Biology subjects

Oliva, A.

Publications and source records attributed to Oliva, A..

28 records · Page 2Linked to original sources

bioRxiv2020

High sensitivity detection of SARS-CoV-2 using multiplex PCR and a multiplex-PCR-based metagenomic method

Many detection methods have been used or reported for the diagnosis and/or surveillance of COVID-19. Among them, reverse transcription polymerase chain reaction (RT-PCR) is the most commonly used because of its high sensitivity, typically claiming detection of about 5 copies of viruses. However, it has been reported that only 47-59% of the positive cases were identified by some RT-PCR methods, probably due to low viral load, timing of sampling, degradation of virus RNA in the sampling process, or possible mutations spanning the primer binding sites. Therefore, alternative and highly sensitive methods are imperative. With the goal of improving sensitivity and accommodating various application settings, we developed a multiplex-PCR-based method comprised of 343 pairs of specific primers, and demonstrated its efficiency to detect SARS-CoV-2 at low copy numbers. The assay produced clean characteristic target peaks of defined sizes, which allowed for direct identification of positives by electrophoresis. We further amplified the entire SARS-CoV-2 genome from 8 to half a million viral copies purified from 13 COVID-19 positive specimens, and detected mutations through next generation sequencing. Finally, we developed a multiplex-PCR-based metagenomic method in parallel, that required modest sequencing depth for uncovering SARS-CoV-2 mutational diversity and potentially novel or emerging isolates.

genomics↗

bioRxiv2020

Hippocampal CA2 ripples recruit social replay and promote social memory

The consolidation of spatial memory depends on the reactivation ( replay) of hippocampal place cells that were active during recent behavior. These reactivations are observed during sharp wave-ripples (SWRs), synchronous oscillatory events that occur during slow-wave sleep1-9 and whose disruption impairs spatial memory consolidation 4,6,7,9. Although the hippocampus encodes a wide range of non-spatial forms of declarative memory, it is not yet known whether SWRs are necessary for non-spatial memory. Moreover, although SWRs can arise from either the hippocampal CA38 or CA210 regions, the relative importance of these sources for memory consolidation is unknown. Here we examined the role of SWRs during the consolidation of social memory, the ability of an animal to recognize and remember a conspecific, focusing on CA2 because of its critical role in social memory11,12,13. We found that ensembles of CA2 pyramidal neurons that were active during social exploration of novel conspecifics were reactivated during SWRs. Importantly, disruption or enhancement of CA2 SWRs suppressed or prolonged social memory, respectively. Thus, SWR reactivation of hippocampal firing related to recent experience appears to be a general mechanism for binding spatial, temporal and sensory information into high-order memory representations.

neuroscience↗

bioRxiv2020

Visual Experience is not Necessary for the Development of Face Selectivity in the Lateral Fusiform Gyrus

Here we show robust face-selectivity in the lateral fusiform gyrus of congenitally blind participants during haptic exploration of 3D-printed stimuli, indicating that neither visual experience, nor fovea-biased input, nor visual expertise is necessary for face-selectivity to arise in its characteristic location. Similar resting fMRI correlation fingerprints in individual blind and sighted participants suggest a role for long-range connectivity in the specification of the cortical locus of face-selectivity.

neuroscience↗

bioRxiv2020

Emergence of Visual Center-Periphery Spatial Organization in Deep Convolutional Neural Networks

Research at the intersection of computer vision and neuroscience has revealed hierarchical correspondence between layers of deep convolutional neural networks (DCNNs) and cascade of regions along human ventral visual cortex. Recently, studies have uncovered emergence of human interpretable concepts within DCNNs layers trained to identify visual objects and scenes. Here, we asked whether an artificial neural network (with convolutional structure) trained for visual categorization would demonstrate spatial correspondences with human brain regions showing central/peripheral biases. Using representational similarity analysis, we compared activations of convolutional layers of a DCNN trained for object and scene categorization with neural representations in human brain visual regions. Results reveal a brain-like topographical organization in the layers of the DCNN, such that activations of layer-units with central-bias were associated with brain regions with foveal tendencies (e.g. fusiform gyrus), and activations of layer-units with selectivity for image backgrounds were associated with cortical regions showing peripheral preference (e.g. parahippocampal cortex). The emergence of a categorical topographical correspondence between DCNNs and brain regions suggests these models are a good approximation of the perceptual representation generated by biological neural networks.

neuroscience↗

bioRxiv2019

A neural correlate of image memorability

Some images are easy to remember while others are easily forgotten. While variation in image memorability is consistent across individuals, we lack a full account of its neural correlates. By analyzing data collected from inferotemporal cortex (IT) as monkeys performed a visual memory task, we demonstrate that a simple property of the visual encoding of an image, its population response magnitude, is strongly correlated with its memorability. These results establish a novel behavioral role for the magnitude of the IT response, which lies largely orthogonal to the coding scheme that IT uses to represent object identity. To investigate the origin of IT memorability modulation, we also probed convolutional neural network models trained to categorize objects. We found brain-analogous correlates of memorability that grew in strength across the hierarchy of these networks, suggesting that this memorability correlate is likely to arise from the optimizations required for visual as opposed to mnemonic processing.

neuroscience↗

bioRxiv2018

Reliability and Generalizability of Similarity-Based Fusion of MEG and fMRI Data in Human Ventral and Dorsal Visual Streams

To build a representation of what we see, the human brain recruits regions throughout the visual cortex in cascading sequence. Recently, an approach was proposed to evaluate the dynamics of visual perception in high spatiotemporal resolution at the scale of the whole brain. This method combined functional magnetic resonance imaging (fMRI) data with magnetoencephalography (MEG) data using representational similarity analysis and revealed a hierarchical progression from primary visual cortex through the dorsal and ventral streams. To assess the replicability of this method, here we present results of a visual recognition neuro-imaging fusion experiment, and compare them within and across experimental settings. We evaluated the reliability of this method by assessing the consistency of the results under similar test conditions, showing high agreement within participants. We then generalized these results to a separate group of individuals and visual input by comparing them to the fMRI-MEG fusion data of Cichy et al (2016), revealing a highly similar temporal progression recruiting both the dorsal and ventral streams. Together these results are a testament to the reproducibility of the fMRI-MEG fusion approach and allows for the interpretation of these spatiotemporal dynamic in a broader context.

neuroscience↗

bioRxiv2018

The Perceptual Neural Trace of Memorable Unseen Scenes

Some scenes are more memorable than others: they cement in minds with consistencies across observers and time scales. While memory mechanisms are traditionally associated with the end stages of perception, recent behavioral studies suggest that the features driving these memorability effects are extracted early on, and in an automatic fashion. This raises the question: is the neural signal of memorability detectable during early perceptual encoding phases of visual processing? Using the high temporal resolution of magnetoencephalography (MEG), during a rapid serial visual presentation (RSVP) task, we traced the neural temporal signature of memorability across the brain. We found an early and prolonged memorability related signal recruiting a network of regions in both dorsal and ventral streams, detected outside of the constraints of subjective awareness. This enhanced encoding could be the key to successful storage and recognition.

neuroscience↗

bioRxiv2018

Accounting for ambiguity in ancestral sequence reconstruction

The reconstruction of ancestral genetic sequences from the analysis of contemporaneous data is a powerful tool to improve our understanding of molecular evolution. Various statistical criteria defined in a phylogenetic framework can be used to infer nucleotide, aminoa-cid or codon states at internal nodes of the tree, for every position along the sequence. These criteria generally select the state that maximises (or minimises) a given criterion. Although it is perfectly sensible from a statistical perspective, that strategy fails to convey useful information about the level of uncertainty associated to the inference. The present study introduces a new criterion for ancestral nucleotide reconstruction that selects a single state whenever the signal conveyed by the data is strong, and a combination of multiple states otherwise. Simulations demonstrate the benefit of this approach with a substantial increase in the accuracy of ancestral sequence reconstruction without significantly compromising on the precision of the solutions returned.

evolutionary biology↗

bioRxiv2017

Image Memorability In The Eye Of The Beholder: Tracking The Decay Of Visual Scene Representations

Some images stick in your mind for days or even years, while others seem to vanish quickly from memory. We tested whether differences in image memorability 1) are already evident immediately after encoding, 2) produce different rates of forgetting, and 3) whether the retrieval of images with different memorability scores affords differential degrees of cognitive load, mirrored by graded pupillary and blink rate responses. We monitored participants eye activity while they viewed a sequence of >1200 images in a repetition detection paradigm. 240 target images from 3 non-overlapping memorability classes were repeated at 4 different lags. Overall, performance decreased log-linearly with time. Differences in memorability were already visible at the shortest lag (~ 20 sec) and became more pronounced as time passed on. The rate of forgetting was steepest for low memorable images. We found that pupils dilated significantly more to correctly identified targets than correctly rejected distractors. Importantly, this \"pupil old/new effect\" increased with increasing number of lags and decreasing image memorability. A similar modulation of blink rates corroborated these findings. These results suggest that during memory retrieval of scenes, image inherent characteristics pose differential degrees of cognitive load on observers as seen in their eyes.

neuroscience↗

bioRxiv2017

Visual memories are stored along a compressed timeline

In continuous recognition the recency effect manifests as a decrease in accuracy and a sublinear increase in response time (RT) with the lag of a repeated stimulus. The recency effect could result from the gradual weakening of mnemonic traces. Alternatively, the recency effect could result from a search through a compressed timeline of recent experience. These two hypotheses make very different predictions about the shape of response time distributions. Using highly-memorable pictures to mitigate changes in accuracy enabled a detailed examination of the effect of recency on retrieval dynamics. The recency at which pictures were repeated ranged over two orders of magnitude across three experiments. Analysis of the RT distributions showed that the time at which memories became accessible changed with the recency of the probe, as predicted by a serial search model suggesting that visual memories can be accessed by sequentially scanning along a compressed representation of the past.

animal behavior and cognition↗