Miracle-dz/UniFAR-FTUs huggingface dataset:
Neural responses to natural visual motion are spatially selective across the visual field, with selectivity differing across brain areas and task

It is well established that neural responses to visual stimuli are enhanced at select locations in the visual field. While spatial selectivity and the effects of spatial attention are well-understood for discrete tasks (e.g., visual cueing paradigms), little is known about neural response during a naturalistic visual experience that involves complex dynamic visual stimuli, for instance, driving. In this study, we assess the strength of neural responses across the visual space during a kart race video game. Specifically, we measure the correlation strength of scalp evoked potentials with optical flow magnitude at individual locations on the screen. We find the strongest neural responses for task-relevant locations in visual space, selectively extending to areas beyond the focus of overt attention: while the driver’s gaze is directed upon the heading direction at the center of the screen, we observe robust neural evoked responses also to peripheral areas such as the road and surrounding buildings. Importantly, this spatial selectivity of neural responses differs across scalp locations. Moreover, during active gameplay, the strength of the spatially-selective neural responses are enhanced compared to passive viewing. Spatially selective neural gains have previously been interpreted as an attentional gain mechanism. In this view, the present data suggest that different brain areas focus attention on different task-relevant portions of the visual field, reaching beyond the focus of overt attention.
Vibrio cholerae’s mysterious Seventh Pandemic island (VSP-II) encodes novel Zur-regulated zinc starvation genes involved in chemotaxis and cell congregation

Vibrio cholerae is the causative agent of cholera, a notorious diarrheal disease that is typically transmitted via contaminated drinking water. The current pandemic agent, the El Tor biotype, has undergone several genetic changes that include horizontal acquisition of two genomic islands (VSP-I and VSP-II). VSP presence strongly correlates with pandemicity; however, the contribution of these islands to V. cholerae’s life cycle, particularly the 26-kb VSP-II, remains poorly understood. VSP-II-encoded genes are not expressed under standard laboratory conditions, suggesting that their induction requires an unknown signal from the host or environment. One signal that bacteria encounter under both host and environmental conditions is metal limitation. While studying V. cholerae’s zinc-starvation response in vitro, we noticed that a mutant constitutively expressing zinc starvation genes (Δzur) congregates at the bottom of a culture tube when grown in a nutrient-poor medium. Using transposon mutagenesis, we found that flagellar motility, chemotaxis, and VSP-II encoded genes were required for congregation. The VSP-II genes encode an AraC-like transcriptional activator (VerA) and a methyl-accepting chemotaxis protein (AerB). Using RNA-seq and lacZ transcriptional reporters, we show that VerA is a novel Zur target and an activator of the nearby AerB chemoreceptor. AerB interfaces with the chemotaxis system to drive oxygen-dependent congregation and energy taxis. Importantly, this work suggests a functional link between VSP-II, zinc-starved environments, and energy taxis, yielding insights into the role of VSP-II in a metal-limited host or aquatic reservoir.
A rapid and efficient learning rule for biological neural circuits

The dominant view in neuroscience is that changes in synaptic weights underlie learning. It is unclear, however, how the brain is able to determine which synapses should change, and by how much. This uncertainty stands in sharp contrast to deep learning, where changes in weights are explicitly engineered to optimize performance. However, the main tool for that, backpropagation, has two problems. One is neuro-science related: it is not biologically plausible. The other is inherent: networks trained with this rule tend to forget old tasks when learning new ones. Here we introduce the Dendritic Gated Network (DGN), a variant of the Gated Linear Network, which offers a biologically plausible alternative to backpropagation. DGNs combine dendritic ‘gating’ (whereby interneurons target dendrites to shape neuronal responses) with local learning rules to yield provably efficient performance. They are significantly more data efficient than conventional artificial networks, and are highly resistant to forgetting. Consequently, they perform well on a variety of tasks, in some cases better than backpropagation. Importantly, DGNs have structural and functional similarities to the cerebellum, a link that we strengthen by using in vivo two-photon calcium imaging to show that single interneurons suppress activity in individual dendritic branches of Purkinje cells, a key feature of the model. Thus, DGNs leverage targeted dendritic inhibition and local learning – two features ubiquitous in the brain – to achieve fast and efficient learning.
Glucose decoration on wall-teichoic acid is required for phage adsorption and InlB-mediated virulence in Listeria ivanovii

Listeria ivanovii (Liv) is an intracellular Gram-positive pathogen that primarily infects ruminants, but also occasionally causes enteric infections in humans. Albeit rare, this bacterium possesses the capacity to cross the intestinal epithelium of humans, similar to its more frequently pathogenic cousin, Listeria monocytogenes (Lmo). Recent studies in Lmo have shown that specific glycosyl modifications on the cell wall-associated glycopolymers (termed wall-teichoic acid, or WTA) of Lmo are responsible for bacteriophage adsorption and retention of the major virulence factor, Internalin B (InlB). However, the relationship between InlB and WTA in Liv remains unclear. Here, we report the identification of the unique gene, liv1070 that encodes a putative glucosyltransferase in the polycistronic WTA gene cluster of the Liv WSLC 3009 genome. We found that in-frame deletion of liv1070 led to loss of the glucose substitution on WTA, as revealed by UPLC-MS analysis. Interestingly, the glucose-deficient mutant became resistant to phage B025 infection due to an inability of the phage to adsorb to the bacterial surface, a binding process mediated by the receptor-binding protein B025_Gp17. As expected, deletion of liv1070 led to loss of InlB retention to the bacterial cell wall, which corresponded to a drastic decrease in cellular invasion. Genetic complementation of liv1070 restored the characteristic phenotypes, including glucose decoration, phage adsorption, and cellular invasion. Taken together, our data demonstrate that an interplay between phage, bacteria, and host cells also exists in Listeria ivanovii, suggesting the trade-off between phage resistance and virulence attenuation may be a general feature in the Listeria genus. Importance Listeria ivanovii is a Gram-positive bacterial pathogen known to cause enteric infection in rodents and ruminants, and occasionally in immunocompromised humans. Recent investigations revealed that, in its better-known cousin Listeria monocytogenes, strains develop resistance to bacteriophage attack due to loss of glycosylated surface receptors, which subsequently resulting in disconnection of one of the bacterium’s major virulence factors, InlB. However, the situation in L. ivanovii remains unclear. Here, we show that L. ivanovii acquires phage resistance following deletion of a unique glycosyltransferase. This deletion also leads to dysfunction of InlB, making the resulting strain unable to invade host cells. Overall, this study suggests that the interplay between phage, bacteria and the host may be a feature common to the Listeria genus.
SOIL DEFORMATION AND SHEAR STRENGTH CHARACTERISTICS OF SOME CLAY SOILS AT DIFFERENT MOISTURE CONTENTS

Summary The soil deformation and shear strength characteristics of three clay soils were determined at different moisture contents and spherical pressures, using a quick un-drained triaxial compression test. The soils were found to deform either in a compressive way or by brittle fissuring, depending upon the relative values of moisture content, dry density and spherical pressure. The critical state concept of soil deformation can explain qualitatively the behaviour of these spils at high moisture contents but not at low. The Bridgman concept for fracture in brittle materials describes the soil behaviour at low moisture contents. The shear strength of the clay soils tested was more closely related to the soil moisture suction and to the amount of shrinkage which occurred on drying than to the absolute dry bulk density. The influence of moisture content and spherical pressure on the effectiveness of certain cultivation operations are considered.
Exposure to sevoflurane results in changes of transcription factor occupancy in sperm and inheritance of autism

Abstract One in 54 children in the United States is diagnosed with autism spectrum disorder. De novo germline and somatic mutations cannot account for all cases of autism spectrum disorder, suggesting that epigenetic alterations triggered by environmental exposures may be responsible for a subset of autism spectrum disorder cases. Human and animal studies have shown that exposure of the developing brain to general anesthetic agents can trigger neurodegeneration and neurobehavioral abnormalities, but the effects of general anesthetics on the germline have not been explored in detail. We exposed pregnant mice to sevoflurane during the time of embryonic development when the germ cells undergo epigenetic reprogramming and found that more than 38% of the directly exposed F1 animals exhibit impairments in anxiety and social interactions. Strikingly, 44–47% of the F2 and F3 animals, which were not directly exposed to sevoflurane, show the same behavioral problems. We performed ATAC-seq and identified more than 1200 differentially accessible sites in the sperm of F1 animals, 69 of which are also present in the sperm of F2 animals. These sites are located in regulatory regions of genes strongly associated with autism spectrum disorder, including Arid1b, Ntrk2, and Stmn2. These findings suggest that epimutations caused by exposing germ cells to sevoflurane can lead to autism spectrum disorder in the offspring, and this effect can be transmitted through the male germline inter- and transgenerationally. Summary sentence Pregnant mouse F0 females exposed to sevoflurane give rise to F1 males with sociability and anxiety defects. These behaviors are transmitted to F2 and F3 males. Their sperm show changes in transcription factor occupancy in genes implicated in autism. Graphical Abstract
Pediatric nasal epithelial cells are less permissive to SARS-CoV-2 replication compared to adult cells

Children typically experience more mild symptoms of COVID-19 when compared to adults. There is a strong body of evidence that children are also less susceptible to SARS-CoV-2 infection with the ancestral viral isolate. However, the emergence of SARS-CoV-2 variants of concern (VOCs) has been associated with an increased number of pediatric infections. Whether this is the result of widespread adult vaccination or fundamental changes in the biology of SARS-CoV-2 remains to be determined. Here, we use primary nasal epithelial cells from children and adults, differentiated at an air-liquid interface to show that the ancestral SARS-CoV-2 replicates to significantly lower titers in the nasal epithelial cells of children compared to those of adults. This was associated with a heightened antiviral response to SARS-CoV-2 in the nasal epithelial cells of children. Importantly, the Delta variant also replicated to significantly lower titres in the nasal epithelial cells of children. This trend was markedly less pronounced in the case of Omicron. It is also striking to note that, at least in terms of viral RNA, Omicron replicated better in pediatric NECs compared to both Delta and the ancestral virus. Taken together, these data show that the nasal epithelium of children supports lower infection and replication of ancestral SARS-CoV-2, although this may be changing as the virus evolves.
Transfer Entropy Based Causality From Head Motion To Eye Movement

Eye movement behavior, which provides the visual information acquisition and processing, plays an important role in performing sensorimotor tasks, such as driving, by human beings in everyday life. In the procedure of performing sensorimotor tasks, eye movement is contributed through a specific coordination of head and eye in gaze changes, with head motions preceding eye movements. Notably we believe that this coordination in essence indicates a kind of causality. In this paper, we investigate transfer entropy to set up a quantity for measuring an unidirectional causality from head motion to eye movement. A normalized version of the proposed measure, demonstrated by virtual reality based psychophysical studies, behaves very well as a proxy of driving performance, suggesting that quantitative exploitation of coordination of head and eye may be an effective behaviometric of sensorimotor activity.
Identifying regions in prefrontal cortex related to working memory improvement: A novel meta-analytic method using electric field modeling

Altering cortical activity using transcranial direct current stimulation (tDCS) has been shown to improve working memory (WM) performance. Due to large inter-experimental variability in the tDCS montage configuration and strength of induced electric fields, results have been mixed. Here, we present a novel meta-analytic method relating behavioral effect sizes to electric field strength to identify brain regions underlying largest tDCS-induced WM improvement. Simulations on 69 studies targeting left prefrontal cortex showed that tDCS electric field strength in lower dorsolateral prefrontal cortex (Brodmann area 45/47) relates most strongly to improved WM performance. This region explained 7.8% of variance, equaling a medium effect. A similar region was identified when correlating WM performance and electric field strength of right prefrontal tDCS studies (n = 18). Maximum electric field strength of five previously used tDCS configurations were outside of this location. We thus propose a new tDCS montage which maximizes the tDCS electric field strength in that brain region. Our findings can benefit future tDCS studies that aim to affect WM function. Highlights - We summarize the effect of 87 tDCS studies on working memory performance - We introduce a new meta-analytic method correlating tDCS electric fields and performance - tDCS-induced electric fields in lower DLPFC correlate significantly with improved working memory - The lower DLPFC was not maximally targeted by most tDCS montages and we provide an optimized montage
Stereo Slant Discrimination of Planar 3D Surfaces: Standard vs. Planar Cross-Correlation

Binocular stereo cues are important for discriminating 3D surface orientation, especially at near distances. We devised a single-interval task where observers discriminated the slant of a densely textured planar test surface relative to a textured planar surround reference surface. Although surfaces were rendered with correct perspective, the stimuli were designed so that the binocular cues dominated performance. Slant discrimination performance was measured as a function of the reference slant and the level of uncorrelated white noise added to the test-plane images in the left and right eye. We compared human performance with an approximate ideal observer (planar cross correlation, PCC) and two sub-ideal observers. The PCC observer uses the image in one eye and back projection to predict the test image in the other eye for all possible slants, tilts, and distances. The estimated slant, tilt, and distance are determined by the prediction that most closely matches the measured image in the other eye. The first sub-ideal observer (local PCC, LPCC) applies planar cross correlation over local neighborhoods and then pools estimates across the test plane. The second sub-optimal observer (standard cross correlation, SCC), uses only positional disparity information. We find that the ideal observer (PCC) and the first sub-ideal observer (LPCC) outperform the second sub-ideal observer (SCC), demonstrating the benefits of structural disparities. We also find that all three model observers can account for human performance, if two free parameters are included: a fixed small level of internal estimation noise, and a fixed overall efficiency scalar on slant discriminability. Precis We measured human stereo slant discrimination thresholds for accurately-rendered textured surfaces designed so that performance is dominated by binocular-disparity cues. We compared human performance with an approximate ideal observer and two sub-ideal observers.
Bruton’s Tyrosine Kinase Supports Gut Mucosal Immunity and Commensal Microbiome Recognition in Autoimmune Arthritis

Bruton’s tyrosine kinase (Btk) deficiency preferentially eliminates autoreactive B cells while sparing normal humoral responses, but has not been studied in mucosal immunity. Commensal microbes are essential for arthritis in K/BxN mice, used here to examine how BTK-mediated signaling interfaces with the microbiome. Btk-deficient K/BxN mice were found to have small Peyer’s Patches with reduced germinal center and IgA+ B cells. Although lamina propria IgA+ plasma cells were numerically normal, intestinal IgA was low and IgA coating of commensal bacteria was reduced. IgA-seq showed a shift in microbes that are normally IgA-coated into the uncoated fraction in Btk-deficient mice. In this altered microbial milieau, the proportion of Parabacteroides distasonis was reduced in Btk-deficient K/BxN mice. To determine whether P. distasonis contributes to arthritis, it was reintroduced into antibiotic-protected K/BxN mice, where it restored disease. This suggests that P. distasonis’ inability to thrive in Btk-deficient mice may be a factor in disease protection. Thus, BTK supports normal intestinal IgA development, with downstream effects on the microbiome that may contribute to autoimmunity.
Distinct generation of subjective vividness and confidence during naturalistic memory retrieval in angular gyrus

Our subjective experience of remembering guides and monitors the reconstruction of past and simulation of the future, which enables us to identify mistakes and adjust our behavior accordingly. However, it remains incompletely understood what underlies the process of subjective mnemonic experience. Here, we combined behavior, repetitive transcranial magnetic stimulation (rTMS), and functional neuroimaging to probe whether vividness and confidence are generated differently during retrieval. We found that preretrieval rTMS targeting the left angular gyrus (AnG) selectively attenuated the vividness efficiency compared to control stimulation while keeping metacognitive efficiency and objective memory accuracy unaffected. Using trial-wise data, we showed that AnG stimulation altered the mediating role of vividness in confidence in the accuracy of memory judgment. Moreover, resting-state functional connectivity of hippocampus and AnG was specifically associated with vividness efficiency, but not metacognitive efficiency across individuals. Together, these results identify the causal involvement of AnG in gauging the vividness, but not the confidence, of memory, thereby suggesting a differentiation account of conscious assessment of memory by functionally and anatomically dissociating the monitoring of vividness from confidence.
Endogenous retrovirus rewired the gene regulatory network shared between primordial germ cells and naïve pluripotent cells in hominoids

Although the gene regulatory network controlling germ cell development is critical for gamete integrity, this network has been substantially diversified during mammalian evolution. Here, we show that several hundred loci of LTR5_Hs, a hominoid-specific endogenous retrovirus (ERV), function as enhancers in both human primordial germ cells (PGCs) and naïve pluripotent cells. PGCs and naïve pluripotent cells exhibit a similar transcriptome signature, and the enhancers derived from LTR5_Hs contribute to establishing such similarity. LTR5_Hs appears to be activated by transcription factors critical in both cell types (KLF4, TFAP2C, NANOG, and CBFA2T2). Comparative transcriptome analysis between humans and macaques suggested that the expression of many genes in PGCs and naïve pluripotent cells has been upregulated by LTR5_Hs insertions in the hominoid lineage. Together, this study suggests that LTR5_Hs insertions have rewired and finetuned the gene regulatory network shared between PGCs and naïve pluripotent cells during hominoid evolution. Teaser A hominoid-specific ERV has rewired the gene regulatory network shared between PGCs and naïve pluripotent cells.
The genetic basis of differential autodiploidization in evolving yeast populations

Spontaneous whole-genome duplication, or autodiploidization, is a common route to adaptation in experimental evolution of haploid budding yeast populations. The rate at which autodiploids fix in these populations appears to vary across strain backgrounds, but the genetic basis of these differences remains poorly characterized. Here we show that the frequency of autodiploidization differs dramatically between two closely related laboratory strains of Saccharomyces cerevisiae, BY4741 and W303. To investigate the genetic basis of this difference, we crossed these strains to generate hundreds of unique F1 segregants and tested the tendency of each segregant to autodiplodize across hundreds of generations of laboratory evolution. We find that variants in the SSD1 gene are the primary genetic determinant of differences in autodiploidization. We then used multiple laboratory and wild strains of S. cerevisiae to show that clonal populations of strains with a functional copy of SSD1 autodiploidize more frequently in evolution experiments, while knocking out this gene or replacing it with the W303 allele reduces autodiploidization propensity across all genetic backgrounds tested. These results suggest a potential strategy for modifying rates of spontaneous whole-genome duplications in laboratory evolution experiments in haploid budding yeast. They may also have relevance to other settings in which eukaryotic genome stability plays an important role, such as biomanufacturing and the treatment of pathogenic fungal diseases and cancers.