Miracle-dz/UniFAR-FTUs huggingface dataset:
Evidence for generative homology of cerebellum and cerebellum‐like structures in an elasmobranch fish based on Pax6, Cbln1 and Grid2 expression

The majority of neurons in the mammalian brain reside within the cerebellum (Cb). Yet, the evolutionary origins of the Cb are not well understood. There are several sensory nuclei present across vertebrate phylogeny collectively termed cerebellum‐like structures (CbLS) due to a shared anatomy and physiology with the Cb. Despite the similarities, the CbLS are clearly not phylogenetically homologous with the Cb. Common structure and function may arise due to a shared genetic and developmental toolkit. To examine this possibility, we used sequence analysis, western blotting, immunohistochemistry and RT‐qPCR to test for the expression of three genes that are critical for mammalian cerebellar development in the Cb and CbLS of an elasmobranch fish, Leucoraja erinacea. In the mammalian Cb, Pax6 is necessary for parallel fiber development, while Cbln1 and Grid2 code for proteins necessary for parallel fiber‐principal cell synaptogenesis. Pax6 and Cbln1 are expressed by granule cells in the Cb and CbLS of the adult skate and stage 31 embryo. Grid2 is expressed by principal cells in the Cb and CbLS of the adult and stage 31 embryo. RT‐qPCR showed this expression is spatially and temporally restricted to the Cb and CbLS. If Pax6, Cbln1 and Grid2 perform the same functions in the skate Cb and CbLS as they do in the mammalian Cb, then these structures may develop using a shared genetic toolkit and be considered generatively homologous. It is possible that the evolutionary genesis of the Cb was the result of duplication or expansion of the cerebellum‐like developmental toolkit.
Regulation of cytochrome P450 gene expression by ketamine: a review

ABSTRACT Introduction: Although used as an anesthetic drug for decades, ketamine appears to have garnered renewed interest due to its potential therapeutic uses in pain therapy, neurology, and psychiatry. Ketamine undergoes extensive oxidative metabolism by cytochrome P450 (CYP) enzymes. Considerable efforts have been expended to elucidate the ketamine-induced regulation of CYP gene expression. The safety profile of chronic ketamine administration is still unclear. Understanding how ketamine regulates CYP gene expression is clinically meaningful. Areas covered: In this article, the authors provide a brief review of clinical applications of ketamine and its metabolism by CYP enzymes. We discuss the effects of ketamine on the regulation of CYP gene expression, exploring aspects of cytoskeletal remodeling, mitochondrial functions, and calcium homeostasis. Expert opinion: Ketamine may inhibit CYP gene expression through inhibiting calcium signaling, decreasing ATP levels, producing excessive reactive oxygen species, and subsequently perturbing cytoskeletal dynamics. Further research is still needed to avoid possible ketamine–drug interactions during long-term use in the clinic.
Generalizing Duchenne to Sad Expressions With Binocular Rivalry and Perception Ratings

Discrete emotion theories emphasize the modularity of facial expressions, while functionalist theories suggest that a single facial action may have a common meaning across expressions. Smiles involving the Duchenne marker, eye constriction causing crow’s feet, are perceived as intensely positive and sincere. To test whether the Duchenne marker is a general index of intensity and sincerity, we contrasted positive and negative expressions with and without the Duchenne marker in a binocular rivalry paradigm. Both smiles and sad expressions involving the Duchenne marker were perceived longer than non-Duchenne expressions, and participants rated all Duchenne expressions as more affectively intense and more sincere than their non-Duchenne counterparts. Correlations between perceptual dominance and ratings suggested that the Duchenne marker increased the dominance of smiles and sad expressions by increasing their perceived affective intensity. The results provide evidence in favor of Darwin’s hypothesis that specific facial actions have a general function (conveying affect intensification and sincerity) across expressions.
Color Sails: Discrete-Continuous Palettes for Deep Color Exploration

We present color sails, a discrete-continuous color gamut representation that extends the color gradient analogy to three dimensions and allows interactive control of the color blending behavior. Our representation models a wide variety of color distributions in a compact manner, and lends itself to applications such as color exploration for graphic design, illustration and similar fields. We propose a Neural Network that can fit a color sail to any image. Then, the user can adjust color sail parameters to change the base colors, their blending behavior and the number of colors, exploring a wide range of options for the original design. In addition, we propose a Deep Learning model that learns to automatically segment an image into color-compatible alpha masks, each equipped with its own color sail. This allows targeted color exploration by either editing their corresponding color sails or using standard software packages. Our model is trained on a custom diverse dataset of art and design. We provide both quantitative evaluations, and a user study, demonstrating the effectiveness of color sail interaction. Interactive demos are available at www.colorsails. com.
Molecular signatures of antibody responses derived from a systems biology study of five human vaccines

Many vaccines induce protective immunity via antibodies. Recent studies have used systems biological approaches to determine signatures that predict vaccine immunity in humans, but whether there is a ‘universal signature’ that can predict antibody responses to any vaccine, is unknown. Here we performed systems analyses of immune responses to the meningococcal polysaccharide and conjugate vaccines in healthy adults, in the broader context of our previous studies with the yellow fever and two influenza vaccines. To achieve this, we performed a largescale network integration of public human blood transcriptomes, and systems-scale databases in specific biological contexts, and deduced a set of blood transcription modules. These modules revealed distinct transcriptional signatures of antibody responses to different classes of vaccines providing key insights into primary viral, protein recall and anti-polysaccharide responses. These results illuminate the early transcriptional programs orchestrating vaccine immunity in humans, and demonstrate the power of integrative network modeling.
Avoiding/inducing dynamic buckling in a thermomechanically coupled plate: a local and global analysis of slow/fast response

The nonlinear response of a reduced model of an orthotropic single-layered plate with thermomechanical coupling is investigated in the presence of thermal excitations, in addition to mechanical ones. Different issues are addressed via accurate and extended local and global analyses. (i) Assessing the possible occurrence, disappearance or modification of mechanical buckling as a result of thermal aspects; (ii) exploiting global dynamics to unveil the effects of coupling; (iii) highlighting the crucial role played by the slow thermal transient evolution in modifying the fast steady mechanical response; (iv) framing the influence of coupling and underlining the need to use a thermomechanical model to grasp the actual plate dynamics; and (v) getting hints of technical interest as to the outcome robustness with respect to variations in the external/internal thermal parameters.
Inaccuracies in epitope repertoire estimations when using multilocus allele‐level HLA genotype imputation tools

Limited availability of allele‐level HLA genotypes prompts their imputation from allele‐group genotypes to estimate epitope mismatches. We evaluated the accuracy of epitope load and repertoire assignment when imputing allele‐level HLA genotypes. Analyses were conducted on 175 hematopoietic stem cell (HSC) donors from the Héma‐Québec registry (HQR) and 57 HSC donor‐recipient pairs from McGill University Health Centre (MUHC), Québec, Canada, genotyped for HLA‐A, ‐B, ‐C, ‐DRB1, and ‐DQB1. Multilocus allele‐level imputation was performed using HaploStats. Disagreement in B‐ and T‐cell epitope assignment and epitope mismatches were ascertained for imputed vs measured allele‐level HLA genotypes in HSC donors and donor‐recipient pairs, respectively. Imputation resulted in no differences in overall eplet mismatches and Predicted Indirectly ReCognizable HLA Epitopes (PIRCHE‐II) for HLA‐A, ‐B, and ‐C in 83.4% and 93.7% of HQR donors and 87.7% and 87.7% of MUHC donors, respectively. HLA‐DRB1‐ and ‐DQB1‐derived eplet mismatches and PIRCHE‐II were correctly assigned in 72.0% and 85.1% of HQR donors and 70.2% and 71.9% of MUHC donors, respectively. No discrepancies in eplet load or PIRCHE‐II were observed in 96.5% and 86.0% of HSC donor‐recipient pairs and in 70.2% and 70.1% of pairs for HLA‐A, ‐B, ‐C, ‐DRB1, and ‐DQB1, respectively. Kappa statistics of 0.9708 and 0.9725, 0.8724 and 0.8177, 0.9827 and 0.9022, 0.5644 and 0.4939, 0.5085 and 0.6361 were estimated when assessing agreement between eplet mismatches and PIRCHE‐II of imputed vs measured HLA‐A, ‐B, ‐C, ‐DRB1, and ‐DQB1 types, respectively. To avoid inaccuracies in epitope compatibility estimation, mainly for HLA class II, multilocus allele‐level genotype measurement is recommended.
Tweedie family of generalized linear models with distribution‐free random effects for skewed longitudinal data

Generalized linear mixed models have played an important role in the analysis of longitudinal data; however, traditional approaches have limited flexibility in accommodating skewness and complex correlation structures. In addition, the existing estimation approaches generally rely heavily on the specifications of random effects distributions; therefore, the corresponding inferences are sometimes sensitive to the choice of random effect distributions under certain circumstance. In this paper, we incorporate serially dependent distribution‐free random effects into Tweedie generalized linear models to accommodate a wide range of skewness and covariance structures for discrete and continuous longitudinal data. An optimal estimation of our model has been developed using the orthodox best linear unbiased predictors of random effects. Our approach unifies population‐averaged and subject‐specific inferences. Our method is illustrated through the analyses of patient‐controlled analgesia data and Framingham cholesterol data.
25-Hydroxyvitamin D in African-origin populations at varying latitudes challenges the construct of a physiologic norm 1 – 3

Background: The vitamin D–endocrine system is thought to play a role in physiologic processes that range from mineral metabolism to immune function. Serum 25-hydroxyvitamin D [25(OH)D] is the accepted biomarker for vitamin D status. Skin color is a key determinant of circulating 25(OH)D concentrations, and genes responsible for melanin content have been shown to be under strong evolutionary selection in populations living in temperate zones. Little is known about the effect of latitude on mean concentrations of 25(OH)D in dark-skinned populations. Objective: The objective was to describe the distribution of 25(OH)D and its subcomponents in 5 population samples of African origin from the United States, Jamaica, Ghana, South Africa, and the
Dexterous manipulation and control with volumetric muscles

We propose a framework for simulation and control of the human musculoskeletal system, capable of reproducing realistic animations of dexterous activities with high-level coordination. We present the first controllable system in this class that incorporates volumetric muscle actuators, tightly coupled with the motion controller, in enhancement of line-segment approximations that prior art is overwhelmingly restricted to. The theoretical framework put forth by our methodology computes all the necessary Jacobians for control, even with the drastically increased dimensionality of the state descriptors associated with three-dimensional, volumetric muscles. The direct coupling of volumetric actuators in the controller allows us to model muscular deficiencies that manifest in shape and geometry, in ways that cannot be captured with line-segment approximations. Our controller is coupled with a trajectory optimization framework, and its efficacy is demonstrated in complex motion tasks such as juggling, and weightlifting sequences with variable anatomic parameters and interaction constraints.
Primary and secondary discourse connectives: definitions and lexicons

Starting from the perspective that discourse structure arises from the presence of coherence relations, we provide a map of linguistic discourse structuring devices (DRDs), and focus on those for written text. We propose to structure these items by differentiating between primary and secondary connectives on the one hand, and free connecting phrases on the other. For the former, we propose that their behavior can be described by lexicons, and we show one concrete proposal that by now has been applied to three languages, with others being added in ongoing work. The lexical representations can be useful both for humans (theoretical investigations, transfer to other languages) and for machines (automatic discourse parsing and generation).
The Relationship of Spiritual Health with Quality of Life, Mental Health, and Burnout: The Mediating Role of Emotional Regulation

Objective: The World Health Organization's definition of health now stands open to severe criticism due to changes in today's world and the accompanying mental void; in addition to physical, psychological, and social aspects, spiritual health and its interaction with the other aspects has been studied in scientific literature and recent research. The present study was conducted to investigate the mediating role of emotional regulation in the relationship between spiritual health with quality of life, psychological health, and burnout. Method : In this study, 231 staff from Baqiyatallah University of Medical Sciences completed Spiritual Well-Being Scale (SWBS), Difficulties in Emotion Regulation Scale (DERS), World Health Organization Quality of Life-BREF (WHOQOL-BREF), General Health Questionnaire-28 (GHQ-28), and Maslach Burnout Inventory (MBI). The gathered data were analyzed using Pearson correlation, Hierarchical Regression analysis, and Sobel’s test. Results: All variables were correlated with one another (p<0.001). The hierarchical regression analysis and Sobel’s test indicated that the emotional regulation have a relative mediating role in the relationship between spiritual health and quality of life (ß=0.53, Z=4.05, p<0.001) and a complete mediating role in the relationship between spiritual health with mental health (ß=0.68, Z=5.62, p<0.001) and burnout (ß=0.70, Z=6.12, p<0.001). Conclusion: There is a complex and non-linear relationship between spiritual health and the areas of quality of life, mental health and burnout. This relationship is potentially influenced by emotional regulation.
Readability of Prostate Cancer Information Online: A Cross-Sectional Study

Reading and understanding health information, both components of health literacy, can influence patient decisions related to disease management. Older adults, the population of males at greatest risk for prostate cancer, may have compromised capacity to understand and use health information. The purpose of this study was to determine the readability of prostate cancer materials on the Internet using five recommended readability tests. Using a cleared Internet browser, a search was conducted for “prostate cancer. ” The URLs of the first 100 websites in English were recorded to create the sample. The readability scores for each website were determined using an online, recommended service. This service generates five commonly recommended readability tests. All five tests revealed that the majority of websites had difficult readability. There were no significant differences identified between websites with . org, . gov, or . edu extension versus those with . com, . net, or other extension. It is apparent that the Internet is used often as a resource for health-related information. This study demonstrates that the large majority of information available on the Internet about prostate cancer will not be readable for many individuals.
Long-term periodontal status of palatally and buccally impacted canines after closed surgical-orthodontic approach.

Introduction The aim of this study is to evaluate the periodontal status of palatally and buccally impacted canines exposed with closed technique, and to compare them with the controlateral canines that served as control teeth as well as to compare them each other. Methods 28 patients, 14 with unilateral palatally impacted canines and 14 with unilateral buccally impacted canines comprised the subjects of the study. Mean recall observational period was 2 years 4 months ± 1 year 1 month. Closed eruption technique without the tunnel was performed to expose both the palatally and the buccally impacted canines. Six periodontal variables were considered: probing pocket depth (PPD); width of keratinized tissue (KT); gingival thickness (GT); plaque index (PI); gingival bleeding index (GBI); gingival recession (REC). Results Palatally impacted canines exhibited significant greater PPD on the mesiolingual site compared to their controlaterals (P<0.05). Buccally impacted canines had significant increased KT compared to their contralaterals (P<0.05). Palatally impacted canines had significant greater PPD on the midbuccal site and on all the palatal sites when compared to the buccally impacted canines (P<0.05). Conclusion The changes observed in the periodontal status of impacted canines, although statistically significant, did not reach clinical significance.
Kernel Machines With Missing Responses

Missing responses is a missing data format in which outcomes are not always observed. In this work we develop kernel machines that can handle missing responses. First, we propose a kernel machine family that uses mainly the complete cases. For the quadratic loss, we then propose a family of doubly-robust kernel machines. The proposed kernel-machine estimators can be applied to both regression and classification problems. We prove oracle inequalities for the finite-sample differences between the kernel machine risk and Bayes risk. We use these oracle inequalities to prove consistency and to calculate convergence rates. We demonstrate the performance of the two proposed kernel machine families using both a simulation study and a real-world data analysis.
Biophysical basis of the linear electrical receptive fields of retinal ganglion cells

Responses of retinal ganglion cells to direct electrical stimulation have been shown experimentally to be well described by linear–nonlinear models. These models rely on the simplifying assumption that retinal ganglion cell responses to stimulation with an array of electrodes are driven by a simple linear weighted sum of stimulus current amplitudes from each electrode, known as the ‘electrical receptive field’. Objective. This paper aims to demonstrate the biophysical basis of the linear–nonlinear model and the electrical receptive field to facilitate the development of improved stimulation strategies for retinal implants. Approach. We compare the linear–nonlinear model of subretinal electrical stimulation with a multi-layered, biophysical, volume conductor model of retinal stimulation. Main results. Our results show that the linear electrical receptive field of the linear–nonlinear model matches the transmembrane currents induced by electrodes (the activating function) at the site of the high-density sodium channel band with only minor discrepancies. The discrepancies are mostly eliminated by including axial current flow originating from adjacent cell compartments. Furthermore, for cells where a single linear electrical receptive field is insufficient, we show that cell responses are likely driven by multiple sites of action potential initiation with multiple distinct receptive fields, each of which can be accurately described by the activating function. Significance. This result establishes that the biophysical basis of the electrical receptive field of the linear–nonlinear model is the superposition of transmembrane currents induced by different electrodes at and near the site of action potential initiation. Together with existing experimental support for linear–nonlinear models of electrical stimulation, this provides a firm basis for using this much simplified model to generate more optimal stimulation patterns for retinal implants.
Joint Part-of-Speech and Language ID Tagging for Code-Switched Data

Code-switching is the fluent alternation between two or more languages in conversation between bilinguals. Large populations of speakers code-switch during communication, but little effort has been made to develop tools for code-switching, including part-of-speech taggers. In this paper, we propose an approach to POS tagging of code-switched English-Spanish data based on recurrent neural networks. We test our model on known monolingual benchmarks to demonstrate that our neural POS tagging model is on par with state-of-the-art methods. We next test our code-switched methods on the Miami Bangor corpus of English Spanish conversation, focusing on two types of experiments: POS tagging alone, for which we achieve 96.34% accuracy, and joint part-of-speech and language ID tagging, which achieves similar POS tagging accuracy (96.39%) and very high language ID accuracy (98.78%). Finally, we show that our proposed models outperform other state-of-the-art code-switched taggers.
Accumulation of Dense Core Vesicles in Hippocampal Synapses Following Chronic Inactivity

The morphology and function of neuronal synapses are regulated by neural activity, as manifested in activity-dependent synapse maturation and various forms of synaptic plasticity. Here we employed cryo-electron tomography (cryo-ET) to visualize synaptic ultrastructure in cultured hippocampal neurons and investigated changes in subcellular features in response to chronic inactivity, a paradigm often used for the induction of homeostatic synaptic plasticity. We observed a more than 2-fold increase in the mean number of dense core vesicles (DCVs) in the presynaptic compartment of excitatory synapses and an almost 20-fold increase in the number of DCVs in the presynaptic compartment of inhibitory synapses after 2 days treatment with the voltage-gated sodium channel blocker tetrodotoxin (TTX). Short-term treatment with TTX and the N-methyl-D-aspartate receptor (NMDAR) antagonist amino-5-phosphonovaleric acid (AP5) caused a 3-fold increase in the number of DCVs within 100 nm of the active zone area in excitatory synapses but had no significant effects on the overall number of DCVs. In contrast, there were very few DCVs in the postsynaptic compartments of both synapse types under all conditions. These results are consistent with a role for presynaptic DCVs in activity-dependent synapse maturation. We speculate that these accumulated DCVs can be released upon reactivation and may contribute to homeostatic metaplasticity.