julilili42/papers huggingface dataset:
Increased H3K27 trimethylation contributes to cone survival in a mouse model of cone dystrophy
2022-02-09

Abstract Inherited retinal diseases (IRDs) are a heterogeneous group of blinding disorders, which result in dysfunction or death of the light-sensing cone and rod photoreceptors. Despite individual IRDs being rare, collectively, they affect up to 1:2000 people worldwide, causing a significant socioeconomic burden, especially when cone-mediated central vision is affected. This study uses the Pde6c cpfl1 mouse model of achromatopsia, a cone-specific vision loss IRD, to investigate the potential gene-independent therapeutic benefits of a histone demethylase inhibitor GSK-J4 on cone cell survival. We investigated the effects of GSK-J4 treatment on cone cell survival in vivo and ex vivo and changes in cone-specific gene expression via single-cell RNA sequencing. A single intravitreal GSK-J4 injection led to transcriptional changes in pathways involved in mitochondrial dysfunction, endoplasmic reticulum stress, among other key epigenetic pathways, highlighting the complex interplay between methylation and acetylation in healthy and diseased cones. Furthermore, continuous administration of GSK-J4 in retinal explants increased cone survival. Our results suggest that IRD-affected cones respond positively to epigenetic modulation of histones, indicating the potential of this approach in the development of a broad class of novel therapies to slow cone degeneration.
Pion fragmentation functions at high energy colliders
2022-02-09

We revisit the description of pion production in proton-proton collisions in the light of the very precise data taken at the Large Hadron Collider (LHC) over the past decade. First attempts to include LHC results in next-to-leading order global QCD analyses of parton-to-pion fragmentation functions insinuated some conflict between data sets at different center-of-mass system energies. We show that the data can be well described within their uncertainties by a consistent set of pion fragmentation functions once the theoretical scale dependence is taken into account in the global QCD analysis.
Comment on bg-2021-343
2022-02-09

<strong class="journal-contentHeaderColor">Abstract.</strong> Soil erosion continues to be one of the most serious environmental problems of our time, which is exacerbated by progressive climate change. Until now, forests have been considered an ideal erosion control in this regard. However, even minor disturbances of the forest floor for example from heavy vehicle used for timber harvesting can cause substantial sediment transport. An important countermeasure is the quick restoration of the uncovered soil surface by vegetation. In this context, biological soil crusts (biocrusts) can play a vital role, as they are known for their soil-protective effect. This study examined the natural succession of pioneer vegetation in skid trails on four soil substrates in a central European temperate forest and investigated their influence on surface runoff and sediment discharge. We applied rainfall simulation experiments on small-scale runoff plots and continuously surveyed vegetation during the same period, primarily to map biocrust development. Skid trails on clayey substrates showed considerably higher biocrust cover and species richness. Biocrust cover was higher in center tracks than in wheel tracks, while there was no clear difference for biocrust species richness with regard to track position. Although biocrusts were quickly overtopped by vascular plants, they managed to coexist until their growth was restricted due to leaf litter fall. <em>Brachythecium rutabulum</em> and <em>Oxyrrhynchium hians</em> were the most important and persistent pioneer biocrust species, while <em>Dicranella schreberiana</em> and <em>Pohlia lutescens</em> were volatile and quickly disappeared after spreading in summer. Soil erosion was reduced with pioneer biocrust vegetation in summer, and again increased in winter. Total amount of sediment discharge was clearly site-dependent, indicating a high relevance of underlying substrates. Sediment discharge was 13.2 times higher in wheel tracks compared to undisturbed forest soil, and bare soil runoff plots produced 22-fold sediment discharge compared to undisturbed forest soil. Overall, bryophyte-dominated biocrusts contributed more to mitigating soil erosion than vascular plants. When soil coverage exceeded 50 %, biocrusts resulted in an average of 18 times less sediment loss compared to vascular plants.
Semantic object-scene inconsistencies affect eye movements, but not in the way predicted by contextualized meaning maps - data
2022-02-09

Data from the article<strong><em> Semantic object-scene inconsistencies affect eye movements, but not in the way predicted by contextualized meaning maps</em></strong> published in Journal of Vision. code: https://zenodo.org/record/5999215<br> data: https://zenodo.org/record/5999046 <br> Marek A. Pedziwiatr<br> marek.pedziwi@gmail.com<br> February 2022
Exponential decay of mutual information for Gibbs states of local Hamiltonians
2022-02-10

The thermal equilibrium properties of physical systems can be described using Gibbs states. It is therefore of great interest to know when such states allow for an easy description. In particular, this is the case if correlations between distant regions are small. In this work, we consider 1D quantum spin systems with local, finite-range, translation-invariant interactions at any temperature. In this setting, we show that Gibbs states satisfy uniform exponential decay of correlations and, moreover, the mutual information between two regions decays exponentially with their distance, irrespective of the temperature. In order to prove the latter, we show that exponential decay of correlations of the infinite-chain thermal states, exponential uniform clustering and exponential decay of the mutual information are equivalent for 1D quantum spin systems with local, finite-range interactions at any temperature. In particular, Araki&amp;apos;s seminal results yields that the three conditions hold in the translation-invariant case. The methods we use are based on the Belavkin-Staszewski relative entropy and on techniques developed by Araki. Moreover, we find that the Gibbs states of the systems we consider are superexponentially close to saturating the data-processing inequality for the Belavkin-Staszewski relative entropy.
Digital twin reveals combinatorial code of non-linear computations in the mouse primary visual cortex
2022-02-10

More than a dozen excitatory cell types have been identified in the mouse primary visual cortex (V1) based on transcriptomic, morphological and in vitro electrophysiological features. However, the functional landscape of excitatory neurons with respect to their responses to visual stimuli is currently unknown. Here, we combined large-scale two-photon imaging and deep learning neural predictive models to study the functional organization of mouse V1 using digital twins. Digital twins enable exhaustive in silico functional characterization providing a bar code summarizing the input-output function of each neuron. Clustering the bar codes revealed a continuum of function with around 30 modes. Each mode represented a group of neurons that exhibited a specific combination of stimulus selectivity and nonlinear response properties such as cross-orientation inhibition, size-contrast tuning and surround suppression. These non-linear properties were expressed independently spanning all possible combinations across the population. This combinatorial code provides the first large-scale, data-driven characterization of the functional organization of V1. This powerful approach based on digital twins is applicable to other brain areas and to complex non-linear systems beyond the brain.
Sex-dependent multimodal response profiles to psychosocial stress
2022-02-10

Abstract Introduction Sex differences in stress reactions are often reported in the literature. However, the sex-dependent interplay of different facets of stress is still not fully understood. Particularly in neuroimaging research, studies on large samples combining different indicators of stress remain scarce. Materials and Methods In a functional magnetic resonance imaging study, a sample of 140 healthy participants (67 females using oral contraceptives) underwent a standardized stress induction protocol, the ScanSTRESS. During the experiment, salivary cortisol and subjective ratings were obtained at multiple time points and heart rate was recorded. Results Sex differences emerged in different facets of the stress response:Women reacted with enhanced subjective feelings of stress and increases in heart rate, while men showed more pronounced neural activation in stress-related brain regions such as the inferior frontal gyrus and insula. Subjective feelings of stress and (para) hippocampal activity were negatively related in women,whereas a slightly positive association was observed in men. Discussion These results provide further insight in the sex-specific stress response patterns. Moreover, they emphasize the role of the hippocampus in the regulation of the stress response. This paves the way for the identification of sex-dependent vulnerability factors that can, in the future, be implemented in the prevention and treatment of stress-related disorders.
Express detection and discrimination of visual objects by primate superior colliculus neurons
2022-02-10

Abstract Primate superior colliculus (SC) neurons exhibit rich visual feature tuning properties and are implicated in a subcortical network hypothesized to mediate fast threat and/or conspecific detection. However, the mechanisms through which generalized object detection may be mediated by SC neurons remain unclear. Here we explored whether, and how quickly, SC neurons detect and discriminate real-life object stimuli. We presented experimentally-controlled gray-scale images of seven different object categories within the response fields (RF’s) of SC neurons, and we also presented a variety of luminance- and spectral-matched image controls. We found that all of our functionally-identified SC neuron types preferentially detected real-life objects even in their very first stimulus-evoked visual bursts (starting within approximately 50 ms from image onset). Intriguingly, even visually-responsive motor-related neurons exhibited such robust early object detection, and they also preferentially discriminated between object categories in their initial visual bursts. We further identified spatial frequency information in visual images as a critical source for early object detection and discrimination by SC neurons. Our results demonstrate rapid and robust SC processing of visual objects, and they underline how the visual processing capabilities of the primate SC support perception and action.
Directional Absolute Coherence: a phase-based measure of effective connectivity for neurophysiology data
2022-02-10

Abstract Communication between neural structures is a topic of much clinical and scientific interest and has been linked to a variety of behavioural, cognitive, and psychiatric measures. Here, we introduce a novel effective connectivity measure, termed the directional absolute coherence (DAC). Combining aspects of magnitude squared coherence, imaginary coherence, and phase slope index, DAC provides an estimate of connectivity that is resistant to volume conduction, encapsulates the directionality of neural communication, and is bound to the interval of –1 and 1. To highlight the properties of this newly proposed method, we compare DAC to a number of established connectivity methods using data recorded from the subthalamic nucleus of patients with Parkinson’s disease with deep brain stimulation electrodes. By applying a combination of real and simulated data, we demonstrate that DAC provides a reliable estimate of the magnitude and direction of connectivity, independent of the phase difference between brain signals. As such, DAC facilitates a reliable investigation of inter-regional neural communication, rendering it a valuable tool for gaining a deeper understanding of the functional architecture of the brain and its relationship to behaviour and cognition. A Python implementation of DAC is freely available at https://github.com/neurophysiological-analysis/FiNN . Highlights - Volume conduction and limited interpretability affect many connectivity methods. - DAC is a combined approach to overcome these pitfalls. - DAC augments information content and interpretability in comparison to other methods. - DAC allows for reliable estimation of effective connectivity.
Decoding geochemical signals of the Schwalbenberg Loess-Palaeosol-Sequences — A key to Upper Pleistocene ecosystem responses to climate changes in western Central Europe
2022-02-10

Loess deposits are the most extent continental archives of climatic- and environmental change and represent important components of local and global dust systems. Consequently, their geochemistry provides an excellent basis for studying climate oscillations on land and how these affect processes in the terrestrial system. It is, however, challenging to assess information archived in loess records due to complexities in their formation, causing interfering geochemical signatures. In particular, the use of element ratios to derive weathering indices may be complicated since dust sources change through time, and since ecosystems respond differently to changing conditions. Whilst this complexity appears as limiting factor, the explanatory potential of proxies increases when the diversity of geochemical processes is acknowledged. To make use of this potential, we integrate the decadic logarithm of element ratios indicative for provenance shifts, mineral sorting during transport and sediment reworking as well as weathering into multivariate statistical analysis. We test, if the sensitivity of Principal Component Analyses (PCA) and Linear Discriminant Analysis (LDA) can be increased by applying both to sub-datasets of diagnostic Stratigraphic Units (SU) of the Schwalbenberg Loess-Palaeosol-Sequences (Middle Rhine valley, Germany). The selected site recorded sub-millennial Upper Pleistocene ecological changes in an unprecedented resolution for Central European LPS. Differences in operating functions of PCA and LDA and our age model highlight timing and intensity of provenance shifts, sediment relocation, decalcification, redox dynamic and clay-mineral formation associated with Atlantic-driven climate oscillations. Based on this we provide evidence for the accretionary character of interstadial palaeosols caused by a close interplay of dust input and soil formation. Automated re-detection of SU across the site using LDA functions contributes important insights into slope dynamics through regional erosion events. Overall, our approach provides a key for tracing ecological changes during climate oscillations across continents.
Competition and Fan Substitution Between Professional Sports Leagues
2022-02-10

Abstract A peculiarity in professional sports is the fact that leagues regularly hold monopoly power within their sports. However, whether and to what extent these leagues may compete with other leagues across sports is relatively unexplored. This paper contributes to the literature by analyzing competition and fan substitution in Germany, where top-tier league managers in handball, basketball, and ice hockey have recently claimed that their teams suffer from football’s dominant position. Our attendance demand models confirm the existence of significant substitution effects in this setting, which suggests that leagues indeed do compete economically across sports for fan attendance .
Using cGMP analogues to modulate photoreceptor light sensitivity: Perspectives for the treatment of retinal degeneration
2022-02-10

Abstract Cyclic nucleotide-gated (CNG) channels play an essential role within the phototransduction cascade in vertebrates. Although rod and cone light responses are mediated through similar pathways, each photoreceptor type relies on a specific CNG-channel isoform. In many forms of retinal degeneration, increased cGMP levels initiate a pathophysiological rollercoaster, which starts with an enhanced CNG-channel activation, often in rod photoreceptors. This causes cell death of both rods and cones, and eventually leads to complete blindness. Unfortunately, the targeting of the desired channel isoform still constitutes the bottleneck for many therapeutic schemes. Here, we present a novel strategy, based on cGMP analogues with opposite types of action, which allows for the selective modulation of either rod or cone photoreceptors. A combined treatment with a weak rod-selective CNG-channel inhibitor (Rp-8-Br-PET-cGMPS) and a cone-selective CNG-channel activator (8-pCPT-cGMP) preserved the normal CNG-channel function at physiological and pathological cGMP levels. The effectiveness of this approach was tested and confirmed in explanted mouse retina. Under physiological conditions, the inhibitor silenced the rods selectively and decreased the dependency of cone responses on light intensity. Remarkably, the activator, when applied together with the inhibitor, reinstated only the light responsiveness of cones. Yet, when applied alone, the activator dampened rod responses more strongly than those of cones. Hence, combinations of cGMP analogues with desired properties may elegantly address the isoform-specificity problem in future pharmacological therapies. Beyond therapies for retinal degeneration diseases, treatments based on this strategy may allow modulation of visual performance in certain light environments or disease conditions. One Sentence Summary A combination of cGMP analogues with opposite types of action can selectively modulate either rod or cone photoreceptor function.
CRACking the Molecular Regulatory Mechanism of SOCE during Platelet Activation in Thrombo-Occlusive Diseases
2022-02-10

Thrombo-occlusive diseases such as myocardial infarction, ischemic stroke and deep vein thrombosis with subsequent pulmonary embolism still represent a major health burden worldwide. Besides the cells of the vasculature or other hematopoietic cells, platelets are primarily responsible for the development and progression of an occluding thrombus. The activation and function of platelets crucially depend on free cytosolic calcium (Ca2+) as second messenger, which modulates platelet secretion, aggregation and thrombus formation. Ca2+ is elevated upon platelet activation by release of Ca2+ from intracellular stores thus triggering of the subsequent store-operated Ca2+ entry (SOCE), which is facilitated by Ca2+ release-activated channels (CRACs). In general, CRACs are assembled by the pore-forming unit Orai in the plasma membrane and the Ca2+-sensing stromal interaction molecule (STIM) in the endoplasmic reticulum after the depletion of internal Ca2+ stores. In the last few years, there is a growing body of the literature demonstrating the importance of STIM and Orai-mediated mechanism in thrombo-occlusive disorders. Thus, this review provides an overview of the recent understanding of STIM and Orai signaling in platelet function and its implication in the development and progression of ischemic thrombo-occlusive disorders. Moreover, potential pharmacological implications of STIM and Orai signaling in platelets are anticipated and discussed in the end.
Direct Modulation Index: a measure of phase amplitude coupling for neurophysiology data
2022-02-10

Abstract Neural communication across different spatial and temporal scales is a topic of great interest in clinical and basic science. Phase-amplitude coupling (PAC) has attracted particular interest due to its functional role in a wide range of cognitive and motor functions. Here, we introduce a novel measure termed the direct modulation index (dMI). Based on the classical modulation index, dMI provides an estimate of PAC that is bound to an absolute interval between 0 and +1, resistant against noise, and reliable even for small amounts of data. To highlight the properties of this newly-proposed measure, we evaluated dMI by comparing it to the classical modulation index, mean vector length, and phase-locking value using simulated data. We ascertained that dMI provides a more accurate estimate of PAC than the existing methods and that is resilient to varying noise levels and signal lengths. As such, dMI permits a reliable investigation of PAC, which may reveal insights crucial to our understanding of functional brain architecture in key contexts such as behaviour and cognition. A Python toolbox that implements dMI and other measures of PAC is freely available at https://github.com/neurophysiological-analysis/FiNN . Highlights - Neural coupling measures are sensitive to higher harmonics of the target oscillation. - dMI achieves frequency-specificity by sine-fitting the phase-amplitude histogram. - Increased robustness to noise and signal duration in comparison to other measures. - dMI allows for reliable estimation of phase-amplitude coupling.
Growing Phylogenetic Trees Using Hierarchical Clustering
2022-02-10

Abstract We compare mitochondrial DNA of different species to build a phylogenetic tree. The main challenge is that the calculation of the Levenshtein distance is very slow for large sequences. We introduce an approximate scheme which uses Levenshtein for lower-level details and a fast distance based on sequence length for high-level attributes. The tree is built using average linkage hierarchical clustering.
The impact of face masks on emotion recognition performance and perception of threat
2022-02-11

Facial emotion recognition is crucial for social interaction. However, in times of a global pandemic, where wearing a face mask covering mouth and nose is widely encouraged to prevent the spread of disease, successful emotion recognition may be challenging. In the current study, we investigated whether emotion recognition, assessed by a validated emotion recognition task, is impaired for faces wearing a mask compared to uncovered faces, in a sample of 790 participants between 18 and 89 years (condition mask vs . original ). In two more samples of 395 and 388 participants between 18 and 70 years, we assessed emotion recognition performance for faces that are occluded by something other than a mask, i.e., a bubble as well as only showing the upper part of the faces (condition half vs . bubble ). Additionally, perception of threat for faces with and without occlusion was assessed. We found impaired emotion recognition for faces wearing a mask compared to faces without mask, for all emotions tested (anger, fear, happiness, sadness, disgust, neutral). Further, we observed that perception of threat was altered for faces wearing a mask. Upon comparison of the different types of occlusion, we found that, for most emotions and especially for disgust, there seems to be an effect that can be ascribed to the face mask specifically, both for emotion recognition performance and perception of threat. Methodological constraints as well as the importance of wearing a mask despite temporarily compromised social interaction are discussed.