julilili42/papers huggingface dataset:
Birds multiplex spectral and temporal visual information via retinal On- and Off-channels
2022-10-21

SUMMARY Early retinal circuits divide incoming visual information into functionally opposite elementary signals: On and Off, transient and sustained, chromatic and achromatic. Together these signals can yield an efficient representation of the scene for transmission to the brain via the optic nerve. For example, primate On- and Off-parasol circuits are transient, while On- and Off-midget circuits are sustained. But this long-standing interpretation of retinal function is based on mammals, and it is unclear whether this functional arrangement is common to all vertebrates. Here we show that poultry chicks use a fundamentally different strategy to communicate information from the eye to the brain. Rather than using functionally opposite pairs of retinal output channels, chicks encode the polarity, timing, and spectral composition of visual stimuli in a highly correlated manner: fast achromatic information is encoded by Off-circuits, and slow chromatic information overwhelmingly by On-circuits. Moreover, most retinal output channels combine On- and Off-circuits to simultaneously encode, or multiplex, both achromatic and chromatic information. Our results from birds conform to evidence from fish, amphibians, and reptiles which retain the full ancestral complement of four spectral types of cone photoreceptors. By contrast, mammals lost two of these cones early in their evolution, and we posit that this loss drove a radical simplification and reorganisation of retinal circuits, while birds and many other extant non-mammalian lineages retain the ancestral strategy for retinal image processing. HIGHLIGHTS First large-scale survey of visual functions in an avian retina Off-circuits are fast and achromatic, On-circuits are slow and chromatic Most avian RGCs are OnOff and encode both types of information Colour and greyscale information can be decoded based on the kinetics
Gamification improves antidepressant effects of cognitive control training—A pilot trial
2022-10-21

Objective Computerised cognitive trainings have been put forward to improve control over negatively biased information processing and associated depressive symptomatology. Yet, disease-related impairments of motivation and endurance, as well as insufficient accessibility hinder use of this promising therapeutic opportunity. Here, we developed an app ( de:)press © ) that utilizes a cognitive control training (paced auditory serial addition task) enriched with gamification and information elements. We compared a six-week training with de:)press © to a non-gamified version (active control group). Methods Thirty-two depressed participants were included. Each received either de:)press © or the non-gamified version and was instructed to train three times per week for two weeks. Afterwards (four weeks) they were free to train at their own discretion. Depression severity was assessed during training and two follow-up sessions. Primary endpoint was defined as difference between groups [change of Montgomery-Åsberg Depression Rating Scale (MADRS)] four weeks after end of training. Results Depression severity decreased in both groups. At primary endpoint, MADRS scores were significantly lower in the de:)press © -group compared to the control group. No differences were observed at three months' follow-up. Intervention usability was consistently rated positively. Participants who had trained with de:)press © maintained the recommended training frequency without further prompting. Besides transient fatigue or frustration, no adverse effects were observed. Conclusion This pilot demonstrates that gamification and information elements can substantially increase cognitive control training efficacy in alleviating depressive symptoms. Moreover, it provides first evidence for the feasibility and efficacy of de:)press © as an add-on intervention to treat depression. Clinical trial registration The study is registered under ClinicalTrials.gov, identifier: NCT04400162.
An evolutionary conserved division-of-labor between hippocampal and neocortical sharp-wave ripples organizes information transfer during sleep
2022-10-21

Abstract The hippocampal sharp-wave ripple (SW-R) is the key substrate of the hippocampal-neocortical dialogue underlying memory formation. Recently, it became evident that SW-R are not unique to archicortex, but constitute a wide-spread neocortical phenomenon. To date, little is known about morphological and functional similarities between archi- and neocortical SW-R. Leveraging intracranial recordings from the human hippocampus and prefrontal cortex during sleep, our results reveal region-specific functional specializations, albeit a near-uniform morphology. While hippocampal SW-R trigger directional hippocampal-to-neocortical information flow, neocortical SW-R reduce information flow to minimize interference. At the population level, hippocampal SW-R confined population dynamics to a low-dimensional subspace, while neocortical SW-R diversified the population response; functionally uncoupling the hippocampal-neocortical network. Critically, our replication in rodents demonstrated the same division-of-labor between archi-and neocortical SW-R. These results uncover an evolutionary preserved mechanism where coordinated interplay between hippocampal and neocortical SW-R temporally segregates hippocampal information transfer from neocortical processing.
Peer Review Report For: Exploring the structural characteristics of the Adult Social Care Outcomes Toolkit (ASCOT) and ASCOT-Carer [version 1; peer review: 2 approved with reservations]
2022-10-21

Background: Measurement models inform the approach to assess a measure’s validity and also how a measure is understood, applied and interpreted. With preference-based measures, it is generally accepted that they are formative ; however, if they are applied without preferences, they may be reflective , formative or mixed . In this study, we sought to empirically test whether the reflective , formative or mixed measurement model best describes PBMs of social care-related quality of life (ASCOT, ASCOT-Carer). We also explored the network approach, as an alternative. Methods: ASCOT and ASCOT-Carer data were analyzed using confirmatory factor analysis and Multiple Indicators Multiple Causes models to test reflective, formative or mixed measurement models, respectively. Network analysis of partial correlations using the Gaussian graphical model was also conducted. Results: The results indicated that the reflective measurement model is the worst fit for ASCOT and ASCOT-Carer. The formative or mixed models may apply to ASCOT. The mixed model was the best fit for ASCOT-Carer. The network analysis indicated that the most important or influential items were Occupation and Personal cleanliness and comfort (ASCOT) and Time and space and Self-care (ASCOT-Carer). Conclusions: The ASCOT and ASCOT-Carer are best described as formative/mixed or mixed models, respectively. These findings may guide the approach to the validation of cross-culturally adapted and translated versions. Specifically, we recommend that EFA be applied to establish structural characteristics, especially if the measure will be applied as a PBM and as a measure of SCRQoL. Network analysis may also provide further useful insights into structural characteristics.
Multi-histone ChIP-Seq Analysis with DecoDen
2022-10-21

Abstract Epigenetic mechanisms coordinate packaging, accessibility and read-out of the DNA sequence within the chromatin context. They significantly contribute to the regulation of gene expression. Thus, they play fundamental roles during differentiation on the one hand and maintenance and propagation of cell identity on the other. Epigenetic malfunctioning is associated with a large range of diseases, from neurodevelopmental disorders to cancer progression. In humans, hundreds of known epigenetic factors and complexes are involved in establishing covalent modifications on the DNA sequence itself and on associated histone proteins. Within the cellular context, the resulting combinatorial epigenomic patterns are neither established nor interpreted independently of each other and therefore exhibit high correlations in a region-specific manner. Post-translational modifications of histone proteins can be analysed using Chromatin Immunoprecipitation followed by sequencing (ChIP-Seq). Often, several assays for a number of different histone modifications are performed as part of the same experimental design. These measurements are, however, confounded by shared biases including chromatin accessibility and mappability. Existing computational methods analyse each histone modification separately. We introduce DecoDen, a new approach that leverages replicates and multi-histone ChIP-Seq experiments for a fixed cell type to learn and remove shared biases. DecoDen (Deconvolve and Denoise) consists of two major steps: We use non-negative matrix factorisation (NMF) to learn a joint cell-type specific background signal. Half-sibling regression (HSR) is then used to correct for these biases in the histone modification signals. We demonstrate that DecoDen is a robust and interpretable method that enables the unbiased discovery of subtle peaks, which are particularly important in an individual-specific context.
Reflections of manual labor in the hand entheses of early industrial women workers with extensively documented life histories
2022-10-23

Abstract Objectives Sex‐based occupational variability constitutes a fundamental component of human behavior and a major focus of research focusing on biocultural evolution. However, the reliability of reconstructing physical activity in past women is often compromised by the lack of female skeletal collections with adequately documented lifetime occupations, domestic living conditions, medical records, and socioeconomic status. Here, we attempt to reconstruct habitual manual activity in a skeletal sample of early industrial women with uniquely archived life histories. Materials and Methods We rely on the application of our “Validated Entheses‐based Reconstruction of Activity” method on the hand skeletons of 38 extensively documented individuals from the Basel‐Spitalfriedhof collection. Our comparisons also include 40 documented males from the same collection. Results As expected, we found evidence of increased entheseal variability among women sharing the same unspecialized occupation (maids and factory workers). Moreover, certain entheseal patterns were almost exclusive to the men involved in occupations not associated with the female sex (mainly construction workers). Importantly, all six women known to have practiced more specific occupational activities (e.g., seamstresses) showed distinctive entheseal patterns, seemingly associated with more demanding physical practices. This within‐sex variation was not correlated with differences in biological age, estimated body size, socioeconomic status, relatedness, or the presence of reported children. Discussion Our findings directly reflect the rich historical sources on the working lives of low‐status women in early industrial Basel. These results highlight the high potential value of our documented sample as a reference basis for reconstructing the division of labor in bioarchaeological contexts.
Talent development environments within sports: a scoping review examining functional and dysfunctional environmental features
2022-10-24

Based on the work of Martindale, R. J., Collins, D., and Daubney, J. (2005, Talent development: A guide for practice and research within sport. Quest (Grand Rapids, Mich ), 57(4), 353–375. https://doi.org/10.1080/00336297.2005.10491862) and Henriksen, K., Stambulova, N., and Roessler, K. K. (2010a, Holistic approach to athletic talent development environments: A successful sailing milieu. Psychology of Sport and Exercise, 11(3), 212–222. https://doi.org/10.1016/j.psychsport.2009.10.005), researchers have increasingly focused on environmental features influencing talent development in sport from an integrated, holistic perspective. These contributions led to a quickly evolving body of literature and a proliferation of findings related to facilitative and debilitative environmental features. With a timely appraisal of this work warranted, this review aims to coalesce salient results from talent development environment research. For this purpose, a holistic perspective is employed on (a) the environmental level, by considering the sport and non-sport domain and by identifying functional and dysfunctional features, as well as on (b) the outcome level, by considering wellbeing and personal development, alongside athletic development, as important athlete-related outcomes. Following a systematic search, 44 articles were identified and findings summarised by conducting a directed content analysis (Hsieh, H. F., & Shannon, S. E. (2005). Three approaches to qualitative content analysis. Qualitative Health Research, 15(9), 1277–1288. https://doi.org/10.1177/1049732305276687). Several functional and dysfunctional features were derived from the literature and grouped into the following main categories within a preliminary conceptual framework: Preconditions of the Sport Environment, Organisational Culture, Integration of Efforts, and Holistic Quality Preparation. The framework's contribution to a more systemic and holistic approach to talent development is discussed and critical future research directions are proposed.
Preclinical Evaluation of CRISPR-Edited CAR-NK-92 Cells for Off-the-Shelf Treatment of AML and B-ALL
2022-10-24

Acute myeloid leukemia (AML) and B-cell acute lymphocytic leukemia (B-ALL) are severe blood malignancies affecting both adults and children. Chimeric antigen receptor (CAR)-based immunotherapies have proven highly efficacious in the treatment of leukemia. However, the challenge of the immune escape of cancer cells remains. The development of more affordable and ready-to-use therapies is essential in view of the costly and time-consuming preparation of primary cell-based treatments. In order to promote the antitumor function against AML and B-ALL, we transduced NK-92 cells with CD276-CAR or CD19-CAR constructs. We also attempted to enhance cytotoxicity by a gene knockout of three different inhibitory checkpoints in NK cell function (CBLB, NKG2A, TIGIT) with CRISPR-Cas9 technology. The antileukemic activity of the generated cell lines was tested with calcein and luciferase-based cytotoxicity assays in various leukemia cell lines. Both CAR-NK-92 exhibited targeted cytotoxicity and a significant boost in antileukemic function in comparison to parental NK-92. CRISPR-Cas9 knock-outs did not improve B-ALL cytotoxicity. However, triple knock-out CD276-CAR-NK-92 cells, as well as CBLB or TIGIT knock-out NK-92 cells, showed significantly enhanced cytotoxicity against U-937 or U-937 CD19/tag AML cell lines. These results indicate that the CD19-CAR and CD276-CAR-NK-92 cell lines’ cytotoxic performance is suitable for leukemia killing, making them promising off-the-shelf therapeutic candidates. The knock-out of CBLB and TIGIT in NK-92 and CD276-CAR-NK-92 should be further investigated for the treatment of AML.
Predicting Soil Textural Classes Using Random Forest Models: Learning from Imbalanced Dataset
2022-10-24

Soil provides a key interface between the atmosphere and the lithosphere and plays an important role in food production, ecosystem services, and biodiversity. Recently, demands for applying machine learning (ML) methods to improve the knowledge and understanding of soil behavior have increased. While real-world datasets are inherently imbalanced, ML models overestimate the majority classes and underestimate the minority ones. The aim of this study was to investigate the effects of imbalance in training data on the performance of a random forest model (RF). The original dataset (imbalanced) included 6100 soil texture data from the surface layer of agricultural fields in northern Iran. A synthetic resampling approach using the synthetic minority oversampling technique (SMOTE) was employed to make a balanced dataset from the original data. Bioclimatic and remotely sensed data, distance, and terrain attributes were used as environmental covariates to model and map soil textural classes. Results showed that based on mean minimal depth (MMD), when imbalanced data was used, distance and annual mean precipitation were important, but when balanced data were employed, terrain attributes and remotely sensed data played a key role in predicting soil texture. Balanced data also improved the accuracies from 44% to 59% and 0.30 to 0.52 with regard to the overall accuracy and kappa values, respectively. Similar increasing trends were observed for the recall and F-scores. It is concluded that, in modeling soil texture classes using RF models through a digital soil mapping approach, data should be balanced before modeling.
Synthesis of Sterically Encumbered Thiourea S‐Oxides through Direct Thiourea Oxidation
2022-10-24

Abstract Thiourea S ‐oxides can be viewed as formal analogs of the currently unknown diamino‐substituted Criegee intermediates (urea O ‐oxides). However, the preparation of such S ‐oxides is rather challenging, and the direct oxidation of thioureas typically only leads to formation of desulfurized products. Employing the accurate revDSD‐PBEP86‐D4 double hybrid density functional, it was found that the peracid mediated oxidation of thiourea S ‐oxides exhibits a lower reaction barrier than the oxidation of the corresponding thiourea itself in contrast to most other ordinary thioketones. The undesired overoxidation reactivity, which is associated with strong π‐donation from the thiourea's nitrogen atoms, can be partially suppressed by introduction of bulky substituents and the utilization of protic solvents. In this regard, we managed to prepare two sterically encumbered thiourea S ‐oxides in isolated yields of 35–40 %. The S ‐oxides are stable in the solid state and in alcoholic solutions at room temperature for extended periods of time, but swiftly decompose in aprotic solvents by disproportionation. A dimesityl‐substituted thiourea S ‐oxide complexed with residual m CBA could be characterized by means of X‐ray crystallography, confirming the importance of hydrogen bonding in the stabilization of the amino‐substituted C=S + −O − moiety.
Multiparametric Longitudinal Profiling of RCAS-tva-Induced PDGFB-Driven Experimental Glioma
2022-10-24

Glioblastomas are incurable primary brain tumors harboring a heterogeneous landscape of genetic and metabolic alterations. Longitudinal imaging by MRI and [18F]FET-PET measurements enable us to visualize the features of evolving tumors in a dynamic manner. Yet, close-meshed longitudinal imaging time points for characterizing temporal and spatial metabolic alterations during tumor evolution in patients is not feasible because patients usually present with already established tumors. The replication-competent avian sarcoma-leukosis virus (RCAS)/tumor virus receptor-A (tva) system is a powerful preclinical glioma model offering a high grade of spatial and temporal control of somatic gene delivery in vivo. Consequently, here, we aimed at using MRI and [18F]FET-PET to identify typical neuroimaging characteristics of the platelet-derived growth factor B (PDGFB)-driven glioma model using the RCAS-tva system. Our study showed that this preclinical glioma model displays MRI and [18F]FET-PET features that highly resemble the corresponding established human disease, emphasizing the high translational relevance of this experimental model. Furthermore, our investigations unravel exponential growth dynamics and a model-specific tumor microenvironment, as assessed by histology and immunochemistry. Taken together, our study provides further insights into this preclinical model and advocates for the imaging-stratified design of preclinical therapeutic interventions.
Detection-time distribution for several quantum particles
2022-10-24

We address the question of how to compute the probability distribution of the time at which a detector clicks, in the situation of non-relativistic quantum particles in a volume in physical space and detectors placed along the boundary of . We have previously [arXiv:1601.03715] argued in favor of a rule for the 1-particle case that involves a Schr\\"odinger equation with an absorbing boundary condition on introduced by Werner; we call this rule the "absorbing boundary rule." Here, we describe the natural extension of the absorbing boundary rule to the -particle case. A key element of this extension is that, upon a detection event, the wave function gets collapsed by inserting the detected position, at the time of detection, into the wave function, thus yielding a wave function of particles. We also describe an extension of the absorbing boundary rule to the case of moving detectors.
Revisiting the electrophysiological correlates of valence and expectancy in reward processing – A Multi-lab replication
2022-10-24

Two event-related brain potential (ERP) components, the frontocentral feedback-related negativity (FRN) and the posterior P300, are key in feedback processing. The FRN typically exhibits greater amplitude in response to negative and unexpected outcomes, whereas the P300 is generally more pronounced for positive outcomes. In an influential ERP study, Hajcak et al., (2005) manipulated outcome valence and expectancy in a guessing task. They found the FRN was larger for negative outcomes regardless of expectancy and the P300 larger for unexpected outcomes regardless of valence. These findings challenged the dominant Reinforcement Learning Theory of the ERN. We aimed to replicate these results within the #EEGManyLabs project (Pavlov et al., 2021) across thirteen labs. Our replication, including robustness tests, a PCA and Bayesian models, found that both FRN and P300 were significantly modulated by outcome valence and expectancy: FRN amplitudes (no-reward - reward) were largest for unexpected outcomes, and P300 amplitudes were largest for reward outcomes. These results were consistent across different methods and analyses. Although our findings only partially replicate the original study, they underscore the complexity of feedback processing and demonstrate how aspects of Reinforcement Learning Theory may apply to the P300 component, reinforcing the need for rigorous ERP research methodologies.
Adult lifespan trajectories of neuromagnetic signals and interrelations with cortical thickness
2022-10-24

Oscillatory power and phase synchronization map neuronal dynamics and are commonly studied to differentiate the healthy and diseased brain. Yet, little is known about the course and spatial variability of these features from early adulthood into old age. Leveraging magnetoencephalography (MEG) resting-state data in a cross-sectional adult sample (n = 350), we probed lifespan differences (18-88 years) in connectivity and power and interaction effects with sex. Building upon recent attempts to link brain structure and function, we tested the spatial correspondence between age effects on cortical thickness and those on functional networks. We further probed a direct structure-function relationship at the level of the study sample. We found MEG frequency-specific patterns with age and divergence between sexes in low frequencies. Connectivity and power exhibited distinct linear trajectories or turning points at midlife that might reflect different physiological processes. In the delta and beta bands, these age effects corresponded to those on cortical thickness, pointing to co-variation between the modalities across the lifespan. Structure-function coupling was frequency-dependent and observed in unimodal or multimodal regions. Altogether, we provide a comprehensive overview of the topographic functional profile of adulthood that can form a basis for neurocognitive and clinical investigations. This study further sheds new light on how the brain’s structural architecture relates to fast oscillatory activity.