Miracle-dz/UniFAR-FTUs huggingface dataset:
Perception of near-threshold visual stimuli is influenced by pre-stimulus alpha-band amplitude but not by alpha phase

Ongoing brain activity preceding visual stimulation has been suggested to shape conscious perception. The underlying mechanisms are still under debate, although alpha oscillations have been pointed out as the main explanatory candidate. According to the pulsed-inhibition framework, bouts of functional inhibition arise in each alpha cycle, allowing information to be processed in a pulsatile manner. Consequently, it has been hypothesized that perceptual outcome can be influenced by the specific phase of alpha oscillations prior to the stimulus onset, although empirical findings are controversial. In this study, we aimed to shed light on the role of pre-stimulus alpha oscillations in visual perception. To this end, we recorded electroencephalographic (EEG) activity while participants performed three near-threshold visual detection tasks with different attentional involvement: a no-cue task, a non-informative cue task (50% cue validity), and an informative cue task (100% cue validity). Cluster-based permutation statistics were complemented with Bayesian analyses to test the effect of pre-stimulus oscillatory amplitude and phase on visual awareness. We additionally examined whether these effects differed on trials with low and high oscillatory amplitude, as expected from the pulsed-inhibition theory. Our results show a clear effect of pre-stimulus alpha amplitude on conscious perception, but only when alpha fluctuated spontaneously and was not modulated by attention, supporting the notion that alpha-band power indexes neural excitability. In contrast, we did not find any evidence that pre-stimulus alpha phase influences the perceptual outcome, not even when differentiating between low and high amplitude trials. Furthermore, Bayesian analysis provided moderate evidence in favor of the absence of phase effects. Taken together, our results challenge the central theoretical predictions of the pulsed-inhibition framework, at least for the particular experimental conditions used here.
Behavioral, molecular and neuronal mechanisms involved in recognition memory retrieval under degraded spatial cues in the rat hippocampus

In a constantly changing environment, organisms face the challenge of adapting their behavior by retrieving previous experiences or acquiring new information. Previous research has postulated that this balance between memory generalization and differentiation manifests in a dichotomic manner. When environmental information exceeds a given threshold, activation of a stored representation could initiate retrieval, but below this threshold, a novel event could be encoded with a concomitant remapping of the internal representation in the hippocampus. Here, we examined the hippocampal molecular and neuronal mechanisms underlying retrieval in a cue-degraded environment by combining in vivo electrophysiological recordings and pharmacological manipulations. We developed a memory recognition task that allows a graded decrease in the contextual cues present during retrieval. We found that the manipulation of the number of visual cues was consistent with the activation or not of the contextual memory trace. Retrieval of a specific context memory was reflected by the level of CA3 remapping, demonstrating a clear relationship between remapping and contextual recognition. Also, manipulation of NMDAR activity in the DG-CA3 circuit bidirectionally modulated contextual memory retrieval. The blockade of NMDAR in CA3 impaired recognition in a cue-degraded, but not in a full-cue context, while their activation has the opposite effect. Conversely, blockade of NMDAR in the DG promoted retrieval under an even more cue-degraded environment, while activation had the opposite effect. Our results provide evidence for a flexible interaction between environmental cues and information stored in the hippocampus and give new insights into the biological mechanisms that balance memory encoding and retrieval.
Cardiopulmonary structural, functional and immune-alterations in a Down syndrome mouse model and upon modulation of EGCG

In individuals with Down syndrome (DS), cardiovascular and pulmonary diseases are the most common health problem and result in increased mortality and morbidity. Although these clinical comorbidities are well described, no preclinical models for DS are fully characterized for cardiopulmonary alterations, preventing research to understanding the development and pharmacological modulation of lungs, heart and immune system. Our objective is to characterize the cardiopulmonary and immunological phenotype in Ts65Dn mice and investigate the modulatory effects green tea extract enriched in epigallocatechin 3 gallate (GTE-EGCG). GTE-EGCG administration started at embryonic day 9 and was discontinued at postnatal day (PD) 180. Newborns were longitudinally monitored until PD210 using micro-computed tomography. At endpoint, we characterized the structural, functional and immunological alterations and persistent effects of GTE-EGCG administration. This study revealed normal lung development in the Ts65Dn mice and highlighted RV hypertrophy and immunological alterations. GTE-EGCG administration resulted in genotype-specific and genotype-independent alterations resulting in lung immaturation and airway hyperreactivity. Our results highlight the cardiovascular and immunological phenotype of Ts65Dn mice and potential use for safety studies of therapeutic agents in a DS-specific context. Summary statement This study longitudinally follows respiratory and cardiac alterations in the Ts65Dn mouse model and describes the impact of prenatal EGCG modulation on the euploid and trisomic phenotype
Effects of selfing on speciation through the accumulation of Dobzhansky-Muller incompatibilities

Phylogenetic analyses suggest that self-compatible lineages have higher speciation rates than self-incompatible lineages. However, the effects of selfing on speciation remain unclear. Although a selfing population can resist gene flow from other populations, selfing may increase gene flow from a focal population to other populations. This study investigates the effects of selfing rates of two populations on the waiting time to speciation through the accumulation of Dobzhansky-Muller incompatibilities (DMI). Generally, a higher mean selfing rate of two populations facilitates speciation when incompatibility-controlling alleles are recessive and are weakly selected, and when gene flow is mainly through pollen dispersal instead of seed dispersal. However, the selfing rate difference between two populations can retard speciation, especially when the selfing rate of immigrants remains unchanged after migration. When the selfing rates of two populations differ, speciation may be fastest when the mean selfing rate is intermediate. Given that selfing rates often vary among conspecific populations in plant species, the results indicate that lineages with higher mean selfing rates may not necessarily have higher rates of speciation through the accumulation of DMI, and also call for an estimation of the dependency of speciation rates on selfing rates.
Modelling the displacement and coexistence of clonal lineages of Phytophthora infestans through revisiting past outbreaks

The continuous changes in the lineage proportions of populations in the clonal plant pathogen Phytophthora infestans on potato and tomato crops have been perplexing to researchers and disease managers. Sudden outbreaks of newly emergent genotypes are often associated with these rapid composition changes. Modelling can predict the persistence and displacement of pathogen genotypes with differential fitness among hosts. Building upon previous models, we combined analytical and simulation methods to model the outcome of interactions between competing lineages on multiple hosts. Model inputs include pathogenesis parameters, and the outputs are fitness and lineage proportions within each host. Analytical solutions yielding complete displacement, partial coexistence-displacement, and complete coexistence were described. In a retrospective study, the lesion growth rate and sporulation density of P. infestans lineages on potato and tomato from pathogenicity trials were used as inputs. Output lineage frequencies were compared with historical epidemiological situations to check model accuracy. The results showed that pathogenesis traits measured from empirical trials could simulate lineage constituents on potato and tomato, and estimate genotypic fitness with reasonable accuracy. The model also showed promise in predicting ongoing lineage displacements in the subsequent year or few years, even when the displaced lineage was still highly prevalent during the time of isolation. However, large uncertainties remain at temporal-spatial scales owing to complex meta-population dynamics in some regions and adaptation to local environmental factors. This simulation model provides a new tool for forecasting pathogen compositions, and can be used to identify potentially problematic genotypes based on pathogen life-history traits.
A CA1 circuit motif that signals the start of information integration

Integrating information from the recent past is critical for guiding predictions and shaping behavior. The process of integrating information, such as tracking distance traveled or time elapsed, begins with establishing a starting point. Yet, the mechanisms by which neural circuits utilize relevant cues to initiate integration remain unknown. Our study sheds light on this question by identifying a subpopulation of CA1 pyramidal neurons called PyrDown. These neurons shut down their activity at the beginning of distance or time integration and then gradually ramp up their firing as the animal approaches the reward. PyrDown neurons provide a mechanism for representing integrated information through ramping activity, complementing the well-known place/time cells that respond to specific distances or time points. Our findings also reveal that parvalbumin inhibitory interneurons mediate the shutdown of PyrDown neurons, uncovering a circuit motif that enables the initiation of subsequent information integration to improve future predictions.
Efficient characterization of multiple binding sites of small molecule imaging ligands on amyloid-beta, 4-repeat/full-length tau and alpha-synuclein

Aim There is an unmet need for compounds that detect alpha-synuclein (αSyn) and 4-repeat tau, which are critical in many neurodegenerative diseases for diagnostic and therapeutic purposes. Here, we aim to develop an efficient surface plasmon resonance (SPR)-based method to facilitate the characterization of small molecule ligands/compounds to these fibrils. Methods SPR measurements were conducted to characterize the binding properties of fluorescent ligands/compounds towards recombinant Aβ42, K18 4-repeat/full-length tau and αSyn fibrils. In silico modelling was performed to examine the binding pockets of ligands on αSyn fibrils. Immunofluorescence staining with fluorescence ligands and specific antibodies on postmortem brain tissue slices from patients with Parkinson’s disease and disease mouse models was performed. Results We optimized the protocol for immobilizing Aβ42, K18 tau, full-length tau and αSyn fibrils in a controlled aggregation state on SPR sensor chips. The results from the analysis of binding kinetics suggested the presence of at least two binding sites for all fibrils, including luminescent conjugated oligothiophenes (HS-169, HS-84, h-FTAA and q-FTAA), pyridine derivative PBB5, nonfluorescent methylene blue and lansoprazole. In silico modelling studies for αSyn (6H6B) showed four binding sites with preference to S4. Immunofluorescence staining validated the detection of pS129-positive αSyn in brain tissue from Parkinson’s disease patients, αSyn PFF-injected mice, 6E10-positive Aβ in arcAβ mice, and AT-8/AT-100-positive in tau pR5 tau mice, respectively. Conclusions SPR measurements of ligands and small molecules binding to Aβ42, 4R and full-length tau and αSyn fibrils suggest the existence of multiple binding sites. This approach may provide efficient characterization of compound binding properties towards these fibrils important in neurodegenerative diseases.
The Electrophysiological Markers of Statistically Learned Attentional Enhancement: Evidence for a Saliency Based Mechanism

It has been well established that attention can be sharpened through the process of statistical learning - whereby visual search is optimally adapted to the spatial probabilities of a target in visual fields. Specifically, attentional processing becomes more efficient when targets appear at high relatively to low probability locations. Statistically learned attentional enhancement has been shown to differ behaviorally from the more well studied top-down and bottom-up forms of attention; and while the electrophysiological characteristics of top-down and bottom-up attention have been well explored, relatively little work has been done to characterize the electrophysiological correlates of statistically learned attentional enhancement. In the current study, EEG data was collected while participants performed the additional singleton task with an unbalanced target distribution. Encephalographic data was then analyzed for two well-known correlates of attentional processing – alpha lateralization and the N2pc component. Our results showed that statistically learned attentional enhancement is not characterized by alpha lateralization, thereby differentiating it from top-down enhancement. Yet targets at high probability locations did reliably produce larger N2pc amplitudes, a known marker of increased bottom-up capture due to higher target-distractor contrasts. These results support an interpretation of the probability cuing effects where the improved processing of targets at expected locations is mediated by a saliency-based mechanism – boosting the salience of targets appearing at high-probability locations relative to those at low-probability locations. Significance statement Things are easier to find when you have a good idea of where they should be – e.g. shoes on the floor and birds in the sky. Expectations of where things are likely to be found can be implicitly learned without much, if any, awareness. Until now, little was known about how these implicit spatial biases change the representation of items in the brain. In the current work, we present EEG recordings which suggest that the brain may represent items in common locations as more salient than in other locations in space. These findings inform how the brain represents implicit search expectations; supporting a model where items in expected areas in space capture attention more frequently because they are represented by the brain as more salient.
PUPILLARY HIPPUS: AN UNRECOGNIZED EXAMPLE OF BIOLOGIC CHAOS

We analyzed the pupil size vs time from six subjects using pupilography and nonlinear techniques. The correlation dimensions ranged from 4.08 to 5.7. The Hurst exponents ranged from 0.132 to 0.546. All data sets contained at least one positive Lyapunov exponent. The use of surrogate yielded statistically significant differences for the correlation dimension. Phase space analysis yields a definite flow, and in subject two, period-doubling is evident. The accumulated evidence supports the notion that dynamics of pupil size are governed by deterministic chaos rather than a stochastic or linear process. This implies that one might discern between well and disease states using pupillography and that the dynamics can be mechanistically modeled.
Use of Contingency Tables in the Analysis of Consumer Preference Studies

A consumer preference study involving three varieties of snap beans was conducted at Mississippi State College. One lot of each of the three varieties (V1 , V2 , and V3) was displayed in retail stores, and each of n consumers was asked to rank the beans according to first, second, alnd third choices. The data obtained in one store on one day are presented in Table 1. I was asked if the usual x2-test with four degrees of freedom could be used to test for independence of varieties and ranks, i.e., that each variety had the same chance (4) of receiving a given rank, regardless of rank.
What is cognitive about ‘plant cognition’? [Preprint]

There is growing evidence that plants possess abilities associated with cognition, such as decision-making, anticipation and learning. And yet, the cognitive status of plants continues to be contested. Among the threats to plant cognitive status is the ‘Representation Demarcation Challenge’ which points to the absence of a seemingly defining aspect of cognition, namely, computation over representation with non-derived content. Defenders of plant cognition may appeal to post-cognitivist perspectives, such as enactivism, which challenge the assumptions of the Representation Demarcation Challenge. This points to an impasse in the debate over plant cognition as it collapses into perennial disagreements over the best way to conceptualise the very nature of cognition. I propose a path that allows us to bypass this quagmire by reconceiving the question of what is cognitive about ‘plant cognition’ in terms of a quest to map the many possible adaptive capacities and behaviours more-or-less associated with cognition, alongside their underlying processes and mechanisms. In turn, we can examine the degrees of similarity between plants and more paradigmatically cognitive creatures. The ‘piecemeal approach’ thus shifts attention away from the abstract and dichotomous question of whether plants are cognitive and towards a series of more precise questions about the many ways and extent to which plants possess features associated with cognition. Ultimately, the value of viewing plants through a cognitive lens may lie less in determining whether they are bona fide cognitive creatures and more in guiding research into concrete abilities and their underlying causes.
Detection of alpine tree line change with high spatial resolution remotely sensed data

Abstract This study examined vegetation distribution and tree line change in the Sangong River watershed in the Tianshan Mountains, Xinjiang, China, using aerial photographs from 1962 and 1981 and a QuickBird image from 2006. An object-oriented classification method was used to map vegetation distribution, and the postclassification comparison approach was used to detect vegetation change. The results were linked to digital elevation model data for exploring the relationships between vegetation distribution/expansion and topographic factors. It shows that Schrenkiana is mainly distributed in the region with elevations less than 2,600 m, but its tree line can reach 2,880 m. Sabina is mainly distributed in the region with elevations within 2,600 to 2,900 m, and its highest elevation can be 3,270 m. Approximately 73% of Schrenkiana areas are distributed in aspects of 0 to 45 deg and 270 to 360 deg and 52% of Sabina areas are in aspects of 45 to 90 deg and 225 to 270 deg. The Schrenkiana expansion is mainly distributed in slopes of 20 to 40 deg (accounting for 82%) and aspects of 0 to 90 deg and 270 to 315 deg (accounting for 77%). The elevation of Schrenkiana tree lines increased by 2 to 3 m from 1962 to 2006 and of Sabina increased by 7 to 12 m from 1981 to 2006. Both Schrenkiana and Sabina expansion is mainly located in vegetation frontiers.
Derivatives of complex eigenvectors with distinct and repeated eigenvalues

In this paper, we investigate the computation of the first‐order derivatives of complex eigenvectors for general non‐defective eigensystems. A new normalization condition is proposed, with which we can compute unique first‐order derivatives of arbitrary differentiable eigenvectors of systems with distinct and repeated eigenvalues. We also present an efficient algorithm to compute the particular solutions to the governing equations of the first‐order derivatives of eigenvectors. Finally, numerical examples are included to demonstrate the validity of the proposed method. Copyright © 2007 John Wiley & Sons, Ltd.
Fully Quantum Mechanical Description of Ultrashort Time Dynamics of Semiconductor Quantum Dots

In this thesis, the quantum kinetics of semiconductor quantum dots coupled to the radiation field, the vibrational modes of the crystalline lattice, and another quantum confined electron are studied using the density matrix formalism in the full quantization regime. To address and characterize the influence of the environment on the optical properties of quantum dots, the experimentally observable quantities in quantum optics are described by the radiation field correlation functions which are coupled to quantum confined electrons and phonons via the electron-photon and -phonon interaction. The influence of dispersive, absorbing, and inhomogeneous media on the local photon density of quantum dots is investigated by a quantized radiation field with the Green function formalism. The influence of the electron-phonon interaction on the quantum dot interband coherence, which consequently yields incoherent photon emission, is explained by the ratio of the electron-phonon scattering time to the duration of the coherent laser pulse. As another aspect of the electron-phonon interaction, the radiation induced by coherent acoustic waves in the intersubband region of quantum dots is investigated. This is a highly off-resonant nonlinear excitation due to the energetically large discrepancy between the acoustic waves and the electronic intersubband transition. As a basic building block for quantum information processes, the excitation energy transfer in a coupled quantum dot system is investigated. Here, the dipole-dipole interaction, where the longitudinal and the transversal electric field couplings are given by the Coulomb and the radiation field coupling, respectively, is a main energy exchange mechanism. Using 8 band kptheory wave functions of self-growth semiconductor quantum dots, all coupling constants are calculated. In linear optics and local excitation regime, quantum kinetic equations of motion for the electrons are analytically solved by using the Hartree-Fock approximation, and its validity is verified. The absorption and the resonance fluorescence spectrum are given in an analytical form. In nonlinear optics, each coupling and dephasing mechanism influencing the energy transfer between the two quantum dots is discussed in the differential transmission spectrum, the resonance fluorescence spectrum, and the joint counting rate of two photons.
Coherent Propagation of Charged Particle Bunches in Random Magnetic Fields

When the distribution function for energetic particles moving in interplanetary space is expressed in terms of eigenfunctions of an operator which describes pitch-angle scattering by random magnetic fields, the familiar phenomenon of diffusion is the dominant solution of the transport equations provided that the spectrum of magnetic fluctuations is not too steep. However, if the power-versus-wavenumber spectrum of the random fields has a spectral index greater than 2, the dominant solution of the same equations is a qualitatively different mode of transport in which density inhomogeneities propagate coherently along the guiding field with a characteristic velocity equal to half the particle speed. The present work, which extends classical transport theory to give a detailed treatment of the new mode, presents explicit formulae which describe the spatial and temporal structure of the coherent disturbance. It is shown that this disturbance evolves asymptotically into a moving Gaussian pulse whose width increases with time.