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Shi, Z.

Publications and source records attributed to Shi, Z..

11 recordsLinked to original sources

Probability cueing of singleton-distractor locations in visual search: priority-map- or dimension-based inhibition?

Observers can learn the likely locations of salient distractors in visual search, reducing their potential to capture attention (Ferrante et al., 2018; Sauter et al., 2018a; Wang & Theeuwes, 2018a). While there is agreement that this involves positional suppression of the likely distractor location(s), it is contentious at which stage of search guidance the suppression operates: the supra-dimensional priority map or feature-contrast signals within the distractor dimension. On the latter account, advocated by Sauter et al., target processing should be unaffected by distractor suppression when the target is defined in a different (non-suppressed) dimension to the target. At odds with this, Wang and Theeuwes found strong suppression not only of the (color) distractor, but also of the (shape) target when it appeared at the likely distractor location. Adopting their paradigm, the present study ruled out that increased cross-trial inhibition of the single frequent (frequently inhibited) as compared to any of the rare (rarely inhibited) distractor locations is responsible for this target-location effect. However, a reduced likelihood of the target appearing at the frequent vs. a rare distractor location contributes to this effect: removing this negative bias abolished the cost to target processing with increasing practice, indicative of a transition from priority-map- to dimension-based - and thus a flexible locus of - distractor suppression.\n\nPublic Significance StatementDistraction by a salient visual stimulus outside the focus of the task at hand occurs frequently. The present study examined whether and how knowledge of the likely location(s) where the distractors occur helps the observer to mitigate distraction. The results confirmed that observers can learn to suppress distracting stimuli at likely locations. Further, they showed that, the suppression may occur at different levels in the hierarchically organized visual system where the priorities of which objects to be attended in the environment are determined.

neuroscience

150 years of research on Vierordt’s law - Fechner’s fault?

150 years ago, the physiologist Karl Vierordt discovered one type of systematic errors in time perception - an overestimation of long durations and underestimation of short durations, now known as Vierordt's law. Here we review the original study in its historical context and ask whether Vierordt's law is a result of an unnatural experimental randomization protocol. Using iterative Bayesian updating, we simulated the original results with astonishing accuracy. To validate whether the experimental protocol matters, we compared duration reproduction from two sequences with the same sampled distribution and found that trial-wise variation determines the reproduction error. We conclude that Vierordt's law is caused by an unnatural yet widely used experimental protocol.

neuroscience

What you see depends on what you hear: temporal averaging and crossmodal integration

In our multisensory world, we often rely more on auditory information than on visual input for temporal processing. One typical demonstration of this is that the rate of auditory flutter assimilates the rate of concurrent visual flicker. To date, however, this auditory dominance effect has largely been studied using regular auditory rhythms. It thus remains unclear whether irregular rhythms would have a similar impact on visual temporal processing; what information is extracted from the auditory sequence that comes to influence visual timing; and how the auditory and visual temporal rates are integrated together in quantitative terms. We investigated these questions by assessing, and modeling, the influence of a task-irrelevant auditory sequence on the type of \"Ternus apparent motion\": group motion versus element motion. The type of motion seen critically depends on the time interval between the two Ternus display frames. We found that an irrelevant auditory sequence preceding the Ternus display modulates the visual interval, making observers perceive either more group motion or more element motion. This biasing effect manifests whether the auditory sequence is regular or irregular, and it is based on a summary statistic extracted from the sequential intervals: their geometric mean. However, the audiovisual interaction depends on the discrepancy between the mean auditory and visual intervals: if it becomes too large, no interaction occurs - which can be quantitatively described by a partial Bayesian integration model. Overall, our findings reveal a crossmodal perceptual averaging principle that may underlie complex audiovisual interactions in many everyday dynamic situations.

neuroscience

Inter-trial effects in visual pop-out search: Factorial comparison of Bayesian updating models

Many previous studies on visual search have reported inter-trial effects, that is, observers respond faster when some target property, such as a defining feature or dimension, or the response associated with the target repeats versus changes across consecutive trial episodes. However, what processes drive these inter-trial effects is still controversial. Here, we investigated this question using a combination of Bayesian modeling of belief updating and evidence accumulation modeling in perceptual decision-making. In three visual singleton ( pop-out) search experiments, we explored how the probability of the response-critical states of the search display (e.g., target presence/absence) and the repetition/switch of the target-defining dimension (color/ orientation) affect reaction time distributions. The results replicated the mean reaction time (RT) inter-trial and dimension repetition/switch effects that have been reported in previous studies. Going beyond this, to uncover the underlying mechanisms, we used the Drift-Diffusion Model (DDM) and the Linear Approach to Threshold with Ergodic Rate (LATER) model to explain the RT distributions in terms of decision bias (starting point) and information processing speed (evidence accumulation rate). We further investigated how these different aspects of the decision-making process are affected by different properties of stimulus history, giving rise to dissociable inter-trial effects. We approached this question by (i) combining each perceptual decision making model (DDM or LATER) with different updating models, each specifying a plausible rule for updating of either the starting point or the rate, based on stimulus history, and (ii) comparing every possible combination of trial-wise updating mechanism and perceptual decision model in a factorial model comparison. Consistently across experiments, we found that the (recent) history of the response-critical property influences the initial decision bias, while repetition/switch of the target-defining dimension affects the accumulation rate, likely reflecting an implicit top-down modulation process. This provides strong evidence of a disassociation between response- and dimension-based inter-trial effects.

neuroscience

Quasi-neutral molecular evolution -- When positive and negative selection cancel out

In the absence of both positive and negative selection, DNA sequences evolve at the neutral rate, R = 1. Due to the prevalence of negative selection, R[~]1 is rarely achieved in organismal evolution. However, when R [~] 1 is observed, it does not necessarily indicate neutral evolution because positive and negative selection could be equally strong but in opposite directions - hereby referred to as quasi-neutrality. We now show that somatic-cell evolution could be the paradigm of quasi-neutral evolution for these reasons: 1) Quasi-neutrality is much more likely in small populations (size N < 50) than in large ones; 2) Stem cell population sizes in single niches of normal tissues, from which tumors likely emerges, have small Ns (usually < 50); 3) the genome-wide evolutionary rate across tissue types is close to R = 1; 4) Relative to the average of R [~] 1, many genes evolve at a much higher or lower rate, thus hinting both positive and negative selection; 5) When N < 50, selection efficacy decreases rapidly as N decreases even when the selection intensity stays constant; 6) Notably, N is smaller in the small intestine (SmI) than in the colon (CO); hence, the [~] 70 fold higher rate of phenotypic evolution (observed as cancer risk) in the latter can be explained by the greater efficacy of selection, which then leads to the fixation of more advantageous mutations and fewer deleterious ones in the CO. Under quasineutrality, positive and negative selection can be measured in the same system as the two forces are simultaneously present or absent.

evolutionary biology

Cell membranes resist flow

The fluid-mosaic model posits a liquid-like plasma membrane, which can flow in response to tension gradients. It is widely assumed that membrane flow transmits local changes in membrane tension across the cell in milliseconds. This conjectured signaling mechanism has been invoked to explain how cells coordinate changes in shape, motility, and vesicle fusion, but the underlying propagation has never been observed. Here we show that propagation of membrane tension occurs quickly in cell-attached blebs, but is largely suppressed in intact cells. The failure of tension to propagate in cells is explained by a fluid dynamical model that incorporates the flow resistance from cytoskeleton-bound transmembrane proteins. In primary endothelial cells, local increases in membrane tension lead only to local activation of mechanosensitive ion channels and to local vesicle fusion. Thus membrane tension is not a mediator of long-range intra-cellular signaling, but local variations in tension mediate distinct processes in sub-cellular domains.

biophysics

Verified the effectiveness of AsCpf1 system in a variety of vertebrate species

CRISPR/Cpf1 system is a novel genomic editing tool. Because of its more sophisticated components, and lower off-target rate, it has the potential to become a better gene-editing tool. Previous reports showed that CRISPR/Cpf1 could work effectively in multiple species. But our data show that AsCpf1 activity has a big difference in different vertebrates. Using in vitro experiments, we finally learned that the difference between species is due to temperature.

developmental biology

Neural code uses self-information principle to organize the brain’s universal cell-assembly coding

The brain generates cognition and behavior through firing changes of its neurons, yet, with enormous firing variability, the organizing principle underlying real-time neural code remains unclear. Here, we test the Neural Self-Information Theory that neural code is constructed via the self-information principle under which each inter-spike-interval (ISI) is inherently self-tagged with discrete information based on its relation to ISI variability-probability distribution - higher-probability ISIs, which reflect the balanced excitation-inhibition ground state, convey minimal information, whereas lower-probability ISIs, which signify statistical surprisals, carry more information. Moreover, temporally coordinated ISI surprisals across neural cliques intrinsically give rise to real-time cell-assembly neural code. As a result, this self-information-based neural coding is uniquely intrinsic to the neurons themselves, with no need for outside observers to set any reference point to manually mark external or internal inputs. Applying this neural self-information concept, we devised an unbiased general decoding strategy and successfully uncovered 15 distinct cell-assembly patterns from multiple cortical and hippocampal circuits associated with different sleep cycles, earthquake, elevator-drop, foot-shock experiences, navigation or various actions in five-choice visual-discrimination operant-conditioning tasks. Detailed analyses of all 15 cell assemblies revealed that ~20% of the skewed ISI distribution tails were responsible for the emergence of robust cell-assembly codes, conforming to the Pareto Principle. These findings support the notion that neural coding is organized via the self-information principle to generate real-time information across brain regions, cognitive modalities, and behaviors.

neuroscience

IFNα, a potential biomarker for stress vitiligo risk

Neural hypothesis has become an important aspect of vitiligo, yet without corresponding diagnostic indicators. We preliminarily found 32 cases of vitiligo patients with certain aggregation of mental factors. In peripheral blood mononuclear cells (PBMCs) of these patients, transcriptome analyses revealed that the circulation expression of a type I interferon (IFN-I)-dependent genes was induced. Also, serum IFN was elevated in vitiligo patients with depression. Therefore, our hypothesis is whether IFN levels predict the occurrence of psychiatric vitiligo. Through the establishment of stress-induced depigmentation model, serum IFN also showed increase. Intracerebroventricular and subcutaneous IFN injection can both elicit not only depressive behavior but also vitiligo-like characteristics. Mechanistically, central IFN induces the release of dorsal root ganglion (DRG) substance P (SP) to inhibit melanogenesis. Peripheral IFN disturbs cutaneous-neuro-endocrine microenvironment. Type I IFN (IFN) pathway-related genes in stress vitiligo were significantly discriminating from non-stress vitiligo, while that of type II IFN pathway was not.

physiology

Characterization Of Imprinted Genes In Rice Reveals Post-Fertilization Regulation And Conservation At Some Loci Of Imprinting In Plant Species

Genomic imprinting is an epigenetic phenomenon by which certain genes display monoallelic expression in a parent-of-origin-dependent manner. Hundreds of imprinted genes have been identified from several plant species. Here we identified, with a high level of confidence, 208 imprinted candidates from rice. Imprinted genes of rice showed limited association to the transposable elements, which is contrast to the findings in Arabidopsis. Generally, imprinting of rice is conserved within species, but intraspecific variations were confirmed here. Imprinting between cultivated rice and wild rice are likely similar. The imprinted genes of rice do not show significant selective signatures overall, which suggests that domestication imposes limited evolutionary effects on genomic imprinting of rice. Though the conservation of imprinting in plants is limited, here we prove that some loci tend to be imprinted in different species. In addition, our results suggest that differential epigenetic regulation between parental alleles can be established either prior to or post-fertilization. The imprinted 24-nt small RNAs, but not the 21-nt ones, likely involve the regulation of imprinting in an opposite parental-allele targeting manner. Together, our findings suggest that regulation of imprinting can be very diverse, and genomic imprinting as well as imprinted genes have essential evolutionary and biological significance.

plant biology

PolyCut: a computer programme for assignments of MSn signals of metallo-biomolecules by considering the entire isotope patterns

A computer programme PolyCut has been written to assist mass spectrometry-based bioinorganic studies via top-down and bottom-up approaches in positive and negative ion modes. PolyCut is designed to cope with metalloproteins, metallo-polymers and biomolecules with heavy element(s) as one (or more) of the charging agents at defined but different oxidation states. It does automatic assignment by considering the entire experimental and simulated isotopic patterns of an ion rather than reading only the mono-isotopic and average m/z values (and/or mass values). The calculation of chemical formula and the simulation of isotopic pattern for an ion at various charge states require PolyCut to be informed of the user-defined elements, the user-defined abundance of isotopes for each element, the user-defined oxidation state of an element, the user-defined residues and sequence of a polymer, and the user-defined fragmentation (or digestion). The programme successfully assisted MSn studies of two copper proteins coordinated to platinum(II) centres (a functional group possessing an intrinsic positive charge rather than a neutral organic modification), published as J. Biol. Inorg. Chem. 2009, 14(2), 163-165; Metallomics 2013, 5(8), 946-954; and [more]. Besides polypeptides, polynucleotides and polysaccharides, PolyCut can be extended to other polymers using user-defined monomer residues. For the metallo-community.\n\nAbbreviations

biochemistry