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Probability of Seeing Increases Saccadic Readiness  [PDF]
Thérèse Collins
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0049454
Abstract: Associating movement directions or endpoints with monetary rewards or costs influences movement parameters in humans, and associating movement directions or endpoints with food reward influences movement parameters in non-human primates. Rewarded movements are facilitated relative to non-rewarded movements. The present study examined to what extent successful foveation facilitated saccadic eye movement behavior, with the hypothesis that foveation may constitute an informational reward. Human adults performed saccades to peripheral targets that either remained visible after saccade completion or were extinguished, preventing visual feedback. Saccades to targets that were systematically extinguished were slower and easier to inhibit than saccades to targets that afforded successful foveation, and this effect was modulated by the probability of successful foveation. These results suggest that successful foveation facilitates behavior, and that obtaining the expected sensory consequences of a saccadic eye movement may serve as a reward for the oculomotor system.
Saccadic Adaptation to Moving Targets  [PDF]
Katharina Havermann, Robert Volcic, Markus Lappe
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0039708
Abstract: Saccades are so called ballistic movements which are executed without online visual feedback. After each saccade the saccadic motor plan is modified in response to post-saccadic feedback with the mechanism of saccadic adaptation. The post-saccadic feedback is provided by the retinal position of the target after the saccade. If the target moves after the saccade, gaze may follow the moving target. In that case, the eyes are controlled by the pursuit system, a system that controls smooth eye movements. Although these two systems have in the past been considered as mostly independent, recent lines of research point towards many interactions between them. We were interested in the question if saccade amplitude adaptation is induced when the target moves smoothly after the saccade. Prior studies of saccadic adaptation have considered intra-saccadic target steps as learning signals. In the present study, the intra-saccadic target step of the McLaughlin paradigm of saccadic adaptation was replaced by target movement, and a post-saccadic pursuit of the target. We found that saccadic adaptation occurred in this situation, a further indication of an interaction of the saccadic system and the pursuit system with the aim of optimized eye movements.
The Relationship between Saccadic Choice and Reaction Times with Manipulations of Target Value  [PDF]
David M. Milstein,Michael C. Dorris
Frontiers in Neuroscience , 2011, DOI: 10.3389/fnins.2011.00122
Abstract: Choosing the option with the highest expected value (EV; reward probability × reward magnitude) maximizes the intake of reward under conditions of uncertainty. However, human economic choices indicate that our value calculation has a subjective component whereby probability and reward magnitude are not linearly weighted. Using a similar economic framework, our goal was to characterize how subjective value influences the generation of simple motor actions. Specifically, we hypothesized that attributes of saccadic eye movements could provide insight into how rhesus monkeys, a well-studied animal model in cognitive neuroscience, subjectively value potential visual targets. In the first experiment, monkeys were free to choose by directing a saccade toward one of two simultaneously displayed targets, each of which had an uncertain outcome. In this task, choices were more likely to be allocated toward the higher valued target. In the second experiment, only one of the two possible targets appeared on each trial. In this task, saccadic reaction times (SRTs) decreased toward the higher valued target. Reward magnitude had a much stronger influence on both choices and SRTs than probability, whose effect was observed only when reward magnitude was similar for both targets. Across EV blocks, a strong relationship was observed between choice preferences and SRTs. However, choices tended to maximize at skewed values whereas SRTs varied more continuously. Lastly, SRTs were unchanged when all reward magnitudes were 1×, 1.5×, and 2× their normal amount, indicating that saccade preparation was influenced by the relative value of the targets rather than the absolute value of any single-target. We conclude that value is not only an important factor for deliberative decision making in primates, but also for the selection and preparation of simple motor actions, such as saccadic eye movements. More precisely, our results indicate that, under conditions of uncertainty, saccade choices and reaction times are influenced by the relative expected subjective value of potential movements.
Identifying transcriptional targets
Nicola V Taverner, James C Smith, Fiona C Wardle
Genome Biology , 2004, DOI: 10.1186/gb-2004-5-3-210
Abstract: The control of many cellular processes requires the coordinated activation or repression of genes in the correct spatial and temporal patterns. This regulation is carried out in large part by transcription factors, which bind to DNA sequences within chromatin and activate or repress the transcription of nearby genes. This binding is frequently sequence-specific, with sequence recognition being carried out by the transcription factor itself or by other proteins complexed to it. Identification of the targets of each transcription factor provides information about individual processes and how transcription factors interact in a transcriptional network. These networks can then be used to describe a particular cellular process, or even something as complicated as embryonic development [1,2].The first step in identifying targets of a transcription factor usually involves overexpression or knockdown of the factor in question and analysis of the resulting changes in gene expression. The development of microarray technology has facilitated this kind of analysis, allowing identification of many more downstream genes than was previously feasible. But this method gives no information about whether targets are regulated directly by the transcription factor through binding to regulatory sequences within the gene or whether regulation is indirect, through the activation of intermediate genes. Other techniques, such as chromatin immunoprecipitation (ChIP) and Dam methylase identification (DamID), have therefore been developed. These reveal where in the genome the transcription factor is bound; these approaches allow identification of many direct target sequences, particularly when it is combined with microarrays of genomic DNA. This type of information, in combination with genomic sequences, is now being used to develop computational algorithms that scan genomic sequence with the aim of distinguishing functional binding sites and target genes of transcription factors.Comparison of
An analysis of the dependence of saccadic latency on target position and target characteristics in human subjects
Jennifer H Darrien, Katrina Herd, Lisa-Jo Starling, Jay R Rosenberg, James D Morrison
BMC Neuroscience , 2001, DOI: 10.1186/1471-2202-2-13
Abstract: In order to resolve this paradox, we have undertaken an extended series of experiments in which saccadic eye movements were recorded by electro-oculography in response to targets presented in the horizontal meridian in normal young subjects. For stationary or moving targets of either normal beam intensity or reduced red intensity, with the direction of gaze either straight ahead with respect to the head or directed eccentrically, the saccadic latency was shown to remain invariant with respect to a wide range of target angular displacements.These results indicate that, irrespective of the angular displacement of the target, the direction of gaze or the target intensity, the saccade-generating system operates with a constant generation time.Specialization of the foveal region of the human retina necessitates a sophisticated ocular motor system to translate an image appearing on the peripheral retina onto the fovea: this is achieved by the generation of saccadic eye movements which effect rapid fixation of the target. The saccadic latency which is the time from the presentation of the target to the commencement of the saccade consists of the transmission times in the afferent and efferent pathways and the central processing time which is likely to be appreciable due to the complexity of the pathway. An important centre in the generation of saccades is the superior colliculus [1]. While a direct projection from the retina via the superior brachium leads to activation of the visual cells of the superior colliculus, the dominant pathway is via the primary visual cortex [2] which projects to the superior colliculus through the thick cytochrome oxidase stripes of area V2 [3]. Saccadic movements are also driven consciously from the frontal eye fields (area 8) which have a projection to the superior colliculus [4]. For a saccade to be generated, there must be activation of the saccade-related burst neurones of the deep layers of the superior colliculus: these drive the excita
Cortical Contributions to Saccadic Suppression  [PDF]
George Chahine, Bart Krekelberg
PLOS ONE , 2009, DOI: 10.1371/journal.pone.0006900
Abstract: The stability of visual perception is partly maintained by saccadic suppression: the selective reduction of visual sensitivity that accompanies rapid eye movements. The neural mechanisms responsible for this reduced perisaccadic visibility remain unknown, but the Lateral Geniculate Nucleus (LGN) has been proposed as a likely site. Our data show, however, that the saccadic suppression of a target flashed in the right visual hemifield increased with an increase in background luminance in the left visual hemifield. Because each LGN only receives retinal input from a single hemifield, this hemifield interaction cannot be explained solely on the basis of neural mechanisms operating in the LGN. Instead, this suggests that saccadic suppression must involve processing in higher level cortical areas that have access to a considerable part of the ipsilateral hemifield.
The Potential of Metatranscriptomics for Identifying Screening Targets for Bacterial Vaginosis  [PDF]
Jimmy Twin, Catriona S. Bradshaw, Suzanne M. Garland, Christopher K. Fairley, Katherine Fethers, Sepehr N. Tabrizi
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0076892
Abstract: Background The ribosomal RNA content of a sample collected from a woman with bacterial vaginosis (BV) was analysed to determine the active microbial community, and to identify potential targets for further screening. Methodology/Principal Findings The sample from the BV patient underwent total RNA extraction, followed by physical subtraction of human rRNA and whole transcriptome amplification. The metatranscriptome was sequenced using Roche 454 titanium chemistry. The bioinformatics pipeline MG-RAST and desktop DNA analysis platforms were utilised to analyse results. Bacteria of the genus Prevotella (predominately P. amnii) constituted 36% of the 16S rRNA reads, followed by Megasphaera (19%), Leptotrichia/Sneathia (8%) and Fusobacterium (8%). Comparison of the abundances of several bacteria to quantitative PCR (qPCR) screening of extracted DNA revealed comparable relative abundances. This suggests a correlation between what was present and transcriptionally active in this sample: however distinct differences were seen when compared to the microbiome determined by 16S rRNA gene amplicon sequencing. To assess the presence of P. amnii in a larger pool of samples, 90 sexually active women were screened using qPCR. This bacterium was found to be strongly associated with BV (P<0.001, OR 23.3 (95%CI:2.9–190.7)) among the 90 women. Conclusions/Significance This study highlighted the potential of metatranscriptomics as a tool for characterising metabolically active microbiota and identifying targets for further screening. Prevotella amnii was chosen as an example target, being the most metabolically active species present in the single patient with BV, and was found to be detected at a high concentration by qPCR in 31% of cohort with BV, with an association with both oral and penile-vaginal sex.
Identifying MicroRNAs and Transcript Targets in Jatropha Seeds  [PDF]
Vanessa Galli, Frank Guzman, Luiz F. V. de Oliveira, Guilherme Loss-Morais, Ana P. K?rbes, Sérgio D. A. Silva, Márcia M. A. N. Margis-Pinheiro, Rogério Margis
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0083727
Abstract: MicroRNAs, or miRNAs, are endogenously encoded small RNAs that play a key role in diverse plant biological processes. Jatropha curcas L. has received significant attention as a potential oilseed crop for the production of renewable oil. Here, a sRNA library of mature seeds and three mRNA libraries from three different seed development stages were generated by deep sequencing to identify and characterize the miRNAs and pre-miRNAs of J. curcas. Computational analysis was used for the identification of 180 conserved miRNAs and 41 precursors (pre-miRNAs) as well as 16 novel pre-miRNAs. The predicted miRNA target genes are involved in a broad range of physiological functions, including cellular structure, nuclear function, translation, transport, hormone synthesis, defense, and lipid metabolism. Some pre-miRNA and miRNA targets vary in abundance between the three stages of seed development. A search for sequences that produce siRNA was performed, and the results indicated that J. curcas siRNAs play a role in nuclear functions, transport, catalytic processes and disease resistance. This study presents the first large scale identification of J. curcas miRNAs and their targets in mature seeds based on deep sequencing, and it contributes to a functional understanding of these miRNAs.
Inhibition of return, gap effect and saccadic reaction time to a visual target
Guimar?es-Silva, S.;Gawryszewski, L.G.;Portugal, T.S.;Klausner-de-Oliveira, L.;
Brazilian Journal of Medical and Biological Research , 2004, DOI: 10.1590/S0100-879X2004000400010
Abstract: simple manual reaction time (mrt) to a visual target (s2) is shortened when a non-informative cue (s1) is flashed at the s2 location shortly before the onset of s2 (early facilitation). afterwards, mrt to s2 appearing at the s1 location is lengthened (inhibition of return - ior). similar results have been obtained for saccadic reaction time (srt). moreover, when there is a temporal gap between offset of the fixation point (fp) and onset of a target (gap paradigm), srt is shorter than srt in an overlap paradigm (fp remains on). in the present study, we determined srt to s2 (10o) after presenting s1 at the same eccentricity (10o) or at a parafoveal position (2o) in the same or in the opposite hemifield. in addition, we employed both gap and overlap paradigms. twelve subjects were asked not to respond to s1 (2o or 10o) to the right or to the left of fp, but to respond by making a saccadic movement in response to s2. we obtained the following results: 1) a 40-ms gap effect, 2) an interaction between gap effect and ior, 3) a 39-ms delay (ior) when s2 appeared at the cued (s1) position, and 4) a smaller (17 ms) but significant inhibition when s1 occurred at 2o in the ipsilateral hemifield. thus, a parafoveal (2o) s1 elicits an inhibition of srt towards ipsilateral peripheral targets. since an inhibition of the ipsilateral hemifield by a 1o eccentric cue has been reported to occur when manual responses are employed, we suggest that the postulated functional link between covert and overt orienting of attention is also valid for parafoveal cues.
Inhibition of return, gap effect and saccadic reaction time to a visual target  [cached]
Guimar?es-Silva S.,Gawryszewski L.G.,Portugal T.S.,Klausner-de-Oliveira L.
Brazilian Journal of Medical and Biological Research , 2004,
Abstract: Simple manual reaction time (MRT) to a visual target (S2) is shortened when a non-informative cue (S1) is flashed at the S2 location shortly before the onset of S2 (early facilitation). Afterwards, MRT to S2 appearing at the S1 location is lengthened (inhibition of return - IOR). Similar results have been obtained for saccadic reaction time (SRT). Moreover, when there is a temporal gap between offset of the fixation point (FP) and onset of a target (gap paradigm), SRT is shorter than SRT in an overlap paradigm (FP remains on). In the present study, we determined SRT to S2 (10o) after presenting S1 at the same eccentricity (10o) or at a parafoveal position (2o) in the same or in the opposite hemifield. In addition, we employed both gap and overlap paradigms. Twelve subjects were asked not to respond to S1 (2o or 10o) to the right or to the left of FP, but to respond by making a saccadic movement in response to S2. We obtained the following results: 1) a 40-ms gap effect, 2) an interaction between gap effect and IOR, 3) a 39-ms delay (IOR) when S2 appeared at the cued (S1) position, and 4) a smaller (17 ms) but significant inhibition when S1 occurred at 2o in the ipsilateral hemifield. Thus, a parafoveal (2o) S1 elicits an inhibition of SRT towards ipsilateral peripheral targets. Since an inhibition of the ipsilateral hemifield by a 1o eccentric cue has been reported to occur when manual responses are employed, we suggest that the postulated functional link between covert and overt orienting of attention is also valid for parafoveal cues.
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