Institute of Behavioural and Neural Scienceshttps://hdl.handle.net/10023/3012024-03-28T15:15:39Z2024-03-28T15:15:39ZBayesPiles : visualisation support for Bayesian network structure learningVogogias, AthanasiosKennedy, JessieArchambault, DanielBach, BenjaminSmith, V AnneCurrant, Hannahhttps://hdl.handle.net/10023/166362023-04-18T23:47:32Z2018-11-01T00:00:00ZWe 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.
2018-11-01T00:00:00ZVogogias, AthanasiosKennedy, JessieArchambault, DanielBach, BenjaminSmith, V AnneCurrant, HannahWe 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.Images as proximity sensors : the incidence of conspecific foraging in Antarctic fur sealsHooker, Sascha KateBarychka, TatsianaJessopp, Mark JStaniland, Iain Jhttps://hdl.handle.net/10023/75812023-04-25T23:41:46Z2015-09-29T00:00:00ZBackground: 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.
2015-09-29T00:00:00ZHooker, Sascha KateBarychka, TatsianaJessopp, Mark JStaniland, Iain JBackground: 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.Stimulation of glia reveals modulation of mammalian spinal motor networks by adenosineActon, DavidMiles, Gareth B.https://hdl.handle.net/10023/72342023-04-18T10:02:01Z2015-08-07T00:00:00ZDespite 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.
This work was funded by the Wellcome Trust Institutional Strategic Support Fund for University of St. Andrews.
2015-08-07T00:00:00ZActon, DavidMiles, Gareth B.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.A genetic algorithm for face fittingHunter, David WilliamTiddeman, Bernard PaulPerrett, David Ianhttps://hdl.handle.net/10023/54432022-04-14T20:39:20Z2012-02-01T00:00:00ZAccurate 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.
2012-02-01T00:00:00ZHunter, David WilliamTiddeman, Bernard PaulPerrett, David IanAccurate 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.Perceptual integration across natural monocular regionsZeiner, Katharina MariaSpitschan, ManuelHarris, Juliehttps://hdl.handle.net/10023/53492022-04-12T11:30:28Z2014-03-05T00:00:00ZNatural 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.
2014-03-05T00:00:00ZZeiner, Katharina MariaSpitschan, ManuelHarris, JulieNatural 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.Characterizing Visual Attention during Driving and Non-driving Hazard Perception TasksMacKenzie, Andrew KerrHarris, Juliehttps://hdl.handle.net/10023/50662023-04-19T00:38:43Z2014-03-26T00:00:00ZResearch 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.
Funding: EPSRC DTG
2014-03-26T00:00:00ZMacKenzie, Andrew KerrHarris, JulieResearch 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.Behavioral observation of xenopus tadpole swimming for neuroscience labsLi, WenchangWagner, Monica AnnePorter, Nicola Jeanhttps://hdl.handle.net/10023/50382023-04-18T09:51:38Z2014-01-01T00:00:00ZNeuroscience 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.
2014-01-01T00:00:00ZLi, WenchangWagner, Monica AnnePorter, Nicola JeanNeuroscience 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.Evaluating multicenter DTI data in Huntington's disease on site specific effects : an ex post facto approachMüller, Hans-PeterGrön, GeorgSprengelmeyer, ReinerKassubek, JanLudolph, Albert C.Hobbs, NicolaCole, JamesRoos, Raymund A.C.Duerr, AlexandraTabrizi, Sarah J.Landwehrmeyer, G. BernhardSüssmuth, Sigurd D.https://hdl.handle.net/10023/47892023-04-18T09:48:23Z2013-01-01T00:00:00ZPurpose: 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.
2013-01-01T00:00:00ZMüller, Hans-PeterGrön, GeorgSprengelmeyer, ReinerKassubek, JanLudolph, Albert C.Hobbs, NicolaCole, JamesRoos, Raymund A.C.Duerr, AlexandraTabrizi, Sarah J.Landwehrmeyer, G. BernhardSüssmuth, Sigurd D.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.Common HLA alleles associated with health, but not with facial attractivenessCoetzee, VinetBarrett, L.Greeff, J.M.Henzi, S.P.Perrett, David IanWadee, A.A.https://hdl.handle.net/10023/42432023-04-25T23:35:07Z2007-07-01T00:00:00ZThree 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.
This material is based, in part, upon work supported by the National Research Foundation under Grant number 2053809 to JMG.
2007-07-01T00:00:00ZCoetzee, VinetBarrett, L.Greeff, J.M.Henzi, S.P.Perrett, David IanWadee, A.A.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.Femtosecond optoinjection of intact tobacco BY-2 cells using a reconfigurable photoporation platformMitchell, C.A.Kalies, S.Cizmár, T.Heisterkamp, A.Torrance, L.Roberts, A.G.Gunn-Moore, F.J.Dholakia, K.https://hdl.handle.net/10023/42342022-04-26T11:30:20Z2013-11-14T00:00:00ZA 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.
2013-11-14T00:00:00ZMitchell, C.A.Kalies, S.Cizmár, T.Heisterkamp, A.Torrance, L.Roberts, A.G.Gunn-Moore, F.J.Dholakia, K.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.Exploring the ultrashort pulse laser parameter space for membrane permeabilisation in mammalian cells.Rudhall, Andrew PeterAntkowiak, MaciejTsampoula, XanthiMazilu, MichaelMetzger, N KlausGunn-Moore, Frank JDholakia, Kishanhttps://hdl.handle.net/10023/39192023-04-18T09:46:20Z2012-01-01T00:00:00ZThe 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.
2012-01-01T00:00:00ZRudhall, Andrew PeterAntkowiak, MaciejTsampoula, XanthiMazilu, MichaelMetzger, N KlausGunn-Moore, Frank JDholakia, KishanThe 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.Interactions between luminance and colour signals : effects on shapeClery, StephaneBloj, MarinaHarris, Juliehttps://hdl.handle.net/10023/38612022-04-26T08:30:12Z2013-04-18T00:00:00ZAlthough 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
This research was supported by the Engineering and Physical Sciences Research Council (EPSRC).
2013-04-18T00:00:00ZClery, StephaneBloj, MarinaHarris, JulieAlthough 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 maskingFemale putty-nosed monkeys use experimentally altered contextual information to disambiguate the cause of male alarm callsArnold, KateZuberbuehler, Klaushttps://hdl.handle.net/10023/36742023-04-18T09:47:54Z2013-06-05T00:00:00ZMany 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.
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.
2013-06-05T00:00:00ZArnold, KateZuberbuehler, KlausMany 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.Public information use in ninespine sticklebacks (Pungitius pungitius) : isolating the mechanisms using computer-animated stimuliChouinard-Thuly, Laurahttps://hdl.handle.net/10023/33492021-10-12T09:10:24Z2012-01-01T00:00:00ZMany studies demonstrated the use, and strategies of use, of public information -or the ability of an observer to assess a resource’s quality by watching inadvertent behavioural cues- in the ninespine stickleback (Pungitius pungitius) presented with a foraging patch assessment problem. Many aspects of behaviour were seen to vary with an increased feeding rate and identifying the one responsible for transmission of information is difficult with live demonstrators. This project created and utilized computer-animated ninespine sticklebacks to isolate behaviours and test which ones are used by observers to gain information. We predicted and found that out of six different behaviours associated with an increase in feeding rate, strike rate is the one used to assess foraging patches’ quality. Observer ninespine sticklebacks preferred to associate with sides that were formerly associated with an animated shoal of conspecifics different only in the amount of strikes per demonstration period, in a ratio of six versus two.
2012-01-01T00:00:00ZChouinard-Thuly, LauraMany studies demonstrated the use, and strategies of use, of public information -or the ability of an observer to assess a resource’s quality by watching inadvertent behavioural cues- in the ninespine stickleback (Pungitius pungitius) presented with a foraging patch assessment problem. Many aspects of behaviour were seen to vary with an increased feeding rate and identifying the one responsible for transmission of information is difficult with live demonstrators. This project created and utilized computer-animated ninespine sticklebacks to isolate behaviours and test which ones are used by observers to gain information. We predicted and found that out of six different behaviours associated with an increase in feeding rate, strike rate is the one used to assess foraging patches’ quality. Observer ninespine sticklebacks preferred to associate with sides that were formerly associated with an animated shoal of conspecifics different only in the amount of strikes per demonstration period, in a ratio of six versus two.Learning to use illumination gradients as an unambiguous cue to three dimensional shapeHarding, GlenHarris, JulieBloj, Marinahttps://hdl.handle.net/10023/30772022-04-26T08:30:04Z2012-04-30T00:00:00ZThe 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.
2012-04-30T00:00:00ZHarding, GlenHarris, JulieBloj, MarinaThe 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.Perception of relative depth interval : Systematic biases in perceived depthHarris, JulieChopin, AdrienZeiner, Katharina MariaHibbard, Paul Barryhttps://hdl.handle.net/10023/27492022-07-08T10:30:03Z2012-01-01T00:00:00ZGiven 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.
2012-01-01T00:00:00ZHarris, JulieChopin, AdrienZeiner, Katharina MariaHibbard, Paul BarryGiven 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.What visual information is used for stereoscopic depth displacement discrimination?Nefs, HaroldHarris, Juliehttps://hdl.handle.net/10023/27462023-04-18T09:43:04Z2010-01-01T00:00:00ZThere 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.
2010-01-01T00:00:00ZNefs, HaroldHarris, JulieThere 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.Evidence for weak or linear conformity but not for hyper-conformity in an everyday social learning contextClaidiere, NicolasBowler, Mark TimothyWhiten, Andrewhttps://hdl.handle.net/10023/25552023-04-18T09:44:58Z2012-02-20T00:00:00ZConformity 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.
2012-02-20T00:00:00ZClaidiere, NicolasBowler, Mark TimothyWhiten, AndrewConformity 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.Sparse codingFoldiak, PEndres, D Mhttps://hdl.handle.net/10023/4942019-04-01T10:39:23Z2008-01-01T00:00:00ZMammalian 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.
The(frequently updated) original version is avalable at http://www.scholarpedia.org/article/Sparse_coding
2008-01-01T00:00:00ZFoldiak, PEndres, D MMammalian 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.Bayesian binning beats approximate alternatives: estimating peri-stimulus time histogramsEndres, D MOram, M WSchindelin, J.E.Foldiak, Phttps://hdl.handle.net/10023/4732019-04-01T10:36:27Z2008-01-01T00:00:00ZThe 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.
2008-01-01T00:00:00ZEndres, D MOram, M WSchindelin, J.E.Foldiak, PThe 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.