Miracle-dz/UniFAR-FTUs huggingface dataset:
Coevolutionary dynamics via adaptive feedback in collective-risk social dilemma game

Human society and natural environment form a complex giant ecosystem, where human activities not only lead to the change of environmental states, but also react to them. By using collective-risk social dilemma game, some studies have already revealed that individual contributions and the risk of future losses are inextricably linked. These works, however, often use an idealistic assumption that the risk is constant and not affected by individual behaviors. We here develop a coevolutionary game approach that captures the coupled dynamics of cooperation and risk. In particular, the level of contributions in a population affects the state of risk, while the risk in turn influences individuals’ behavioral decision-making. Importantly, we explore two representative feedback forms describing the possible effect of strategy on risk, namely, linear and exponential feedbacks. We find that cooperation can be maintained in the population by keeping at a certain fraction or forming an evolutionary oscillation with risk, independently of the feedback type. However, such evolutionary outcome depends on the initial state. Taken together, a two-way coupling between collective actions and risk is essential to avoid the tragedy of the commons. More importantly, a critical starting portion of cooperators and risk level is what we really need for guiding the evolution toward a desired direction.
The cortico-thalamic loop attunes competitive lateral interactions across retinotopic and orientation preference maps

In the early visual system, corticothalamic feedback projections greatly outnumber thalamocortical feedforward projections. Extensive experimental and modeling work has been devoted to the functional impact of the feedforward pathway, but the role of its denser feedback counterpart remains elusive. Here, we propose a novel unifying framework where thalamic recurrent interactions and corticothalamic feedback act in a closed-loop fashion to attune multiple stimulus representations. At each position of the visual field, the loop puts into competition local representations of the stimulus in thalamus and cortex through direct excitation of narrow topologically-aligned portions of the thalamus, accompanied with peri-geniculate nucleus mediated broad inhibition suppressing the topological surround. We built a detailed conductance-based spiking model incorporating retinal input, lateral geniculate nucleus, peri-geniculate nucleus, primary visual cortex, and all the relevant intra-areal and feedback pathways. For the first time we perform comparative analyses between model configurations with completely or locally inactivated cortico-thalamic feedback, as in the experimental preparations. The model mechanistically explains (i) the existence of intra-thalamic surround suppression, (ii) the sensitivity of thalamic neurons to orientation tuning, (iii) the cortex-dependent center-surround opponency in thalamic cells, (iv) the cortical increase of size and orientation selectivity, (v) the cortically enhanced competition between cross-oriented domains within the hypercolumn, and (vi) the selective suppression of cortical functional connectivity. Our results integrate decades of experimental and theoretical research, supporting the hypothesis that cortico-thalamic loop exerts competitive influence between neighboring regions in the thalamus and cortex, complementing the lateral intra-V1 interactions in center-surround contextual modulation.
Endogenous opioid release following orgasm in man: A combined PET-fMRI study

Sex is one of the most rewarding and motivating behaviours for humans. Endogenous mu-opioid receptor system (MORs) plays a key role in the mammalian reward circuit. Both human and animal experiments suggest the involvements of MORs in human sexual pleasure, yet this hypothesis currently lacks in vivo support. We used positron emission tomography (PET) with the radioligand [11C]carfentanil, which has high affinity for MORs to quantify endogenous opioid release following orgasm in man. Subjects were scanned twice: Once immediately after reaching an orgasm and once in a baseline state. Haemodynamic activity was measured with functional magnetic resonance imaging during penile stimulation from partner. The PET data revealed significant opioid release in hippocampus. Haemodynamic activity in somatosensory and motor cortices as well as hippocampus and thalamus increased during penile stimulation, and thalamic activation was linearly dependent on self-reported sexual arousal. Altogether these data show that endogenous opioidergic activation in the medial temporal lobe is centrally involved in sexual arousal.
Switching between External and Internal Attention in Hippocampal Networks

Everyday experience requires processing external signals from the world around us and internal information retrieved from memory. To do both, the brain must fluctuate between states that are optimized for external versus internal attention. Here, we focus on the hippocampus as a region that may serve at the interface between these forms of attention and ask how it switches between prioritizing sensory signals from the external world versus internal signals related to memories and thoughts. Pharmacological, computational, and animal studies have identified input from the cholinergic basal forebrain as important for biasing the hippocampus toward processing external information, whereas complementary research suggests the dorsal attention network (DAN) may aid in allocating attentional resources toward accessing internal information. We therefore tested the hypothesis that the basal forebrain and DAN drive the hippocampus toward external and internal attention, respectively. We used data from 29 human participants (17 female) who completed two attention tasks during fMRI. One task (memory-guided) required proportionally more internal attention, and proportionally less external attention, than the other (explicitly instructed). We discovered that background functional connectivity between the basal forebrain and hippocampus was stronger during the explicitly instructed versus memory-guided task. In contrast, DAN–hippocampus background connectivity was stronger during the memory-guided versus explicitly instructed task. Finally, the strength of DAN–hippocampus background connectivity was correlated with performance on the memory-guided but not explicitly instructed task. Together, these results provide evidence that the basal forebrain and DAN may modulate the hippocampus to switch between external and internal attention. SIGNIFICANCE STATEMENT How does the brain balance the need to pay attention to internal thoughts and external sensations? We focused on the human hippocampus, a region that may serve at the interface between internal and external attention, and asked how its functional connectivity varies based on attentional states. The hippocampus was more strongly coupled with the cholinergic basal forebrain when attentional states were guided by the external world rather than retrieved memories. This pattern flipped for functional connectivity between the hippocampus and dorsal attention network, which was higher for attention tasks that were guided by memory rather than external cues. Together, these findings show that distinct networks in the brain may modulate the hippocampus to switch between external and internal attention.
Shared neural codes of recognition memory

Recognition memory research has identified several electrophysiological indicators of successful memory retrieval, known as old-new effects. These effects have been observed in different sensory domains using various stimulus types, but little attention has been given to their similarity or distinctiveness and the underlying processes they may share. Here, a data-driven approach was taken to investigate the temporal evolution of shared information content between different memory conditions using openly available EEG data from healthy human participants of both sexes, taken from six experiments. A test dataset involving personally highly familiar and unfamiliar faces was used. The results show that neural signals of recognition memory for face stimuli were highly generalized starting from around 200 ms following stimulus onset. When training was performed on non-face datasets, an early (around 200-300 ms) to late (post-400 ms) differentiation was observed over most regions of interest. Successful cross-classification for non-face stimuli (music and object/scene associations) was most pronounced in late period. Additionally, a striking dissociation was observed between familiar and remembered objects, with shared signals present only in the late window for correctly remembered objects, while cross-classification for familiar objects was successful in the early period as well. These findings suggest that late neural signals of memory retrieval generalize across sensory modalities and stimulus types, and the dissociation between familiar and remembered objects may provide insight into the underlying processes.
pOpsicle: An all-optical reporter system for synaptic vesicle recycling combining pH-sensitive fluorescent proteins with optogenetic manipulation of neuronal activity

pH-sensitive fluorescent proteins are widely used to study synaptic vesicle (SV) fusion and recycling. When targeted to the lumen of SVs, fluorescence of these proteins is quenched by the acidic pH. Following SV fusion, they are exposed to extracellular neutral pH, resulting in a fluorescence increase. SV fusion, recycling and acidification can thus be tracked by tagging integral SV proteins with pH-sensitive proteins. Neurotransmission is generally stimulated by electrophysiology, which is not feasible in small, intact animals, thus limiting the approach to cell culture regimes. Previous in vivo approaches depended on distinct (sensory) stimuli, thus limiting the addressable neuron types. To overcome these limitations, we established an all-optical approach to stimulate and visualize SV fusion and recycling. We combined distinct pH-sensitive fluorescent proteins (inserted into the SV protein synaptogyrin) and light-gated channelrhodopsins (ChRs) for optical stimulation, overcoming optical crosstalk and thus enabling an all-optical approach. We generated two different variants of the pH-sensitive optogenetic reporter of vesicle recycling (pOpsicle) and tested them in cholinergic neurons of intact Caenorhabditis elegans nematodes. First, we combined the red fluorescent protein pHuji with the blue-light gated ChR2(H134R), and second, the green fluorescent pHluorin combined with the novel red-shifted ChR ChrimsonSA. In both cases, fluorescence increases were observed after optical stimulation. Increase and subsequent decline of fluorescence was affected by mutations of proteins involved in SV fusion and endocytosis. These results establish pOpsicle as a non-invasive, all-optical approach to investigate different steps of the SV cycle.
Hippocampal neuronal synchronization in the rat - Dissociation of perception from associative learning

Learning requires flexible switching between perceiving and encoding external sensory stimuli, making associations with representations already stored in memory (retrieval) and acting accordingly to adapt to the environment. Hippocampus is known to be central in creating mnemonic representations, but how it could support the integration of these processes of memory encoding and retrieval during repetitive learning experiences has remained unknown. In this study, we recorded local-field potentials (LFPs) from the dorsal hippocampus during classical trace eyeblink conditioning in rats. An auditory conditioned stimulus (CS) was followed by a periorbital shock-unconditioned stimulus (US). From the LFPs, we separated hippocampal oscillations that were linked with the variation in the trial-by-trial processing of the CS from those linked with the gradual learning of the CS-US association over daily sessions of training. Short latency transient theta and gamma band oscillations were associated with learning so that both the oscillation amplitudes (strength) and phase locking increased as a function of training. In contrast, long-latency sustained alpha and beta oscillations were associated with perception of CS. These data show divergent oscillatory neural signatures for perception and learning in hippocampal subfields.
Transcriptomic reprogramming in a susceptible Phaseolus vulgaris L. variety during Pseudomonas syringae attack: The key role of homogalacturonan methylation

The susceptibility of common bean varieties to Pseudomonas syringae pv. phaseolicola (Pph) has been well-documented. However, the molecular mechanism that drives this susceptibility has not been clarified yet. In an attempt to understand this process, 15-day-old common bean plants, variety riñón, were infected with Pph to analyze the transcriptomic changes during the first steps of the infection (at 2 and 9 h). RNA-seq analysis showed an upregulation of defense-and signaling-related genes at 2h, most of them being downregulated at 9h, suggesting that Pph would inhibit the transcriptomic reprogramming of the plant. This trend was also observed in the modulation of 101 cell wall (CW) related genes, suggesting that Pph could produce/induce changes in the CW. However, the changes in CW composition at early stages of Pph infection were related to homogalacturonan (HG) methylation and the formation of HG egg boxes. From all HG-related genes modulated by the infection, a common bean pectin methylesterase inhibitor 3 (PvPMEI3) gene – closely related to AtPMEI3 — was detected. In addition, PMEI3 protein was located in the apoplast and its PME inhibitory activity was demonstrated. Therefore, PvPMEI3 seems to be a good candidate to play a key role in Pph infection. This premise was supported by the analysis of Arabidopsis pmei3 mutant, which showed susceptibility to Pph, in contrast to resistant Col-0 control plants. All these changes could be an attempt to reinforce the CW structure and thus, hinder the attack of the bacterium. However, these transcriptional and CW-remodeling processes are neither maintained during the necessary time, nor are deep enough to block the action of the pathogen, facilitating the well-known susceptibility of riñón variety to Pph.
Femtosecond microscopy of localized and propagating surface plasmons in silver gratings

Localized and propagating surface plasmons excited with 10 fs, 400 nm laser pulses in silver gratings are imaged with a sub-wavelength spatial resolution. Microscopic images of two-photon photoemission from the nanostructured silver surface representing nonlinear maps of surface plasmon fields are recorded with a photoemission electron microscope (PEEM). Tuning the laser wavelength into the resonance of a silver grating enhances the emission from the propagating mode and attenuates that from the localized modes. Time-resolved interferometric PEEM movies taken at 330 as/frame intervals reveal the dynamics of the oscillation and dephasing of individual localized surface plasmons.
Analyzing postprandial metabolomics data using multiway models: a simulation study

Background Analysis of time-resolved postprandial metabolomics data can improve the understanding of metabolic mechanisms, potentially revealing biomarkers for early diagnosis of metabolic diseases and advancing precision nutrition and medicine. Postprandial metabolomics measurements at several time points from multiple subjects can be arranged as a subjects by metabolites by time points array. Traditional analysis methods are limited in terms of revealing subject groups, related metabolites, and temporal patterns simultaneously from such three-way data. Results We introduce an unsupervised multiway analysis approach based on the CANDECOMP/PARAFAC (CP) model for improved analysis of postprandial metabolomics data guided by a simulation study. Because of the lack of ground truth in real data, we generate simulated data using a comprehensive human metabolic model. This allows us to assess the performance of CP models in terms of revealing subject groups and underlying metabolic processes. We study three analysis approaches: analysis of fasting-state data using principal component analysis, T0-corrected data (i.e., data corrected by subtracting fasting-state data) using a CP model and full-dynamic (i.e., full postprandial) data using CP. Through extensive simulations, we demonstrate that CP models capture meaningful and stable patterns from simulated meal challenge data, revealing underlying mechanisms and differences between diseased versus healthy groups. Conclusions Our experiments show that it is crucial to analyze both fasting-state and T0-corrected data for understanding metabolic differences among subject groups. Depending on the nature of the subject group structure, the best group separation may be achieved by CP models of T0-corrected or full-dynamic data. This study introduces an improved analysis approach for postprandial metabolomics data while also shedding light on the debate about correcting baseline values in longitudinal data analysis.
Forces due to contraction on a cord spanning between two spaceships

A formula is derived estimating the additional tensile forces which a cord must be able to exert to support the Lorentz contraction of itself and of two spaceships, positioned line-ahead, which it spans between, as those ships steadily and identically fire their thrusters. It is found that even a spider's thread of length one metre can exert the forces required to reach half light speed in less than half an hour between ships each weighing a hundred metric tonnes. A critique is also provided of previous published work in this area.
QRATER: a collaborative and centralized imaging quality control web-based application

Quality control (QC) is an important part of all scientific analysis, including neuroscience. With manual curation considered the gold standard, there remains a lack of available tools that make manual neuroimaging QC accessible, fast, and easy. In this article we present Qrater, a containerized web-based python application that enables viewing and rating of previously generated QC images. A group of raters with varying amounts of experience in QC evaluated Qrater in three different tasks: QC of MRI raw acquisition (10,196 images), QC of non-linear registration to a standard template (10,196 images) and QC of skull segmentation (6,968 images). We measured the proportion of failed images, timing and intra- and inter-rater agreement. Raters spent vastly different amounts of time on each image depending on their experience and the task at hand. QC of MRI raw acquisition was the slowest. While an expert rater needed approximately one minute, trained raters spent 2-6 minutes evaluating an image. The fastest was the curation of a skull segmentation image, where expert raters spent on average 3 seconds per image before assigning a rating. Rating agreement also varied depending on the experience of the raters and the task at hand: trained raters’ inter-rater agreement with the expert’s gold standard ranged from fair to substantial in raw acquisition (Cohen’s chance corrected kappa agreement scores up to 0.72) and from fair to excellent in linear registration (kappa scores up to 0.82), while the experts’ inter-rater agreement of the skull segmentation task was excellent (kappa = 0.83). These results demonstrate that Qrater is a useful asset for QC tasks that rely on manual curation of images.
Nigral pathology contributes to microstructural integrity of striatal and frontal tracts in Parkinson’s disease

Background Motor and cognitive impairment in Parkinson’s disease (PD) is associated with dopaminergic dysfunction that stems from substantia nigra (SN) degeneration and concomitant α-synuclein accumulation. Diffusion MRI can detect microstructural alterations of the SN and its tracts to (sub)cortical regions, but their pathological sensitivity is still poorly understood. Objective To unravel the pathological substrate underlying microstructural alterations of the SN, and its tracts to the dorsal striatum and dorsolateral prefrontal cortex (DLPFC) in PD. Methods Combining post-mortem in-situ MRI and histopathology, T1-weighted and diffusion MRI of 9 PD, 6 PD with dementia (PDD), 5 dementia with Lewy bodies (DLB), and 10 control donors were collected. From MRI, mean diffusivity (MD) and fractional anisotropy (FA) were derived from the SN, and tracts between the SN and caudate nucleus, putamen, and DLPFC. Phosphorylated-Ser129-α-synuclein and tyrosine hydroxylase immunohistochemistry was included to quantify nigral Lewy pathology and dopaminergic degeneration, respectively. Results Compared to controls, PD and PDD/DLB showed increased MD of the SN and SN-DLPFC tract, as well as increased FA of the SN-caudate nucleus tract. Both PD and PDD/DLB showed nigral Lewy pathology and dopaminergic loss compared to controls. Increased FA of the SN and SN-caudate nucleus tract was associated with SN dopaminergic loss, while increased MD of the SN-DLPFC tract was associated with increased SN Lewy neurite load. Conclusions In PD and PDD/DLB, diffusion MRI captures microstructural alterations of the SN and tracts to the dorsal striatum and DLPFC, which differentially associates with SN dopaminergic degeneration and Lewy neurite pathology.
The problem of spurious Lyapunov exponents in time series analysis and its solution by covariant Lyapunov vectors

We briefly recall the methods for the determination of Lyapunov exponents from time series data and their limitations. One particular problem is given by the fact that reconstructed phase spaces have usually extra dimensions compared to the true phase space of a dynamical system, leading to extra, so called spurious Lyapunov exponents. Several methods to identify the true ones have been proposed which do not give satisfactory results. We show that the geometric information contained in covariant Lyapunov vectors can be used to identify the true exponents. We illustrate its use and its limitations by applying it to experimental NMR laser data. This article is part of a special issue of Journal of Physics A: Mathematical and Theoretical devoted to ‘Lyapunov analysis: from dynamical systems theory to applications’.
Developing Heat Transfer and Friction in a Ribbed Rectangular Duct With Flow Separation at Inlet

The local heat transfer and pressure drop characteristics of developing turbulent flows in a rectangular duct with an abrupt-contraction entrance and repeated square-rib pairs on the two opposite walls have been investigated experimentally. Both entrance-region and periodic-fully-developed-region results were obtained. Laser holographic interferometry was employed in the local and average heat transfer measurements. The Reynolds number was varied from 5.0x10[sup 3] to 5.0x10[sup 4]; the rib pitch-to-height ratios were 10, 15, and 20; and the rib height-to-duct height ratio was kept at a value of 0.13. The results allowed the entry length to be determined and the regions susceptible to hot spots to be located. Semi-empirical heat transfer and friction correlations for the periodic fully developed region were developed. Moreover, performance comparisons between the ribbed and smooth ducts were made under two types of constraint, namely equal mass flow rate and equal pumping power. Finally, the effect of thermal entry length on the length mean Nusselt number was also investigated. The results showed that the length mean Nusselt number ratio was a function of only the duct length and independent of PR and Re, and could be further correlated by an equation of the form [bar N]u[sub m]/[bar N]u[sub p]=1more » + 1.844/(X/De). « less
Some relations between nonexpansive and order preserving mappings

Abstract : It is shown that nonlinear operators which preserve the integral are order preserving if and only if they are nonexpansive in L(1) and that those wich commute with translation by a constant are order preserving if and only if they are nonexpansive in L(infinity). Examples are presented and involving partial differential equations, difference approximations and rearrangements. (Author)