Biases in Perception of Visual Motion

Perceptual decision making refers to the process of making a choice among a series of options based on sensory information. Several studies have used visual stimuli to gain an understanding of the processes involved in encoding sensory information and its decoding, leading to a perceptual decision. One popular visual modality for studying these questions is motion and the ability to discriminate between axes of motion. Several mathematical models describing the processes of perceptual decision making have been proposed – many of them are based on data from electrophysiological experiments on macaque monkeys. By directly recording neuronal activity while monkeys were presented with different visual stimuli and making categorical choices about the perceived direction of motion, scientists have been able to study how decisions are made when enough perceptual evidence is accumulated to reach a threshold. A particularly interesting aspect of perceptual decision making is that it allows the study of situations in which the choice deviates from the physical features characterising the stimulus (e.g., a leftward motion is presented but the subject reports perceiving a rightward motion). A type of such perceptual bias is called reference repulsion: a systematic bias away from a reference when estimating the direction of motion of a stimulus. Several possible explanations of this phenomenon have been proposed: incorrect encoding of sensory information, influence of prior knowledge about the world, response-related factors such as expectations, rewards, and response history. The aim of this thesis was to shed light on when in the sequence of decision making such perceptual biases arise, as well as further address both sensory and higher-order factors that influence perceptual decisions of visual stimuli. We combined a series of psychophysical, eye-tracking, and neuroimaging studies, together with computational modelling approaches, to selectively look at the effect of: sensory information available during decision making, task-related sensory information processing, response modality, and also look for specific mechanisms involved in processing highly similar / dissimilar stimuli. The findings presented in this thesis show that perceptual biases in estimates of motion direction arise at a later stage than at the encoding of sensory representation, as previously thought. In particular, we show that information present at the time of the response is fundamental for the bias to emerge: the presence of a reference while estimating direction of motion results in reference repulsion, but this effect is not there when the same estimate is given in the absence of a reference. Moreover, the information given by the reference at the time of response – when subjects report the perceived motion, rather than at the time of stimulus presentation – plays a crucial role in the observed perceptual bias. These findings were used to develop a mathematical model able to describe the phenomena observed, as well as making a series of testable predictions. For example, the model could be used in future work to predict responses when more than one reference is present, when order of presentation of target and reference is inverted, and so on. By manipulating the modality with which subjects estimated the direction of motion of the stimuli they were presented with, it was also possible to show that a perceptual bias is observed for manual reproduction of the perceived direction, but not when the response is given by a saccadic eye movement. Finally, by looking at the brain activity recorded when performing a coarse / fine discrimination task in a functional magnetic resonance imaging (fMRI) study, we aimed at distinguishing between activity patterns encoding highly dissimilar / similar stimuli. For these analyses, we used both conventional, univariate analysis techniques, as well as a more advanced and relatively more recent multivariate approaches to the data. First, the retinotopic mapping of areas in early visual cortex and area MT was obtained through phase-encoded methods. Second, a version of the Generalised Linear Model was applied to the data measured while subjects were performing a fine / coarse discrimination task. This allowed to ensure the adequacy of tasks and stimuli used in the imaging study. I also applied the population Receptive Field methodology to fit a more explicit, physiologically relevant model of visual responses to the voxel-wise fMRI time series. Third, given that the spatial scale of the question we addressed in this study required aggregating sub-voxel differences in the fMRI responses during a fine versus coarse visual motion discrimination task, we employed a multivariate approach. This consisted in implementing a forward encoding model aimed at reducing the number of dimensions from several hundreds (given by the number of voxels) to a much smaller set of hypothetical channels. By considering the responses in these channels as a weighted combination from many hundred voxels we re-cast the activity patterns in a physiologically relevant space to predict responses to arbitrary visual motion directions. While there were very interesting aspects to the results from these imaging experiments, the analysis was inconclusive on any task-related shifts in stimulus encoding. Possible explanations, together with alternative paradigms that can be used in future to further address this question are discussed

Metal Interactions in the Ni Hyperaccumulating Population of Noccaea caerulescens Monte Prinzera

Hyperaccumulation is a fascinating trait displayed by a few plant species able to accumulate large amounts of metal ions in above-ground tissues without symptoms of toxicity. Noccaea caerulescens is a recognized model system to study metal hyperaccumulation and hypertolerance. A N. caerulescens population naturally growing on a serpentine soil in the Italian Apennine Mountains, Monte Prinzera, was chosen for the study here reported. Plants were grown hydroponically and treated with different metals, in excess or limiting concentrations. Accumulated metals were quantified in shoots and roots by means of ICP-MS. By real-time PCR analysis, the expression of metal transporters and Fe deficiency-regulated genes was compared in the shoots and roots of treated plants. N. caerulescens Monte Prinzera confirmed its ability to hypertolerate and hyperaccumulate Ni but not Zn. Moreover, excess Ni does not induce Fe deficiency as in Ni-sensitive species and instead competes with Fe translocation rather than its uptake

Positional accuracy assessment of the OpenStreetMap buildings layer through automatic homologous pairs detection: the method and a case study

OpenStreetMap (OSM) is currently the largest openly licensed collection of geospatial data. Being OSM increasingly exploited in a variety of applications, research has placed great attention on the assessment of its quality. This work focuses on assessing the quality of OSM buildings. While most of the studies available in literature are limited to the evaluation of OSM building completeness, this work proposes an original approach to assess the positional accuracy of OSM buildings based on comparison with a reference dataset. The comparison relies on a quasi-automated detection of homologous pairs on the two datasets. Based on the homologous pairs found, warping algorithms like e.g. affine transformations and multi-resolution splines can be applied to the OSM buildings to generate a new version having an optimal local match to the reference layer. A quality assessment of the OSM buildings of Milan Municipality (Northern Italy), having an area of about 180 km2, is then presented. After computing some measures of completeness, the algorithm based on homologous points is run using the building layer of the official vector cartography of Milan Municipality as the reference dataset. Approximately 100000 homologous points are found, which show a systematic translation of about 0.4 m on both the X and Y directions and a mean distance of about 0.8 m between the datasets. Besides its efficiency and high degree of automation, the algorithm generates a warped version of OSM buildings which, having by definition a closest match to the reference buildings, can be eventually integrated in the OSM database

Dynamic Gap Selector: A Smith Waterman Sequence Alignment Algorithm with Affine Gap Model Optimisation

Smith Waterman algorithm (S-W) is nowadays considered one of the best method to perform local alignments of biological sequences characterizing proteins, DNA and RNA molecules. Indeed, S-W is able to ensure better accuracy levels with respect to the heuristic alignment algorithms by extensively exploring all the possible alignment configurations between the sequences under examination. It has been proven that the first amino acid (AA) or nucleotide (NT) inserted/deleted (that identify a gap open) found during the alignment operations performed on sequences is more significant from a biological point of view than the subsequent ones (called gap extension), making the so called Affine Gap model a viable solution for biomolecules alignment. However, this version of S-W algorithm is expensive both in terms of computation as well as in terms of memory requirements with respect to others less demanding solutions such as the ones using a Linear Gap model. In order to overcome these drawbacks we have developed an optimised version of the S-Walgorithm based on Affine Gap model called Dynamic Gap Selector (DGS S-W). Differently from the standard S-W Affine Gap method, the proposed DGS S-W method reduces the memory requirements from 3*N*M to N*M where N and M represents the size of the compared sequences. In terms of computational costs, the proposed algorithm reduces by a factor of 2 the number of operations required by the standard Affine Gap model. DGS S-W method has been tested on two protein and one RNA sequences datasets, showing mapping scores very similar to those reached thanks to the classical S-W Affine Gap method and, at the same time, reduced computational costs and memory usag

A protocol for ultra-high field laminar fMRI in the human brain.

Ultra-high field (UHF) neuroimaging affords the sub-millimeter resolution that allows researchers to interrogate brain computations at a finer scale than that afforded by standard fMRI techniques. Here, we present a step-by-step protocol for using UHF imaging (Siemens Terra 7T scanner) to measure activity in the human brain. We outline how to preprocess the data using a pipeline that combines tools from SPM, FreeSurfer, ITK-SNAP, and BrainVoyager and correct for vasculature-related confounders to improve the spatial accuracy of the fMRI signal. For complete details on the use and execution of this protocol, please refer to Jia et al. (2020) and Zamboni et al. (2020).This work was supported by grants to Z.K. from the Biotechnology and Biological Sciences Research Council (H012508 and BB/P021255/1), the Wellcome Trust (205067/Z/16/Z) and European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska Curie grant agreement No 840271

AVALIAÇÕES DAS CARACTERÍSTICAS NA CULTURA DO MILHO COM A APLICAÇÃO DOSE DE FUNGICIDA

O cultivo de milho safrinha ocorre em todo o território nacional, representando uma das culturas de grande importância socioeconômico para a população brasileira. O presente trabalho objetivou avaliar as características na utilização de fungicida no milho safrinha. O trabalho foi conduzido no município de Cunha Porã/SC. Foram analisados agronomicamente a utilização em doses crescente de fungicida no milho safrinha: Foram avaliados a quantidade de massa verde por hectare, inserção de espiga e altura de planta. O estudo foi conduzido com aplicação de diferentes doses de fungicida no milho. Sendo que a ausencia de fungicida (0%) obteve melhores resultados para massa verde, inserção de espiga e altura de planta

A protocol for ultra-high field laminar fMRI in the human brain.

Ultra-high field (UHF) neuroimaging affords the sub-millimeter resolution that allows researchers to interrogate brain computations at a finer scale than that afforded by standard fMRI techniques. Here, we present a step-by-step protocol for using UHF imaging (Siemens Terra 7T scanner) to measure activity in the human brain. We outline how to preprocess the data using a pipeline that combines tools from SPM, FreeSurfer, ITK-SNAP, and BrainVoyager and correct for vasculature-related confounders to improve the spatial accuracy of the fMRI signal. For complete details on the use and execution of this protocol, please refer to Jia et al. (2020) and Zamboni et al. (2020).This work was supported by grants to Z.K. from the Biotechnology and Biological Sciences Research Council (H012508 and BB/P021255/1), the Wellcome Trust (205067/Z/16/Z) and European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska Curie grant agreement No 840271

Recurrent Processing Drives Perceptual Plasticity.

Learning and experience are critical for translating ambiguous sensory information from our environments to perceptual decisions. Yet evidence on how training molds the adult human brain remains controversial, as fMRI at standard resolution does not allow us to discern the finer scale mechanisms that underlie sensory plasticity. Here, we combine ultra-high-field (7T) functional imaging at sub-millimeter resolution with orientation discrimination training to interrogate experience-dependent plasticity across cortical depths that are known to support dissociable brain computations. We demonstrate that learning alters orientation-specific representations in superficial rather than middle or deeper V1 layers, consistent with recurrent plasticity mechanisms via horizontal connections. Further, learning increases feedforward rather than feedback layer-to-layer connectivity in occipito-parietal regions, suggesting that sensory plasticity gates perceptual decisions. Our findings reveal finer scale plasticity mechanisms that re-weight sensory signals to inform improved decisions, bridging the gap between micro- and macro-circuits of experience-dependent plasticity

Use of 31P Magnetisation Transfer Magnetic Resonance Spectroscopy to Measure ATP changes after 670 nm transcranial photobiomodulation in older adults

Mitochondrial function declines with age, and many pathological processes in neurodegenerative diseases stem from this dysfunction when mitochondria fail to produce the necessary energy required. Photobiomodulation (PBM), long‐wavelength light therapy, has been shown to rescue mitochondrial function in animal models and improve human health, but clinical uptake is limited due to uncertainty around efficacy and the mechanisms responsible. Using 31P magnetisation transfer magnetic resonance spectroscopy (MT‐MRS) we quantify, for the first time, the effects of 670 nm PBM treatment on healthy ageing human brains. We find a significant increase in the rate of ATP synthase flux in the brain after PBM in a cohort of older adults. Our study provides initial evidence of PBM therapeutic efficacy for improving mitochondrial function and restoring ATP flux with age, but recognises that wider studies are now required to confirm any resultant cognitive benefits