 , no. 2 , e30970 . https://doi.org/10.1371/journal.pone.0030970
1932-6203
PURE: 19317236
PURE UUID: a640cfff-45ac-469a-bd18-efa2225faa81
Scopus: 84857400769
ORCID: /0000-0003-2426-5890/work/65014003
http://hdl.handle.net/10023/2555
https://doi.org/10.1371/journal.pone.0030970
094440/Z/10/Z
Conformity is thought to be an important force in cultural evolution because it has the potential to stabilize cooperation in large groups, potentiate group selection and thus explain uniquely human behaviors. However, the effects of such conformity on cultural and biological evolution will depend much on the way individuals are influenced by the frequency of alternative behavioral options witnessed. Theoretical modeling has suggested that only what we refer to as ‘hyper-conformity’, an exaggerated tendency to perform the most frequent behavior witnessed in other individuals, is able to increase within-group homogeneity and between-group diversity, for instance. Empirically however, few experiments have addressed how the frequency of behavior witnessed affects behavior. Accordingly we performed an experiment to test for the presence of conformity in a natural situation with humans. Visitors to a Zoo exhibit were invited to write or draw answers to questions on A5 cards and potentially win a small prize. We manipulated the proportion of existing writings versus drawings visible to visitors and measured the proportion of written cards submitted. We found a strong and significant effect of the proportion of text displayed on the proportion of text in the answers, thus demonstrating social learning. We show that this effect is approximately linear, with potentially a small, weak-conformist component but no hyper-conformist one. The present experiment therefore provides evidence for linear conformity in humans in a very natural context.
Publisher PDF
Peer reviewed
eng
PLoS One
© 2012 Claidière et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Cultural evolution
QL Zoology
QL
Evidence for weak or linear conformity but not for hyper-conformity in an everyday social learning context
Journal article
THUMBNAIL
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oai:research-repository.st-andrews.ac.uk:10023/2555
2023-04-18 10:44:58.935
St Andrews Research Repository
Digital-Repository@st-andrews.ac.uk
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oai:research-repository.st-andrews.ac.uk:10023/54432022-04-14T20:39:20Zcom_10023_184com_10023_39com_10023_301com_10023_130com_10023_32com_10023_879com_10023_878col_10023_185col_10023_303col_10023_131col_10023_880
Hunter, David William
Tiddeman, Bernard Paul
Perrett, David Ian
University of St Andrews. School of Psychology and Neuroscience
University of St Andrews. Institute of Behavioural and Neural Sciences
University of St Andrews. Centre for Social Learning & Cognitive Evolution
2014-09-18T09:31:01Z
2014-09-18T09:31:01Z
2012-02
Hunter , D W , Tiddeman , B P & Perrett , D I 2012 , ' A genetic algorithm for face fitting ' , Paper presented at GRAPP - International Conference on Computer Graphics Theory and Applications , Rome, Italy , United Kingdom , 24/02/12 - 26/02/12 pp. 115-120 . https://doi.org/10.5220/0003816101150120
conference
PURE: 20248043
PURE UUID: 418b9dc7-0654-4967-9732-6a89ddc25867
Scopus: 84862218570
ORCID: /0000-0002-6025-0939/work/64360959
http://hdl.handle.net/10023/5443
https://doi.org/10.5220/0003816101150120
Accurate estimation of the shape of human faces has many applications from computer-imaging to psychological research. One well known method is to fit a Three Dimensional Morphable Model to a target image. This method is attractive as the faces it constructs are already projected onto an orthogonal basis making further manipulation and analysis easier. So far its use in these fields has been limited the inaccuracy and inconvenience of current face-fitting methods. We present a method based on Genetic Algorithms that avoid the local minima and gradient image errors that current methods suffer from. It has the added advantage of requiring no manual interaction to initialise or guide the fitting process.
Postprint
Peer reviewed
6
eng
©2012. SCITEPRESS Lda. This is the accepted manuscript of a Conference Paper originally submitted to the International Conference on Computer Graphics Theory and Applications (GRAPP 2012) available from http://www.scitepress.org/DigitalLibrary/Link.aspx?doi=10.5220/0003816101150120
Genetic algorithm
Face recognition models
Three dimensional morphable models
QA75 Electronic computers. Computer science
QA75
A genetic algorithm for face fitting
Conference paper
THUMBNAIL
Final.pdf.jpg
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4450
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Final.pdf
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license.txt
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Final.pdf.txt
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24441
https://research-repository.st-andrews.ac.uk/bitstream/10023/5443/3/Final.pdf.txt
4d6bf480a5b9016bd79bd647c5be6f25
MD5
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10023/5443
oai:research-repository.st-andrews.ac.uk:10023/5443
2022-04-14 21:39:20.407
St Andrews Research Repository
Digital-Repository@st-andrews.ac.uk
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oai:research-repository.st-andrews.ac.uk:10023/50382023-04-18T09:51:38Zcom_10023_301com_10023_39com_10023_130com_10023_32com_10023_879com_10023_878col_10023_303col_10023_131col_10023_880
Li, Wenchang
Wagner, Monica Anne
Porter, Nicola Jean
The Royal Society
University of St Andrews. School of Psychology and Neuroscience
University of St Andrews. Institute of Behavioural and Neural Sciences
2014-07-17T14:31:01Z
2014-07-17T14:31:01Z
2014
Li , W , Wagner , M A & Porter , N J 2014 , ' Behavioral observation of xenopus tadpole swimming for neuroscience labs ' , Journal of Undergraduate Neuroscience Education , vol. 12 , no. 2 , pp. A107-A113 .
1544-2896
PURE: 117053509
PURE UUID: 846beb56-9694-4263-9026-ebacca91953b
Scopus: 84896349372
ORCID: /0000-0002-1179-6636/work/64361126
http://hdl.handle.net/10023/5038
http://www.funjournal.org/images/stories/downloads/2014_Volume_12_Issue_2/june-12-107.pdf
516002.K5880/ROG
Neuroscience labs benefit from reliable, easily - monitored neural responses mediated by well - studied neural pathways . Xenopus laevis tadpoles have been used as a simple vertebrate model preparation in motor control studies. Most of the neuronal pathways underlying different aspects of tadpole swimming behavior have been revealed. These include the skin mechanosensory touch and pineal eye light - sensing pathways whose activation can initiate swimming , and the cement gland pressure - sensing pathway responsible for stopping swimming. A simple transection in the hindbrain can cut off the pineal eye and cement gland pathways from the swimming circuit in the spinal cord, resulting in losses of corresponding functions. Additionally, some pharmacological experiments targeting neurotransmission can be designed to affect swimming and, fluorescence - conjugated α -bungarotoxin can be used to label nicotinic receptors at neuromuscular junctions. These experiments can be readily adapted for undergraduate neuroscience teaching labs. Possible expansions of some experiments for more sophisticated pharmacological or neurophysiological labs are also discussed.
Publisher PDF
Peer reviewed
7
eng
Journal of Undergraduate Neuroscience Education
© 2014 The Authors. This is an Open Access article published in the Journal of Undergraduate Neuroscience Education Spring 2014, available online: http://www.funjournal.org/
Xenopus
Tadpole
Swimming
Neuromuscular junction behaviour
Pharmacology
Physiology
QP Physiology
QP
Behavioral observation of xenopus tadpole swimming for neuroscience labs
Journal article
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oai:research-repository.st-andrews.ac.uk:10023/5038
2023-04-18 10:51:38.814
St Andrews Research Repository
Digital-Repository@st-andrews.ac.uk
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oai:research-repository.st-andrews.ac.uk:10023/53492022-04-12T11:30:28Zcom_10023_301com_10023_39com_10023_130com_10023_32com_10023_879com_10023_878col_10023_303col_10023_131col_10023_880
Zeiner, Katharina Maria
Spitschan, Manuel
Harris, Julie
The Leverhulme Trust
EPSRC
University of St Andrews. School of Psychology and Neuroscience
University of St Andrews. Institute of Behavioural and Neural Sciences
2014-09-04T23:01:37Z
2014-09-04T23:01:37Z
2014-03-05
2014-09-05
Zeiner , K M , Spitschan , M & Harris , J 2014 , ' Perceptual integration across natural monocular regions ' , Journal of Vision , vol. 14 , no. 3 , 5 . https://doi.org/10.1167/14.3.5
1534-7362
PURE: 97152271
PURE UUID: c7e49888-3ee8-4ac6-805f-58da17a4877d
Scopus: 84897078121
ORCID: /0000-0002-3497-4503/work/46085827
WOS: 000334344500005
http://hdl.handle.net/10023/5349
https://doi.org/10.1167/14.3.5
RF-2011-019
EP/G038708/1
Natural scenes contain hidden regions, or occlusions, that differ in the two eyes, resulting in monocular regions that can only be seen by one eye. Such monocular regions appear to not be suppressed but seem to be integrated into the scene percept. Here we explore how the two eyes' views are combined to represent a scene that contains monocular regions, partially hidden behind a foreground occluding “fence.” We measured performance in a density/numerosity discrimination task for scenes containing differing amounts of binocular and monocular information. We find that information from a number of separate monocular regions can be integrated into our overall percept of dot density/numerosity, although different observers use different strategies. If, however, both monocular and binocular information is present, observers appear to ignore the purely monocular regions, relying solely on the binocular information when making density/numerosity judgments. Our work suggests that binocular regions are favored over monocular regions, such that information from monocular regions is effectively ignored when binocular regions are present in a scene.
Publisher PDF
Peer reviewed
eng
Journal of Vision
Copyright 2014, ARVO. This is open access article.
Binocular vision
Half-occlusion
Occlusion
Monocular
Representation
BF Psychology
BF
Perceptual integration across natural monocular regions
Journal article
THUMBNAIL
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6236
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license.txt
license.txt
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JoV2014.pdf.txt
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10023/5349
oai:research-repository.st-andrews.ac.uk:10023/5349
2022-04-12 12:30:28.897
St Andrews Research Repository
Digital-Repository@st-andrews.ac.uk
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oai:research-repository.st-andrews.ac.uk:10023/27492022-07-08T10:30:03Zcom_10023_301com_10023_39com_10023_130com_10023_32com_10023_879com_10023_878col_10023_303col_10023_131col_10023_880
Harris, Julie
Chopin, Adrien
Zeiner, Katharina Maria
Hibbard, Paul Barry
The Leverhulme Trust
EPSRC
University of St Andrews. School of Psychology and Neuroscience
University of St Andrews. Institute of Behavioural and Neural Sciences
2012-06-12T14:31:02Z
2012-06-12T14:31:02Z
2012
Harris , J , Chopin , A , Zeiner , K M & Hibbard , P B 2012 , ' Perception of relative depth interval : Systematic biases in perceived depth ' , The Quarterly Journal of Experimental Psychology , vol. 65 , no. 1 , pp. 73-91 . https://doi.org/10.1080/17470218.2011.589520
1747-0218
PURE: 16281292
PURE UUID: ed53dba8-f578-4775-865a-ae13f283ad34
Scopus: 84859336897
ORCID: /0000-0002-3497-4503/work/46085840
http://hdl.handle.net/10023/2749
https://doi.org/10.1080/17470218.2011.589520
RF-2011-019
EP/G038708/1
Given an estimate of the binocular disparity between a pair of points and an estimate of the viewing distance, or knowledge of eye position, it should be possible to obtain an estimate of their depth separation. Here we show that, when points are arranged in different vertical geometric configurations across two intervals, many observers find this task difficult. Those who can do the task tend to perceive the depth interval in one configuration as very different from depth in the other configuration. We explore two plausible explanations for this effect. The first is the tilt of the empirical vertical horopter: Points perceived along an apparently vertical line correspond to a physical line of points tilted backwards in space. Second, the eyes can rotate in response to a particular stimulus. Without compensation for this rotation, biases in depth perception would result. We measured cyclovergence indirectly, using a standard psychophysical task, while observers viewed our depth configuration. Biases predicted from error due either to cyclovergence or to the tilted vertical horopter were not consistent with the depth configuration results. Our data suggest that, even for the simplest scenes, we do not have ready access to metric depth from binocular disparity.
Preprint
Peer reviewed
eng
The Quarterly Journal of Experimental Psychology
This is a preprint of an article whose final and definitive form has been published in The Quarterly Journal of Experimental Psychology © 2012, copyright Taylor & Francis and The Experimental Psychology Society. The Quarterly Journal of Experimental Psychology is available online at http://dx.doi.org/10.1080/17470218.2011.589520
Binocular disparity
Depth
Depth interval
Metric depth
Cyclovergence
Vertical horopter
BF Psychology
BF
Perception of relative depth interval : Systematic biases in perceived depth
Journal article
THUMBNAIL
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depth_bias_qjep_inpress.pdf.jpg
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oai:research-repository.st-andrews.ac.uk:10023/2749
2022-07-08 11:30:03.133
St Andrews Research Repository
Digital-Repository@st-andrews.ac.uk
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oai:research-repository.st-andrews.ac.uk:10023/36742023-04-18T09:47:54Zcom_10023_184com_10023_39com_10023_301com_10023_130com_10023_32com_10023_879com_10023_878col_10023_185col_10023_303col_10023_131col_10023_880
Arnold, Kate
Zuberbuehler, Klaus
University of St Andrews. School of Psychology and Neuroscience
University of St Andrews. Institute of Behavioural and Neural Sciences
University of St Andrews. Centre for Social Learning & Cognitive Evolution
2013-06-12T15:01:01Z
2013-06-12T15:01:01Z
2013-06-05
Arnold , K & Zuberbuehler , K 2013 , ' Female putty-nosed monkeys use experimentally altered contextual information to disambiguate the cause of male alarm calls ' , PLoS ONE , vol. 8 , no. 6 , e65660 . https://doi.org/10.1371/journal.pone.0065660
1932-6203
PURE: 51290969
PURE UUID: 7468cf02-ccde-4da8-bda4-6d9e58343e34
Scopus: 84878758053
ORCID: /0000-0001-8378-088X/work/64360641
http://hdl.handle.net/10023/3674
https://doi.org/10.1371/journal.pone.0065660
Funding was provided by The Leverhulme Trust (http://www.leverhulme.ac.uk/). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Many animal vocal signals are given in a wide range of contexts which can sometimes have little in common. Yet, to respond adaptively, listeners must find ways to identify the cause of a signal, or at least rule out alternatives. Here, we investigate the nature of this process in putty-nosed monkeys, a forest primate. In this species, adult males have a very restricted repertoire of vocalizations which are given in response to a wide variety of events occurring under conditions of limited visibility. We carried out a series of field playback experiments on females (N = 6) in a habituated group in Gashaka Gumti National Park, Nigeria, in which male alarm/loud calls were presented either alone, or following acoustic information that simulated the occurrence of natural disturbances. We demonstrate that listeners appear to integrate contextual information in order to distinguish among possible causes of calls. We conclude that, in many cases, pragmatic aspects of communication play a crucial role in call interpretation and place a premium on listeners' abilities to integrate information from different sources.
Publisher PDF
Peer reviewed
eng
PLoS ONE
© 2013 Arnold and Zuberbühler. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
QL Zoology
QL
Female putty-nosed monkeys use experimentally altered contextual information to disambiguate the cause of male alarm calls
Journal article
THUMBNAIL
Context_Arnold_Zuberbuhler.pdf.jpg
Context_Arnold_Zuberbuhler.pdf.jpg
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MD5
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Context_Arnold_Zuberbuhler.pdf.txt
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oai:research-repository.st-andrews.ac.uk:10023/3674
2023-04-18 10:47:54.847
St Andrews Research Repository
Digital-Repository@st-andrews.ac.uk
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oai:research-repository.st-andrews.ac.uk:10023/50662023-04-19T00:38:43Zcom_10023_301com_10023_39com_10023_130com_10023_32com_10023_879com_10023_878col_10023_303col_10023_131col_10023_880
MacKenzie, Andrew Kerr
Harris, Julie
University of St Andrews. School of Psychology and Neuroscience
University of St Andrews. Institute of Behavioural and Neural Sciences
2014-07-23T11:31:01Z
2014-07-23T11:31:01Z
2014-03-26
MacKenzie , A K & Harris , J 2014 , Characterizing Visual Attention during Driving and Non-driving Hazard Perception Tasks . in Proceedings of the Symposium on Eye Tracking Research and Applications . ACM siggraph , pp. 127-130 . https://doi.org/10.1145/2578153.2578171
9781450327510
PURE: 107268222
PURE UUID: 952c6430-4fbd-40d6-adae-dde8f58c53a4
Scopus: 84899674104
ORCID: /0000-0002-3497-4503/work/46085835
http://hdl.handle.net/10023/5066
https://doi.org/10.1145/2578153.2578171
Funding: EPSRC DTG
Research into driving skill, particularly of hazard perception, often involves studies where participants either view pictures of driving scenarios or use movie viewing paradigms. However oculomotor strategies tend to change between active and passive tasks and attentional limitations are introduced during real driving. Here we present a study using eye tracking methods, to contrast oculomotor behaviour differences across a passive video based hazard perception task and an active hazard perception simulated driving task. The differences presented highlight a requirement to study driving skill under more active conditions, where the participant is engaged with a driving task. Our results suggest that more standard, passive tests, may have limited utility when developing visual models of driving behaviour. The results presented here have implications for driver safety measures and provide further insights into how vision and action interact during natural activity.
Postprint
eng
ACM siggraph
Proceedings of the Symposium on Eye Tracking Research and Applications
© 2014. ACM. This is an Accepted Manuscript of an article published in the ETRA '14 Proceedings of the Symposium on Eye Tracking Research, available online: http://dx.doi.org/10.1145/2578153.2578171
Eye movements and cognition
Visual search behaviour
Scanning strategies
Natural scene perception
BF Psychology
BF
Characterizing Visual Attention during Driving and Non-driving Hazard Perception Tasks
Conference item
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oai:research-repository.st-andrews.ac.uk:10023/5066
2023-04-19 01:38:43.752
St Andrews Research Repository
Digital-Repository@st-andrews.ac.uk
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oai:research-repository.st-andrews.ac.uk:10023/30772022-04-26T08:30:04Zcom_10023_301com_10023_39com_10023_130com_10023_32com_10023_879com_10023_878col_10023_303col_10023_131col_10023_880
Harding, Glen
Harris, Julie
Bloj, Marina
EPSRC
University of St Andrews. School of Psychology and Neuroscience
University of St Andrews. Institute of Behavioural and Neural Sciences
2012-09-19T11:31:05Z
2012-09-19T11:31:05Z
2012-04-30
Harding , G , Harris , J & Bloj , M 2012 , ' Learning to use illumination gradients as an unambiguous cue to three dimensional shape ' , PLoS One , vol. 7 , no. 4 , e35950 . https://doi.org/10.1371/journal.pone.0035950
1932-6203
PURE: 20133413
PURE UUID: 864e4987-54d2-4cb6-a3c9-80ecffdae202
Scopus: 84860456844
ORCID: /0000-0002-3497-4503/work/46085826
http://hdl.handle.net/10023/3077
https://doi.org/10.1371/journal.pone.0035950
EP/G038708/1
The luminance and colour gradients across an image are the result of complex interactions between object shape, material and illumination. Using such variations to infer object shape or surface colour is therefore a difficult problem for the visual system. We know that changes to the shape of an object can affect its perceived colour, and that shading gradients confer a sense of shape. Here we investigate if the visual system is able to effectively utilise these gradients as a cue to shape perception, even when additional cues are not available. We tested shape perception of a folded card object that contained illumination gradients in the form of shading and more subtle effects such as inter-reflections. Our results suggest that observers are able to use the gradients to make consistent shape judgements. In order to do this, observers must be given the opportunity to learn suitable assumptions about the lighting and scene. Using a variety of different training conditions, we demonstrate that learning can occur quickly and requires only coarse information. We also establish that learning does not deliver a trivial mapping between gradient and shape; rather learning leads to the acquisition of assumptions about lighting and scene parameters that subsequently allow for gradients to be used as a shape cue. The perceived shape is shown to be consistent for convex and concave versions of the object that exhibit very different shading, and also similar to that delivered by outline, a largely unrelated cue to shape. Overall our results indicate that, although gradients are less reliable than some other cues, the relationship between gradients and shape can be quickly assessed and the gradients therefore used effectively as a visual shape cue.
Publisher PDF
Peer reviewed
eng
PLoS One
© 2012 Harding et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
RC0321 Neuroscience. Biological psychiatry. Neuropsychiatry
RC0321
Learning to use illumination gradients as an unambiguous cue to three dimensional shape
Journal article
THUMBNAIL
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oai:research-repository.st-andrews.ac.uk:10023/3077
2022-04-26 09:30:04.02
St Andrews Research Repository
Digital-Repository@st-andrews.ac.uk
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oai:research-repository.st-andrews.ac.uk:10023/47892023-04-18T09:48:23Zcom_10023_301com_10023_39com_10023_130com_10023_32com_10023_879com_10023_878col_10023_303col_10023_131col_10023_880
Müller, Hans-Peter
Grön, Georg
Sprengelmeyer, Reiner
Kassubek, Jan
Ludolph, Albert C.
Hobbs, Nicola
Cole, James
Roos, Raymund A.C.
Duerr, Alexandra
Tabrizi, Sarah J.
Landwehrmeyer, G. Bernhard
Süssmuth, Sigurd D.
University of St Andrews. School of Psychology and Neuroscience
University of St Andrews. Institute of Behavioural and Neural Sciences
2014-05-14T12:31:00Z
2014-05-14T12:31:00Z
2013
Müller , H-P , Grön , G , Sprengelmeyer , R , Kassubek , J , Ludolph , A C , Hobbs , N , Cole , J , Roos , R A C , Duerr , A , Tabrizi , S J , Landwehrmeyer , G B & Süssmuth , S D 2013 , ' Evaluating multicenter DTI data in Huntington's disease on site specific effects : an ex post facto approach ' , Neuroimage: Clinical , vol. 2 , pp. 161-167 . https://doi.org/10.1016/j.nicl.2012.12.005
PURE: 61428302
PURE UUID: 55da85a5-7157-42f6-a271-9bdac888ab0b
RIS: urn:09F109A635C85407EF2521A5F662EB51
Scopus: 84872740490
ORCID: /0000-0002-3083-5995/work/64697279
http://hdl.handle.net/10023/4789
https://doi.org/10.1016/j.nicl.2012.12.005
Purpose: Assessment of the feasibility to average diffusion tensor imaging (DTI) metrics of MRI data acquired in the course of a multicenter study. Materials and methods: Sixty-one early stage Huntington's disease patients and forty healthy controls were studied using four different MR scanners at four European sites with acquisition protocols as close as possible to a given standard protocol. The potential and feasibility of averaging data acquired at different sites was evaluated quantitatively by region-of-interest (ROI) based statistical comparisons of coefficients of variation (CV) across centers, as well as by testing for significant group-by-center differences on averaged fractional anisotropy (FA) values between patients and controls. In addition, a whole-brain based statistical between-group comparison was performed using FA maps. Results: The ex post facto statistical evaluation of CV and FA-values in a priori defined ROIs showed no differences between sites above chance indicating that data were not systematically biased by center specific factors. Conclusion: Averaging FA-maps from DTI data acquired at different study sites and different MR scanner types does not appear to be systematically biased. A suitable recipe for testing on the possibility to pool multicenter DTI data is provided to permit averaging of DTI-derived metrics to differentiate patients from healthy controls at a larger scale.
Publisher PDF
Peer reviewed
7
eng
Neuroimage: Clinical
© 2013 The Authors. Published by Elsevier Inc. All rights reserved. This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike License, which permits non-commercial use, distribution, and reproduction in any medium, provided the original author and source are credited.
Multicenter study
Diffusion tensor imaging
Fractional anisotropy
Huntington's disease
R Medicine (General)
R1
Evaluating multicenter DTI data in Huntington's disease on site specific effects : an ex post facto approach
Journal article
THUMBNAIL
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oai:research-repository.st-andrews.ac.uk:10023/4789
2023-04-18 10:48:23.767
St Andrews Research Repository
Digital-Repository@st-andrews.ac.uk
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oai:research-repository.st-andrews.ac.uk:10023/38612022-04-26T08:30:12Zcom_10023_301com_10023_39com_10023_130com_10023_32com_10023_879com_10023_878col_10023_303col_10023_131col_10023_880
Clery, Stephane
Bloj, Marina
Harris, Julie
EPSRC
University of St Andrews. School of Psychology and Neuroscience
University of St Andrews. Institute of Behavioural and Neural Sciences
2013-07-23T12:01:01Z
2013-07-23T12:01:01Z
2013-04-18
Clery , S , Bloj , M & Harris , J 2013 , ' Interactions between luminance and colour signals : effects on shape ' , Journal of Vision , vol. 13 , no. 5 , 16 . https://doi.org/10.1167/13.5.16
1534-7362
PURE: 48195193
PURE UUID: 0dbcd78f-c58c-40bb-a616-020e28479466
Scopus: 84878356283
ORCID: /0000-0002-3497-4503/work/46085844
http://hdl.handle.net/10023/3861
https://doi.org/10.1167/13.5.16
http://www.journalofvision.org/content/13/5/16.full
EP/G038708/1
This research was supported by the Engineering and Physical Sciences Research Council (EPSRC).
Although luminance and color are thought to be processed independently at early stages of visual processing, there is evidence that they interact at later stages. For example, chromatic information has been shown to enhance or suppress depth from luminance depending on whether chromatic edges are aligned or orthogonal with luminance edges. Here we explored more generally how chromatic information interacts with luminance information that specifies shape from shading. Using a depth-matching task, we measured perceived depth in sinusoidal and square-wave gratings (specifying close-to sinusoidal and triangle-wave depth profiles, respectively) in three conditions. In the first, as we varied luminance contrast in the presence of an orthogonal chromatic grating, perceived depth increased (consistent with classical shape from shading). When we held the luminance at a fixed contrast and varied the chromatic grating in the other two conditions (orthogonal or aligned), we found large and inconsistent individual differences. Some participants exhibited the expected pattern of enhancement and suppression, but most did not, either for the sinusoidal or square-wave stimuli. Our results cast doubt on the idea that the interaction demonstrates a single high-level heuristic linked to depth perception. Instead, we speculate that interactions are more likely due to early cross-channel masking
Publisher PDF
Peer reviewed
eng
Journal of Vision
Copyright © 2013 by the Association for Research in Vision and Ophthalmology. This article was made open access through BIS OA funding.
Colour-luminance interaction
Colour contrast
Luminance contrast
Q Science
Q
Interactions between luminance and colour signals : effects on shape
Journal article
THUMBNAIL
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Vision2013.pdf.txt
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oai:research-repository.st-andrews.ac.uk:10023/3861
2022-04-26 09:30:12.729
St Andrews Research Repository
Digital-Repository@st-andrews.ac.uk
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oai:research-repository.st-andrews.ac.uk:10023/166362023-04-18T23:47:32Zcom_10023_45com_10023_17com_10023_2323com_10023_39com_10023_301com_10023_792com_10023_879com_10023_878col_10023_46col_10023_2324col_10023_303col_10023_795col_10023_880
Vogogias, Athanasios
Kennedy, Jessie
Archambault, Daniel
Bach, Benjamin
Smith, V Anne
Currant, Hannah
University of St Andrews. School of Biology
University of St Andrews. Scottish Oceans Institute
University of St Andrews. Institute of Behavioural and Neural Sciences
University of St Andrews. Centre for Biological Diversity
2018-12-06T16:30:08Z
2018-12-06T16:30:08Z
2018-11
2018-11-28
Vogogias , A , Kennedy , J , Archambault , D , Bach , B , Smith , V A & Currant , H 2018 , ' BayesPiles : visualisation support for Bayesian network structure learning ' , ACM Transactions on Intelligent Systems and Technology , vol. 10 , no. 1 , 5 . https://doi.org/10.1145/3230623
2157-6904
PURE: 252830854
PURE UUID: e1b4c0c9-92ce-409a-9494-3bf1f97f11a6
Scopus: 85057586933
ORCID: /0000-0002-0487-2469/work/51470191
WOS: 000458017400005
http://hdl.handle.net/10023/16636
https://doi.org/10.1145/3230623
We address the problem of exploring, combining, and comparing large collections of scored, directed networks for understanding inferred Bayesian networks used in biology. In this field, heuristic algorithms explore the space of possible network solutions, sampling this space based on algorithm parameters and a network score that encodes the statistical fit to the data. The goal of the analyst is to guide the heuristic search and decide how to determine a final consensus network structure, usually by selecting the top-scoring network or constructing the consensus network from a collection of high-scoring networks. BayesPiles, our visualisation tool, helps with understanding the structure of the solution space and supporting the construction of a final consensus network that is representative of the underlying dataset. BayesPiles builds upon and extends MultiPiles to meet our domain requirements. We developed BayesPiles in conjunction with computational biologists who have used this tool on datasets used in their research. The biologists found our solution provides them with new insights and helps them achieve results that are representative of the underlying data.
Postprint
Peer reviewed
23
eng
ACM Transactions on Intelligent Systems and Technology
© 2018, Association for Computing Machinery. This work has been made available online in accordance with the publisher’s policies. This is the author created, accepted version manuscript following peer review and may differ slightly from the final published version. The final published version of this work is available at https://doi.org/10.1145/3230623
Visualisation
Graphs
Bioinformatics
QA75 Electronic computers. Computer science
QA76 Computer software
QH301 Biology
NDAS
QA75
QA76
QH301
BayesPiles : visualisation support for Bayesian network structure learning
Journal article
TEXT
Vogogias_2018_BayesPiles_ACMTIST_AAM.pdf.txt
Vogogias_2018_BayesPiles_ACMTIST_AAM.pdf.txt
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MD5
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THUMBNAIL
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Vogogias_2018_BayesPiles_ACMTIST_AAM.pdf
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MD5
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LICENSE
license.txt
license.txt
text/plain
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08270a77feb23c60a16676b3309cc4cb
MD5
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10023/16636
oai:research-repository.st-andrews.ac.uk:10023/16636
2023-04-19 00:47:32.87
St Andrews Research Repository
Digital-Repository@st-andrews.ac.uk
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oai:research-repository.st-andrews.ac.uk:10023/27462023-04-18T09:43:04Zcom_10023_301com_10023_39com_10023_130com_10023_32com_10023_879com_10023_878col_10023_303col_10023_131col_10023_880
Nefs, Harold
Harris, Julie
EPSRC
University of St Andrews. School of Psychology and Neuroscience
University of St Andrews. Institute of Behavioural and Neural Sciences
2012-06-12T14:01:01Z
2012-06-12T14:01:01Z
2010
Nefs , H & Harris , J 2010 , ' What visual information is used for stereoscopic depth displacement discrimination? ' , Perception , vol. 39 , no. 6 , pp. 727-744 . https://doi.org/10.1068/p6284
0301-0066
PURE: 5286037
PURE UUID: c6e45681-764b-4c4a-b574-24dd651681fa
Scopus: 77954811759
ORCID: /0000-0002-3497-4503/work/46085843
http://hdl.handle.net/10023/2746
https://doi.org/10.1068/p6284
EP/D002281/1
There are two ways to detect a displacement in stereoscopic depth, namely by monitoring the change in disparity over time (CDOT) or by monitoring the inter-ocular velocity difference (IOVD). Though previous studies have attempted to understand which cue is most significant for the visual system, none have designed stimuli that provide a comparison in terms of relative efficiency between them. Here we used two-frame motion and random dot noise to deliver equivalent strengths of CDOT and IOVD information to the visual system. Using three kinds of random dot stimuli, we were able to isolate CDOT or IOVD or deliver both simultaneously. The proportion of dots delivering CDOT or IOVD signals could be varied, and we defined discrimination threshold as the proportion needed to detect the direction of displacement (towards or away)1. Thresholds were similar for stimuli containing CDOT only, and containing both CDOT and IOVD, but only one participant was able to consistently perceive the displacement for stimuli containing only IOVD. We also investigated the effect of disparity pedestals on discrimination. Performance was best when the displacement crossed the reference plane, but was not significantly different for stimuli containing CDOT only, or containing both CDOT and IOVD. When stimuli are specifically designed to provide equivalent two-frame motion or disparity-change, few participants can reliably detect displacement when IOVD is the only cue. This challenges the notion that IOVD is involved in the discrimination of direction of displacement in two-frame motion displays.
Preprint
Peer reviewed
eng
Perception
The definitive, peer-reviewed and edited version of this article is published in Perception 39(6) 727-744. doi:10.1068/p6284 Copyright (c) Pion, 2010.
BF Psychology
BF
What visual information is used for stereoscopic depth displacement discrimination?
Journal article
THUMBNAIL
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10023/2746
oai:research-repository.st-andrews.ac.uk:10023/2746
2023-04-18 10:43:04.12
St Andrews Research Repository
Digital-Repository@st-andrews.ac.uk
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oai:research-repository.st-andrews.ac.uk:10023/72342023-04-18T10:02:01Zcom_10023_301com_10023_39com_10023_130com_10023_32com_10023_879com_10023_878col_10023_303col_10023_131col_10023_880
Acton, David
Miles, Gareth B.
The Wellcome Trust
University of St Andrews. School of Psychology and Neuroscience
University of St Andrews. Institute of Behavioural and Neural Sciences
2015-08-14T14:40:01Z
2015-08-14T14:40:01Z
2015-08-07
Acton , D & Miles , G B 2015 , ' Stimulation of glia reveals modulation of mammalian spinal motor networks by adenosine ' , PLoS One , vol. 10 , no. 8 , e0134488 . https://doi.org/10.1371/journal.pone.0134488
1932-6203
PURE: 209627040
PURE UUID: 2f87c0dc-a3c7-4b88-861f-817893132474
RIS: urn:61276D036968375E034A220001F744CA
Scopus: 84941922403
ORCID: /0000-0002-8624-4625/work/42734891
WOS: 000359121100060
http://hdl.handle.net/10023/7234
https://doi.org/10.1371/journal.pone.0134488
097831/z/11/z
This work was funded by the Wellcome Trust Institutional Strategic Support Fund for University of St. Andrews.
Despite considerable evidence that glia can release modulators to influence the excitability of neighbouring neurons, the importance of gliotransmission for the operation of neural networks and in shaping behaviour remains controversial. Here we characterise the contribution of glia to the modulation of the mammalian spinal central pattern generator for locomotion, the output of which is directly relatable to a defined behaviour. Glia were stimulated by specific activation of protease-activated receptor-1 (PAR1), an endogenous G-protein coupled receptor preferentially expressed by spinal glia during ongoing activity of the spinal central pattern generator for locomotion. Selective activation of PAR1 by the agonist TFLLR resulted in a reversible reduction in the frequency of locomotor-related bursting recorded from ventral roots of spinal cord preparations isolated from neonatal mice. In the presence of the gliotoxins methionine sulfoximine or fluoroacetate, TFLLR had no effect, confirming the specificity of PAR1 activation to glia. The modulation of burst frequency upon PAR1 activation was blocked by the non-selective adenosine-receptor antagonist theophylline and by the A1-receptor antagonist 8-cyclopentyl-1,3-dipropylxanthine, but not by the A2A-receptor antagonist SCH5826, indicating production of extracellular adenosine upon glial stimulation, followed by A1-receptor mediated inhibition of neuronal activity. Modulation of network output following glial stimulation was also blocked by the ectonucleotidase inhibitor ARL67156, indicating glial release of ATP and its subsequent degradation to adenosine rather than direct release of adenosine. Glial stimulation had no effect on rhythmic activity recorded following blockade of inhibitory transmission, suggesting that glial cell-derived adenosine acts via inhibitory circuit components to modulate locomotor-related output. Finally, the modulation of network output by endogenous adenosine was found to scale with the frequency of network activity, implying activity-dependent release of adenosine. Together, these data indicate that glia play an active role in the modulation of mammalian locomotor networks, providing negative feedback control that may stabilise network activity.
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PLoS One
Copyright: © 2015 Acton, Miles. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
BF Psychology
NDAS
BDC
BF
Stimulation of glia reveals modulation of mammalian spinal motor networks by adenosine
Journal article
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oai:research-repository.st-andrews.ac.uk:10023/4942019-04-01T10:39:23Zcom_10023_301com_10023_39com_10023_130com_10023_32col_10023_303col_10023_131
Foldiak, P
Endres, D M
2984
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2008-05-28T08:15:13Z
2008
Scholarpedia 3(1): 2984 January 2008
StAndrews.ResExp.Output.OutputID.17616
http://hdl.handle.net/10023/494
http://www.scholarpedia.org/article/Sparse_coding
The(frequently updated) original version is avalable at http://www.scholarpedia.org/article/Sparse_coding
Mammalian brains consist of billions of neurons, each capable of independent electrical activity. Information in the brain is represented by the pattern of activation of this large neural population, forming a neural code. The neural code defines what pattern of neural activity corresponds to each represented information item. In the sensory system, such items may indicate the presence of a stimulus object or the value of some stimulus parameter, assuming that each time this item is represented the neural activity pattern will be the same or at least similar. One important and relatively simple property of this code is the fraction of neurons that are strongly active at any one time. For a set of N binary neurons (which can either be 'active' or 'inactive'), the average (i.e., expected value) of this fraction across all information items is the sparseness of the code. This average fraction can vary from close to 0 to about 1/2. Average fractions above 1/2 can always be decreased below 1/2 without loss of information by replacing each active neuron with an inactive one, and vice versa. Sparse coding is the representation of items by the strong activation of a relatively small set of neurons. For each stimulus, this is a different subset of all available neurons.
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sparse coding
computational neuroscience
neurons
neural code
Sparse coding
Journal article
School : Psychology
Published
Peer reviewed
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St Andrews Research Repository
Digital-Repository@st-andrews.ac.uk
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oai:research-repository.st-andrews.ac.uk:10023/42432023-04-25T23:35:07Zcom_10023_301com_10023_39com_10023_130com_10023_32com_10023_879com_10023_878col_10023_303col_10023_131col_10023_880
Coetzee, Vinet
Barrett, L.
Greeff, J.M.
Henzi, S.P.
Perrett, David Ian
Wadee, A.A.
University of St Andrews. School of Psychology and Neuroscience
University of St Andrews. Institute of Behavioural and Neural Sciences
2013-12-03T10:01:06Z
2013-12-03T10:01:06Z
2007-07
Coetzee , V , Barrett , L , Greeff , J M , Henzi , S P , Perrett , D I & Wadee , A A 2007 , ' Common HLA alleles associated with health, but not with facial attractiveness ' , PLoS ONE , vol. 2 , no. 7 , e640 . https://doi.org/10.1371/journal.pone.0000640
1932-6203
PURE: 5516269
PURE UUID: 6a3c5edb-afc8-4d4f-a8f5-d96a332cd79e
Scopus: 39849093592
ORCID: /0000-0002-6025-0939/work/64360916
http://hdl.handle.net/10023/4243
https://doi.org/10.1371/journal.pone.0000640
This material is based, in part, upon work supported by the National Research Foundation under Grant number 2053809 to JMG.
Three adaptive hypotheses have been proposed to explain the link between the human leucocyte antigen (HLA) genes, health measures and facial attractiveness: inbreeding avoidance, heterozygote advantage and frequency-dependent selection. This paper reports findings that support a new hypothesis relating HLA to health. We suggest a new method to quantify the level of heterozygosity. HLA heterozygosity did not significantly predict health measures in women, but allele frequency did. Women with more common HLA alleles reported fewer cold and flu bouts per year, fewer illnesses in the previous year and rated themselves healthier than women with rare alleles. To our knowledge, this is the first study to show a positive correlation between HLA allele frequency and general health measures. We propose that certain common HLA alleles confer resistance to prevalent pathogens. Nevertheless, neither HLA heterozygosity nor allele frequency significantly predicted how healthy or attractive men rated the female volunteers. Three non-mutually exclusive explanations are put forward to explain this finding.
Publisher PDF
Peer reviewed
eng
PLoS ONE
© 2007 Coetzee et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Human leucocyte antigen (HLA) genes
Health measures
Facial attractiveness
Inbreeding avoidance
Heterozygote advantage
Frequency-dependent selection
SDG 3 - Good Health and Well-being
Common HLA alleles associated with health, but not with facial attractiveness
Journal article
THUMBNAIL
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oai:research-repository.st-andrews.ac.uk:10023/4243
2023-04-26 00:35:07.912
St Andrews Research Repository
Digital-Repository@st-andrews.ac.uk
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oai:research-repository.st-andrews.ac.uk:10023/75812023-04-25T23:41:46Zcom_10023_45com_10023_17com_10023_301com_10023_39com_10023_181com_10023_792com_10023_309com_10023_879com_10023_878col_10023_46col_10023_303col_10023_182col_10023_795col_10023_311col_10023_880
Hooker, Sascha Kate
Barychka, Tatsiana
Jessopp, Mark J
Staniland, Iain J
The Royal Society
University of St Andrews. School of Biology
University of St Andrews. Marine Alliance for Science & Technology Scotland
University of St Andrews. Scottish Oceans Institute
University of St Andrews. Institute of Behavioural and Neural Sciences
University of St Andrews. St Andrews Sustainability Institute
University of St Andrews. Sea Mammal Research Unit
2015-10-01T23:12:40Z
2015-10-01T23:12:40Z
2015-09-29
Hooker , S K , Barychka , T , Jessopp , M J & Staniland , I J 2015 , ' Images as proximity sensors : the incidence of conspecific foraging in Antarctic fur seals ' , Animal Biotelemetry , vol. 3 , 37 . https://doi.org/10.1186/s40317-015-0083-2
2050-3385
PURE: 193890101
PURE UUID: 5e5e860f-a9b1-42aa-af33-c701de5b7611
Scopus: 85018192858
ORCID: /0000-0002-7518-3548/work/47136149
http://hdl.handle.net/10023/7581
https://doi.org/10.1186/s40317-015-0083-2
Background: Although there have been recent advances in the development of animal-attached ‘proximity’ tags to remotely record the interactions of multiple individuals, the efficacy of these devices depends on the instrumentation of sufficient animals that subsequently have spatial interactions. Among densely colonial mammals such as fur seals, this remains logistically difficult, and interactions between animals during foraging have not previously been recorded. Results: We collected data on conspecific interactions during diving at sea using still image and video cameras deployed on 23 Antarctic fur seals. Animals carried cameras for a total of 152 days, collecting 38,098 images and 369 movies (total time 7.35 h). Other fur seals were detected in 74% of deployments, with a maximum of five seals seen at one time (n = 122 images, 28 videos). No predators other than conspecifics were observed. Detection was primarily limited by light conditions, since conspecifics were usually further from each other than the 1-m range illuminated by camera flash under low light levels. Other seals were recorded at a range of depths (average 27 ± 14.3 m, max 66 m). In terms of bouts of dives, still images of other seals were recorded in 5 single dives (of 330) and 28 bouts of dives <2 min apart (of 187). Linear mixed models suggested a relationship between conspecific observations per dive and the number of krill images recorded per dive. Using light conditions as a proxy for detectability, other seals were more likely to be observed at the bottom of dives than during descent or ascent. Seals were also more likely to be closer to each other and oriented perpendicular to each other at the bottom of dives, and in the same direction as each other during ascent. Conclusions: These results are contrary to animal-attached camera observations of penguin foraging, suggesting differing group-foraging tactics for these marine predators. Group foraging could have consequences for models linking predator behaviour to prey field densities since this relationship may be affected by the presence of multiple predators at the same patch.
Publisher PDF
Peer reviewed
11
eng
Animal Biotelemetry
© 2015 Hooker et al. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
Pinniped
Animal-attached camera
Sociality
Foraging
Groups
Arctocephalus gazella
QH301 Biology
SDG 14 - Life Below Water
QH301
Images as proximity sensors : the incidence of conspecific foraging in Antarctic fur seals
Journal article
THUMBNAIL
hooker2015animalbiotelem37.pdf.jpg
hooker2015animalbiotelem37.pdf.jpg
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hooker2015animalbiotelem37.pdf
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hooker2015animalbiotelem37.pdf.txt
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10023/7581
oai:research-repository.st-andrews.ac.uk:10023/7581
2023-04-26 00:41:46.225
St Andrews Research Repository
Digital-Repository@st-andrews.ac.uk
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oai:research-repository.st-andrews.ac.uk:10023/39192023-04-18T09:46:20Zcom_10023_45com_10023_17com_10023_175com_10023_39com_10023_301com_10023_126com_10023_31com_10023_879com_10023_878col_10023_46col_10023_176col_10023_303col_10023_128col_10023_880
Rudhall, Andrew Peter
Antkowiak, Maciej
Tsampoula, Xanthi
Mazilu, Michael
Metzger, N Klaus
Gunn-Moore, Frank J
Dholakia, Kishan
University of St Andrews. School of Biology
University of St Andrews. Institute of Behavioural and Neural Sciences
University of St Andrews. Biomedical Sciences Research Complex
University of St Andrews. School of Physics and Astronomy
2013-08-05T16:01:01Z
2013-08-05T16:01:01Z
2012
Rudhall , A P , Antkowiak , M , Tsampoula , X , Mazilu , M , Metzger , N K , Gunn-Moore , F J & Dholakia , K 2012 , ' Exploring the ultrashort pulse laser parameter space for membrane permeabilisation in mammalian cells. ' , Nature Science Reports , vol. 2 , no. 858 , pp. 1-5 . https://doi.org/10.1038/srep00858
PURE: 27611994
PURE UUID: 35faf452-b6b9-48e9-90e8-fdbe5b0136dc
Scopus: 84870814873
ORCID: /0000-0003-3422-3387/work/34730443
http://hdl.handle.net/10023/3919
https://doi.org/10.1038/srep00858
The use of ultrashort femtosecond pulsed lasers to effect membrane permeabilisation and initiate both optoinjection and transfection of cells has recently seen immense interest. We investigate femtosecond laser-induced membrane permeabilisation in mammalian cells as a function of pulse duration, pulse energy and number of pulses, by quantifying the efficiency of optoinjection for these parameters. Depending on pulse duration and pulse energy we identify two distinct membrane permeabilisation regimes. In the first regime a nonlinear dependence of order 3.4-9.6 is exhibited below a threshold peak power of at least 6 kW. Above this threshold peak power, the nonlinear dependence is saturated resulting in linear behaviour. This indicates that the membrane permeabilisation mechanism requires efficient multiphoton absorption to produce free electrons but once this process saturates, linear absorption dominates. Our experimental findings support a previously proposed theoretical model and provide a step towards the optimisation of laser-mediated gene delivery into mammalian cells.
Publisher PDF
Peer reviewed
eng
Nature Science Reports
© 2012 Nature Publishing Group. This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-nd/3.0/
Ultrashort femtosecond pulsed lasers
Membrane permeabilisation
Mammalian cells
Q Science
Q
Exploring the ultrashort pulse laser parameter space for membrane permeabilisation in mammalian cells.
Journal article
THUMBNAIL
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srep00858.pdf.txt
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oai:research-repository.st-andrews.ac.uk:10023/3919
2023-04-18 10:46:20.991
St Andrews Research Repository
Digital-Repository@st-andrews.ac.uk
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oai:research-repository.st-andrews.ac.uk:10023/42342022-04-26T11:30:20Zcom_10023_45com_10023_17com_10023_175com_10023_39com_10023_1943com_10023_24com_10023_301com_10023_48com_10023_16com_10023_126com_10023_31com_10023_879com_10023_878col_10023_46col_10023_176col_10023_1944col_10023_303col_10023_49col_10023_128col_10023_880
Mitchell, C.A.
Kalies, S.
Cizmár, T.
Heisterkamp, A.
Torrance, L.
Roberts, A.G.
Gunn-Moore, F.J.
Dholakia, K.
EPSRC
EPSRC
University of St Andrews. School of Biology
University of St Andrews. University of St Andrews
University of St Andrews. School of Physics and Astronomy
University of St Andrews. School of Medicine
University of St Andrews. Geography & Sustainable Development
University of St Andrews. Institute of Behavioural and Neural Sciences
University of St Andrews. Biomedical Sciences Research Complex
2013-12-02T10:31:02Z
2013-12-02T10:31:02Z
2013-11-14
Mitchell , C A , Kalies , S , Cizmár , T , Heisterkamp , A , Torrance , L , Roberts , A G , Gunn-Moore , F J & Dholakia , K 2013 , ' Femtosecond optoinjection of intact tobacco BY-2 cells using a reconfigurable photoporation platform ' , PLoS One , vol. 8 , no. 11 , e79235 . https://doi.org/10.1371/journal.pone.0079235
1932-6203
PURE: 71205869
PURE UUID: eae2748c-d5e9-4cb7-92b4-718acd4e1100
Scopus: 84893643628
Scopus: 84893643628
ORCID: /0000-0003-3422-3387/work/34730434
http://hdl.handle.net/10023/4234
https://doi.org/10.1371/journal.pone.0079235
EP/H045368/1
EP/J01771X/1
A tightly-focused ultrashort pulsed laser beam incident upon a cell membrane has previously been shown to transiently increase cell membrane permeability while maintaining the viability of the cell, a technique known as photoporation. This permeability can be used to aid the passage of membrane-impermeable biologically-relevant substances such as dyes, proteins and nucleic acids into the cell. Ultrashort-pulsed lasers have proven to be indispensable for photoporating mammalian cells but they have rarely been applied to plant cells due to their larger sizes and rigid and thick cell walls, which significantly hinders the intracellular delivery of exogenous substances. Here we demonstrate and quantify femtosecond optical injection of membrane impermeable dyes into intact BY-2 tobacco plant cells growing in culture, investigating both optical and biological parameters. Specifically, we show that the long axial extent of a propagation invariant (“diffraction-free”) Bessel beam, which relaxes the requirements for tight focusing on the cell membrane, outperforms a standard Gaussian photoporation beam, achieving up to 70% optoinjection efficiency. Studies on the osmotic effects of culture media show that a hypertonic extracellular medium was found to be necessary to reduce turgor pressure and facilitate molecular entry into the cells.
Publisher PDF
Peer reviewed
10
eng
PLoS One
© 2013 Mitchell et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Pulsed laser beam
Cell membrane permeability
Photoporation
Femtosecond optical injection
Tobacco BY-2 cells
Q Science
Q
Femtosecond optoinjection of intact tobacco BY-2 cells using a reconfigurable photoporation platform
Journal article
THUMBNAIL
e79235.pdf.jpg
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license.txt
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17927ad4e2686587f84067b17682d5d9
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10023/4234
oai:research-repository.st-andrews.ac.uk:10023/4234
2022-04-26 12:30:20.229
St Andrews Research Repository
Digital-Repository@st-andrews.ac.uk
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