Miracle-dz/UniFAR-FTUs huggingface dataset:
Auditory Brainstem Response as an Objective Measure of Temporal Resolution

Background and Aims Temporal resolution is assessed using behavioral tests, which are highly affected by extraneous variables. We explored the relationship between behavioral Across-Channel Gap Detection Threshold (AC GDT) and different temporal parameters of an objective measure, Auditory Brainstem Response (ABR), to account for the extraneous variables. Settings and Design We conducted an experimental study on thirty native Kannada-speaking adults with normal hearing sensitivity in the age range of 18-25 years. Materials and Methods We estimated the Gap detection threshold (GDT) using an across-channel (AC) paradigm, and Auditory Brainstem Response (ABR) was recorded at 80 dBnHL for three repetition rates of 11.1, 30.1, and 90.1/sec. Statistical Analyses used Normality testing, the Friedman test, post-hoc analysis by Wilcoxon Signed-Rank test, along with descriptive statistics was performed using SPSS v20 (IBM Statistical Package for Social Sciences, New York, USA). Results The results showed a significant positive correlation between AC GDT scores and latency of wave I for the repetition rates of 11.1 and 30.1/sec and latency of wave V at 30.1 and 90.1/sec. There was a negative correlation (but not significant) between AC GDT scores and the slope of wave V across the repetition rates. Conclusions The results suggest a relationship between the behavioral and electrophysiological measures of temporal processing. Measuring the latency of wave I and wave V of ABR would give an estimate of their AC GDT scores, especially in difficult-to-test populations. Key messages To test temporal resolution abilities in individuals with normal hearing sensitivity, we can use an objective measure of latency of wave I and wave V of ABR. ABR can be highly useful in reducing testing time and obtaining reliable estimates in children and individuals with associated disorders like autism, below-average intelligence, and so on.
Mitotic chromosomes scale to nuclear-cytoplasmic ratio and cell size in Xenopus

During the rapid and reductive cleavage divisions of early embryogenesis, subcellular structures such as the nucleus and mitotic spindle scale to decreasing cell size. Mitotic chromosomes also decrease in size during development, presumably to coordinately scale with mitotic spindles, but underlying mechanisms are unclear. Here we combine in vivo and in vitro approaches using eggs and embryos from the frog Xenopus laevis to show that mitotic chromosome scaling is mechanistically distinct from other forms of subcellular scaling. We found that mitotic chromosomes scale continuously with cell, spindle and nuclear size in vivo. However, unlike for spindles and nuclei, mitotic chromosome size cannot be re-set by cytoplasmic factors from earlier developmental stages. In vitro, increasing nucleo-cytoplasmic (N/C) ratio is sufficient to recapitulate mitotic chromosome scaling, but not nuclear or spindle scaling, through differential loading of maternal factors during interphase. An additional pathway involving importin α scales mitotic chromosomes to cell surface area/volume (SA/V) during metaphase. Finally, single-chromosome immunofluorescence and analysis of Hi-C data suggest that mitotic chromosomes scale through decreased recruitment of condensin I, resulting in major rearrangements of DNA loop architecture to accommodate the same amount of DNA on a shorter axis. Together, our findings demonstrate how mitotic chromosome size is set by spatially and temporally distinct developmental cues in the early embryo.
COnstrained Reference frame diffusion TEnsor Correlation Spectroscopic (CORTECS) MRI: A practical framework for high-resolution diffusion tensor distribution imaging

Diffusion MRI studies with resolutions of a few hundred micrometers have consistently shown that in the cortex water diffusion occurs preferentially along radial and tangential orientations with respect to the cortical surface, in agreement with histology. These dominant orientations do not change significantly even if the relative contributions from microscopic water pools to the net voxel signal vary across studies that use different diffusion times, b-values, TEs, and TRs. With this in mind, we propose a practical new framework for measuring non-parametric diffusion tensor distribution (DTD) MRI by constraining the microscopic diffusion tensors of the DTD to be diagonalized using the same orthonormal reference frame of the mesoscopic voxel. In each voxel, the constrained DTD (cDTD) is completely determined by the correlation spectrum of the microscopic principal diffusivities associated with the axes of the voxel reference frame. Consequently, all cDTDs are inherently limited to the domain of positive definite tensors and can be reconstructed efficiently with numerical methods for solving Inverse Laplace Transform problems. Moreover, cDTDs can be measured using only data acquired with conventional single diffusion encoding, which can be obtained more efficiently than measurements with multiple diffusion encoding. In tissues with radial symmetry, such as the cortex, we can further constrain the cDTD to contain only cylindrically symmetric diffusion tensors and measure the 2D correlation spectra of radial and tangential diffusivities. To demonstrate this framework, we perform numerical simulations and analyze high-resolution dMRI data. We image 2D cDTDs in the cortex and derive marginal distributions of radial and tangential diffusivities, distributions of the microscopic fractional anisotropies and mean diffusivities, as well as their 2D correlation spectra to quantify the shape-size characteristics of the microscopic diffusion tensors. Signal components corresponding to specific bands in the measured correlation spectra show high specificity to cortical laminar structures observed with histology. Our framework drastically simplifies the measurement of non-parametric DTDs and may be applied retrospectively to analyze existing high-resolution dMRI data. Moreover, the framework provides a non-parametric generalization of DTI and subsumes existing diffusion signal representations and tissue models, enabling their harmonization, cross-validation, and optimization in specific clinical applications characterizing tissue changes.
Multimodal mapping of cell types and projections in the central nucleus of the amygdala

The central nucleus of the amygdala (CEA) is a brain region that integrates external and internal sensory information and executes innate and adaptive behaviors through distinct output pathways. Despite its complex functions, the diversity of molecularly defined neuronal types in the CEA and their contributions to major axonal projection targets have not been examined systematically. Here, we performed single-cell RNA-sequencing (scRNA-Seq) to classify molecularly defined cell types in the CEA and identified marker-genes to map the location of these neuronal types using expansion assisted iterative fluorescence in situ hybridization (EASI-FISH). We developed new methods to integrate EASI-FISH with 5-plex retrograde axonal labeling to determine the spatial, morphological, and connectivity properties of ∼30,000 molecularly defined CEA neurons. Our study revealed spatio-molecular organization of the CEA, with medial and lateral CEA associated with distinct cell families. We also found a long-range axon projection network from the CEA, where target regions receive inputs from multiple molecularly defined cell types. Axon collateralization was found primarily among projections to hindbrain targets, which are distinct from forebrain projections. This resource reports marker-gene combinations for molecularly defined cell types and axon-projection types, which will be useful for selective interrogation of these neuronal populations to study their contributions to the diverse functions of the CEA.
Phenomenological analysis of the Two Higgs Doublet Model

The Two Higgs Doublet model and its phenomenological implications are discussed. A brief survey on the present status of this model is given. In particular, we concentrate on the Two Higgs Doublet Model with Flavor Changing Neutral Currents. First, we develop some new parametrizations of the 2HDM type III, in such a way that the relation of it with models type I and type II become apparent. Based on this parametrization we get some bounds on the mixing vertex involving the second and third lepton generations, and lower bounds on the mass of the pseudoscalar Higgs boson. Further, by using a parametrization in which one of the vacuum expectation values vanishes, we constrain some lepton flavor violating vertices, based on the $g-2 $muon factor and some lepton flavor violating decays. Moreover, upper limits on the decay widths of $\tau \to e\gamma, $and $\tau \to eee $are calculated, finding them to stay far from the reach of near future experiments. On the other hand, as an addendum to this work, we study the production and decays of top squarks at the Tevatron collider in models of low-energy supersymmetry breaking. We consider that the lightest Standard Model superpartner is a light neutralino that predominantly decays into a photon and a light gravitino, and that the lighter stop is the next-to-lightest Standard Model superpartner. For a modest projection of the final Tevatron luminosity, $L\simeq 4$ fb$^{-1}$, stop masses of order 300 GeV are accessible. We also consider the production and decay of ten degenerate squarks, and we find that common squark masses up to 360 GeV are easily accessible, and that the reach increases further if the gluino is light.
Electrophysiological correlates of associative recognition memory for identity, spatial, and temporal relations

The formation of associative representations and their retrieval from episodic memory are vital cognitive functions. However, it is unclear to what extent retrieval of the basic component relations of episodic memory – identity, time, and space – requires different or shared brain mechanisms. In the current study, we employed EEG to track the time courses of electrophysiological correlates of retrieval processes of memory for identity relations, temporal order, and spatial configuration. Participants engaged in pair-associate learning of serially presented and spatially configured object picture pairs, followed by discrimination of identity, spatially, or temporally intact and rearranged pairs. Event-related brain potentials (ERPs) revealed distinct patterns of activity during successful retrieval of identity, spatial, and temporal relations that differed by the status of association, across the three retrieval time windows examined (300-500, 500-800, and 800-1000 ms). The identity relations condition was distinguished by a widespread greater negative-going deflection for rearranged relative to intact pairs in all three time windows. For the temporal relations condition, we observed a widespread more negative-going deflection for rearranged than intact pairs, significant in the second time window only. For the spatial relations condition, there was a widespread positive-going deflection greater for rearranged than for intact pairs, significant in the early and in middle time windows. These patterns of activity suggest that retrieval of associative memory traces for identity, spatial, and temporal relationships involve dynamically different processes, which may partially rely on different sets of basic associative mechanisms.
METHOD OF AREAS FOR MANIPULATING THE ENTANGLEMENT PROPERTIES OF ONE COPY OF A TWO-PARTICLE PURE ENTANGLED STATE

We consider the problem of how to manipulate the entanglement properties of a general two-particle pure state, shared between Alice and Bob, by using only local operations at each end and classical communication between Alice and Bob. A method is developed in which this type of problem is found to be equivalent to a problem involving the cutting and pasting of certain shapes along with certain coloring problems. We consider two problems. First, we find the most general way of manipulating the state to obtain maximally entangled states. After such a manipulation, the entangled states $|11〉+|22〉+\ensuremath{\cdot}\ensuremath{\cdot}\ensuremath{\cdot}+|\mathrm{mm}〉$ are obtained with probability ${p}_{m}. $ We obtain an expression for the optimal average entanglement obtainable. Also, some results of Lo and Popescu (e-print quant-ph/9707038) pertaining to this problem are given simple geometric proofs. Second, we consider how to manipulate one two-particle entangled state $|\ensuremath{\psi}〉$ to another $|{\ensuremath{\psi}}^{\ensuremath{'}}〉$ with certainty. We derive Nielsen's theorem (which states a necessary and sufficient condition for this to be possible) using the method of areas.
Infralimbic Projections to the Nucleus Accumbens Shell and Amygdala Regulate the Encoding of Cocaine Extinction Learning

Prior evidence indicates that the infralimbic cortex (IL) mediates the ongoing inhibition of cocaine seeking following self-administration and extinction training in rats, specifically through projections to the nucleus accumbens shell (NAshell). Our own data indicate that IL activity immediately following an unreinforced lever press is critical for encoding the extinction contingencies in such procedures. Whether extinction encoding requires activity in the IL exclusively or also activity in its outputs, such as those to the NAshell and amygdala, is unknown. To address this issue, we used a closed-loop optogenetic approach in female and male Sprague Dawley rats to silence IL–NAshell or IL–amygdala activity following an unreinforced lever press during extinction training. Optical illumination (20 s) was given either immediately after a lever press or following a 20 s delay. IL–NAshell inhibition immediately following an unreinforced lever press increased lever pressing during extinction training and impaired retention of extinction learning, as assessed during subsequent extinction sessions without optical inhibition. Likewise, IL–amygdala inhibition given in the same manner impaired extinction retention during sessions without inhibition. Control experiments indicate that critical encoding of extinction learning does not require activity in these pathways beyond the initial 20 s post-lever press period, as delayed IL–NAshell and IL–amygdala inhibition had no effect on extinction learning. These results suggest that a larger network extending from the IL to the NAshell and amygdala is involved in encoding extinction contingencies following cocaine self-administration. SIGNIFICANCE STATEMENT Infralimbic cortex (IL) activity following an unreinforced lever press during extinction learning encodes the extinction of cocaine-seeking behavior. However, the larger circuitry controlling such encoding has not been investigated. Using closed-loop optogenetic pathway targeting, we found that inhibition of IL projections to the nucleus accumbens shell and to the amygdala impaired the extinction of cocaine seeking. Importantly, these effects were only observed when activity was disrupted during the first 20 s post-lever press and not when given following a 20 s delay. These findings suggest that successful cocaine extinction encoding requires activity across a larger circuit beyond simply inputs to the IL.
Selective retrieval revealed by electroencephalographic (EEG) neural pattern reinstatement

For past experiences to guide our actions we need to retrieve the relevant memories. Here, we used electroencephalography (EEG) to investigate how a memory is selected for retrieval from a large store of mnemonic traces, and to evaluate how selection operates during the retrieval cascade. We analyzed data from two studies in which people studied objects in picture or auditory word formats, and later recalled them using either written words (Experiment 1, N=28) or line drawings (Experiment 2, N=28) as retrieval cues. We used multivariate decoding to quantify the reinstatement of study phase neural patterns when people successfully identified items that had been studied in the format currently designated as targets, versus non-targeted items. Neural reinstatement emerged by 500 ms post-stimulus, as did the established left parietal event-related potential (ERP) signature of recollection. Reinstatement was also target-selective (greater for targets than non-targets) when test cues overlapped more with targets, as had previously been shown for the left parietal ERP (Moccia and Morcom, 2021). In contrast, when cues overlapped more with non-targets, neural reinstatement was non-selective or reversed, unlike the left parietal ERP. We also tested for goal-directed reinstatement prior to retrieval cues, hypothesized to drive selection. When words were cues there was strong evidence of this proactive reinstatement, but it was not detected when pictures were cues. Together, the data suggest that selection can act at multiple stages of recovery of a memory and depends on both external cues and goal-directed control.
Local prediction-learning enables neural networks to plan

The capability to plan a sequence of actions toward a given goal is a cornerstone of higher cognitive function. But compelling models for planning in the brain, or more generally in any type of neural network, are missing. We present a simple model for planning in neural networks, the Cognitive Map Learner (CML), that can achieve high performance on a variety of tasks by learning a cognitive map of the environment. The way how the CML constructs a cognitive map is based on a fundamental insight from neuroscience: Observations from the environment acquire meaning for the organism primarily through performing actions that change them. The CML also provides a viable alternative to reinforcement learning in robotics, since it learns faster and becomes more flexible, due to its task-agnostic design principles. The design of the CML is also of interest from the perspective of the relationship between self-attention networks (Transformers) and neural networks, since it combines attractive features of both.
A Grism Design Review and the As-Built Performance of the Silicon Grisms for JWST-NIRCam

Grisms are dispersive transmission optics that find their most frequent use in instruments that combine imaging and spectroscopy. This application is particularly popular in the infrared where imagers frequently have a cold pupil in their optical path that is a suitable location for a dispersive element. In particular, several recent and planned space experiments make use of grisms in slit-less spectrographs capable of multi-object spectroscopy. We present an astronomer-oriented general purpose introduction to grisms and their use in current and future astronomical instruments. We present a simple, step-by-step procedure for adding a grism spectroscopy capability to an existing imager design. This procedure serves as an introduction to a discussion of the device performance requirements for grisms, focusing in particular on the problems of lithographically patterned silicon devices, the most effective grism technology for the 1.1–8 micron range. We begin by summarizing the manufacturing process of monolithic silicon gratings. We follow this with a report in detail on the as-built performance of parts constructed for a significant new space application, the NIRCam instrument on James Webb Space Telescope and compare these measurements to the requirements.
From genome wide SNPs to genomic islands of differentiation: the quest for species diagnostic markers in two scleractinian corals, Pocillopora and Porites

Coral reefs are of paramount importance in marine ecosystems, where they provide support for a large part of the biodiversity. Being quite sensitive to global changes, they are therefore the prime targets for biodiversity conservation policies. However, such conservation goals require accurate species identification, which are notoriously difficult to get in these highly morphologically variable organisms, rich in cryptic species. There is an acute need for easy-to-use and resolutive species diagnostic molecular markers. The present study builds on the huge sequencing effort developed during the TARA Pacific expedition to develop a genotyping strategy to assign coral samples to the correct species within two coral genera (Porites and Pocillopora). For this purpose, we developed a technique that we called “Divergent Fragment” based on the sequencing of a less than 2kb long diagnostic genomic fragment determined from the metagenomic data of a subset of the corals collected. This method has proven to be rapid, resolvable and cost-effective. Sequencing of PCR fragments nested along the species diagnostic fragment allowed us to assign 232 individuals of the genus Pocillopora and 247 individuals of the genus Porites to previously identified independent genetic lineages (i.e. species). This genotyping method will allow to fully analyze the coral samples collected across the Pacific during the Tara Pacific expedition and opens technological perspectives in the field of population genomics-guided conservation.
Synaptopodin Regulates Denervation-Induced Plasticity at Hippocampal Mossy Fiber Synapses

Neurological diseases can lead to the denervation of brain regions caused by demyelination, traumatic injury or cell death. Nevertheless, the molecular and structural mechanisms underlying lesion-induced reorganization of denervated brain regions are a matter of ongoing investigation. In order to address this issue, we performed an entorhinal cortex lesion (ECL) in mouse organotypic entorhino-hippocampal tissue cultures of both sexes and studied denervation-induced plasticity of mossy fiber synapses, which connect dentate granule cells (dGCs) with CA3 pyramidal cells (CA3-PCs) and play important roles in spatial learning. Partial denervation caused a strengthening of excitatory neurotransmission in dGCs, in CA3-PCs, and their direct synaptic connections as revealed by paired recordings (GC-to-CA3). These functional changes were accompanied by ultrastructural reorganization of mossy fiber synapses, which regularly contain the plasticity-related protein synaptopodin and the spine apparatus organelle. We demonstrate that the spine apparatus organelle and its integral protein synaptopodin are associated with ribosomes in close proximity to synaptic sites and unravel a synaptopodin-related transcriptome. Notably, synaptopodin-deficient tissue preparations that lack the spine apparatus organelle, failed to express lesion-induced synaptic adjustments. Hence, synaptopodin and the spine apparatus organelle play a crucial role in regulating lesion-induced synaptic plasticity at hippocampal mossy fiber synapses.