Miracle-dz/UniFAR-FTUs huggingface dataset:
Distilling multi-scale neural mechanisms from diverse unlabeled experimental data using deep domain-adaptive inference framework

Behavior and cognition emerge from the complex interplay of neural properties at different scales. However, inferring these multi-scale properties from diverse experimental data remains a classical challenge in computational and systems neuroscience. Advanced machine learning (ML) techniques, such as deep learning and Bayesian inference, have shown promise in addressing this issue. Nonetheless, the performance of ML models trained on synthetic data generated from computational models degrades dramatically on experimental data. To systematically tackle these challenges, we introduce the concept of “out-of-distribution (OOD)” to quantify distributional shift between synthetic and experimental datasets, and propose a deep domain-adaptive inference framework that aligns the distribution of synthetic data with experimental data by minimizing OOD errors. Our framework achieves state-of-the-art performance on a wide range of real experimental data when inferring neural properties at different scales. We demonstrate the efficacy of our framework in two scenarios: inferring detailed biophysical properties at the neuron and microcircuit scales, and inferring monosynaptic connections in hippocampal CA1 networks from in vivo multi-electrode extracellular recordings in free-running mice. Our approach represents a pioneering systematic solution to the OOD problem in neuroscience research and can potentially facilitate bottom-up modeling of large-scale network dynamics underlying brain function and dysfunction. Teaser Our deep domain-adaptive inference framework addresses the out-of-distribution (OOD) problem in inferring multi-scale neural properties from experimental data, enabling state-of-the-art performance and broad implications for neuroscience research.
Butt-seq: a new method for facile profiling of transcription

A wide range of sequencing methods have been developed to assess nascent RNA transcription and resolve the single-nucleotide position of RNA polymerase genome-wide. These techniques are often burdened with high input material requirements and lengthy protocols. We leveraged the template-switching properties of thermostable group II intron reverse transcriptase (TGIRT) and developed BuTT-Seq (BUlk analysis of nascent Transcript Termini sequencing), which can produce libraries from purified nascent RNA in 6 hours and from as few as 10,000 cells – an improvement of at least 25-fold over existing techniques. BuTT-Seq shows that inhibition of the superelongation complex (SEC) causes promoter-proximal pausing to move upstream in a fashion correlated with subnucleosomal fragments. To address transcriptional regulation in a tissue, BuTT-Seq was used to measure the circadian regulation of transcription from fly heads. All the results indicate that BuTT-Seq is a simple and powerful technique to analyze transcription at a high level of resolution.
Tbx5 overexpression in embryoid bodies increases TAK1 expression but does not enhance the differentiation of sinoatrial node cardiomyocytes

Genetic studies place Tbx5 at the apex of the sinoatrial node (SAN) transcriptional program. To understand its role in SAN differentiation, clonal embryonic stem (ES) cell lines were made that conditionally overexpress Tbx5, Tbx3, Tbx18, Shox2, Islet-1 and Map3k7/TAK1. and cardiac cells differentiated using embryoid bodies (EBs). EBs overexpressing Tbx5, Islet1, and TAK1 beat faster than cardiac cells differentiated from control ES cell lines suggesting possible roles in SAN differentiation. Tbx5 overexpressing EBs showed increased expression of TAK1, but cardiomyocytes did not differentiate as SAN cells. They showed no increase in the expression of Shox2, or Islet1 and decreased expression of HCN4. EBs constitutively overexpressing TAK1 direct cardiac differentiation to the SAN fate, but also have decreased phosphorylation of its targets, p38, and Jnk. This opens the possibility that blocking the phosphorylation of TAK1 targets may have the same impact as forced overexpression. To test this, we treated EBs with 5z-7-Oxozeanol (OXO), an inhibitor of TAK1 phosphorylation. Like TAK1 overexpressing cardiac cells, cardiomyocytes differentiated in the presence of OXO beat faster and showed increased expression of SAN genes (Shox2, HCN4, and Islet1). This suggests that activation of the SAN transcriptional network can be accomplished by blocking the phosphorylation of TAK1.
Sensing volatiles throughout the body: Geographic and tissue-specific olfactory receptor expression in the fig wasp Ceratosolen fusciceps

An essential adaptive strategy in insects is the evolution of olfactory receptors (ORs) to recognize important volatile environmental chemical cues. Our model species, Ceratosolen fusciceps, a specialist wasp pollinator of Ficus racemosa, likely possesses an OR repertoire that allows it to distinguish fig-specific volatiles in highly variable environments. Using a newly assembled genome-guided transcriptome, we annotated 63 ORs in the species and reconstructed the phylogeny of Ceratosolen ORs in conjunction with other hymenopteran species. Expression analysis showed that though ORs were mainly expressed in the antennae, 20 percent were also expressed in non-antennal tissues such as the head, thorax, abdomen, legs, wings, and ovipositor. Specific upregulated expression was observed in OR30C in the head and OR60C in the wings. We identified OR expression from all major body parts of C. fusciceps, suggesting novel roles of ORs throughout the body. Further examination of OR expression of C. fusciceps in widely separated geographical locations, i.e., south (urban) and northeast (rural) India, revealed distinct OR expression levels in different locations. This discrepancy likely parallels the observed variation in fig volatiles between these regions and provides new insights into the evolution of insect ORs and their expression across geographical locations and tissues.
RatXcan: Framework for translating genetic results between species via transcriptome-wide association analyses

We developed a framework for identifying trait-associated genes in rats and facilitating the transfer of polygenic evidence across species by expanding the transcriptome-wide association (TWAS) approach to rats. Our analysis successfully trained transcript predictors for over 8000 genes in each of the five brain regions of rats, revealing several shared properties of gene regulation with humans. Moreover, mirroring trends observed in humans, our findings showed that sparse predictors using variants in cis are more effective than polygenic predictors and that gene expression prediction in rats is highly correlated across brain regions. Importantly, our analysis also identified a significant overlap between genes associated with rat and human body length and BMI, indicating rat models may be useful for studying the genetic basis of complex traits in humans. RatXcan represents a valuable tool for uncovering shared biological mechanisms of complex traits across species, with potential applications in a wide range of research fields.
Optimal energy decay rate in a damped Rayleigh beam

We consider a clamped Rayleigh beam subject to a positive viscous damping. Using an explicit approximation, we first give the asymptotic expansion of eigenvalues and eigenfunctions of the underlying system. We next identify the optimal energy decay rate of the system with the supremum of the real part of the spectrum of the infinitesimal generator of the associated semigroup.
Prediction of the growth rates of VDEs in JET

In this paper we show that the effect of the saddle currents in the rigid sectors slows down the vertical instability of JET elongated plasmas with respect to estimates based on pure axisymmetric models. This, together with an accurate description of the passive structures, significantly improves the agreement between the theoretical predictions and the experimental results. Linearized models taking into account the three-dimensional effects of the eddy currents have been applied to various JET pulses; the growth rates have been estimated within an accuracy of less than 5% for plasmas with a growth time longer than 2 ms. This model can be used for JET and extended to ITER-FEAT to provide a reliable test bed for assessing the performance of the vertical control system and obtain an estimate of the loads on the structures during vertical displacement events (VDEs) and plasma disruptions.
CIENCIAS EPIDEMIOLÓGICAS Y SALUBRISTAS Revista Habanera de Ciencias Médicas

Introduction: The COVID-19 pandemic has revealed high disparities in the world population. Objective: To describe the correlation between competitiveness and mortality from COVID-19 in Peru, with subnational governments as an element of study. Material and Methods: Observational study based on the secondary analysis of deaths from COVID-19 that occurred in 2020 and the regional competitiveness index of subnational governments in 2019. The crude and standardized rates, the effect index, the difference and ratio of crude and standardized rates, the population attributable risk, the inequality gradient, and the relative and absolute gaps in mortality from COVID-19 were calculated. Results: In 2020, the standardized mortality rate for COVID-19 (COVID-19-SMR) was 267,61 deaths per 10 5 inhabitants. Additionally, 21,53 % of the variance from the COVID-19-SMR is explained by the regional competitiveness index 2019 (p= 0,019); the slope inequality index was 29,68 and, for each point in the INCORE 2019, the COVID-19-SMR increased 100,78 points (R 2 a= 0,181). In quintile 1 of regional competitiveness, it was 151,83, while in quintile 5 it reached 449,15. The absolute inequality gap between both quintiles was 297,32 and it reached 2,95 in the relative inequality gap. The concentration curve evidenced the socio-geographic inequality of deaths from COVID-19 in 2020. Conclusions: Mortality increased as subnational governments became more competitive, evidencing the socio-geographical inequality of the impact of the COVID-19 pandemic.
High Pressure Photoluminescence Study of the GaAs/Partially Ordered GaInP Interface

Using time-resolved (TRPL) and continuous-wave photoluminescence (CWPL) we have studied GaAs/partially ordered Ga0.5In0. 5P single quantum well samples at pressures up to ≈5 GPa. In such samples emission from the quantum well is only seen if intermediate GaP layers are grown between the GaAs and GaInP and is otherwise masked by anomalous bands at around 1.46 eV. Examination of the TRPL spectra shows large differences in the pressure dependence of this emission because of the inequivalence of the GaAs/GaInP interfaces. For the sample with no thin GaP layer between the upper interface this emission has a very long PL-decay time and a stronger blueshift with excitation intensity at higher pressures. The pressure-dependent PL behavior at lower excitation intensity is close to that of the GaInP barrier. The 1.46 eV emission can be attributed to the spatially indirect transitions at the interface with no GaP layer.
Service-Learning Project in a First-Year Seminar: A Social Network Analysis

Abstract Understanding the effects of a service-learning component on the classroom culture, socially and academically, brings a novel perspective to designing, executing, and assessing these types of active-learning projects. This paper evaluates the success of a service-learning project from a perspective of social networks by investigating the question: How does a service-learning project affect friendship and academic collaborations in the classroom? We believe that the benefits of service-learning involvement extend beyond helping students' academic success. Especially in a first-year seminar course, building a support system for the incoming student in order to ease the translation to a college setting is beneficial to students and to colleges. Here we use social network analysis tools to analyze relational data where relations are described as friendships or academic collaborations among classmates. Our results show that a group-based service learning project in an introductory level Statistics course has different effects on the evolution of friendship and academic collaboration networks among classmates.
The role of aerodynamic drag in dynamics of coronal mass ejections

Abstract Dynamics of coronal mass ejections (CMEs) is strongly affected by the interaction of the erupting structure with the ambient magnetoplasma: eruptions that are faster than solar wind transfer the momentum and energy to the wind and generally decelerate, whereas slower ones gain the momentum and accelerate. Such a behavior can be expressed in terms of “aerodynamic” drag. We employ a large sample of CMEs to analyze the relationship between kinematics of CMEs and drag-related parameters, such as ambient solar wind speed and the CME mass. Employing coronagraphic observations it is demonstrated that massive CMEs are less affected by the aerodynamic drag than light ones. On the other hand, in situ measurements are used to inspect the role of the solar wind speed and it is shown that the Sun-Earth transit time is more closely related to the wind speed than to take-off speed of CMEs. These findings are interpreted by analyzing solutions of a simple equation of motion based on the standard form for the drag acceleration. The results show that most of the acceleration/deceleration of CMEs on their way through the interplanetary space takes place close to the Sun, where the ambient plasma density is still high. Implications for the space weather forecasting of CME arrival-times are discussed.
Language Resources and Evaluation Conference 20-25 June 2022 Games and Natural Language Processing ( Games & NLP 2022 )

In this work we present an analysis of abusive language annotations collected through a 3D video game. With this approach, we are able to involve in the annotation teenagers, i.e. typical targets of cyberbullying, whose data are usually not available for research purposes. Using the game in the framework of educational activities to empower teenagers against online abuse we are able to obtain insights into how teenagers communicate, and what kind of messages they consider more offensive. While players produced interesting annotations and the distributions of classes between players and experts are similar, we obtained a significant number of mismatching judgements between experts and players.
CONVERGENCE OF STOCHASTIC ALGORITHMS: FROM THE KUSHNER-CLARK THEOREM TO THE LYAPOUNOV FUNCTIONAL METHOD

In the first part of this paper a global Kushner-Clark theorem about the convergence of stochastic algorithms is proved: we show that, under some natural assumptions, one can 'read' from the trajectories of its ODE whether or not an algorithm converges. The classical stochastic optimization results are included in this theorem. In the second part, the above smoothness assumption on the mean vector field of the algorithm is relaxed using a new approach based on a path-dependent Lyapounov functional. Several applications, for non-smooth mean vector fields and/or bounded Lyapounov function settings, are derived. Examples and simulations are provided that illustrate and enlighten the field of application of the theoretical results.
Nonalcoholic fatty liver disease: pathogenesis and intervention

Nonalcoholic fatty liver disease (NAFLD) is the most frequent liver disease in Western nations. NAFLD is characterized by intrahepatic fat accumulation (first “hit”) and can progress to nonalcoholic steatohepatitis by the second “hit,” such as free fatty acid lipotoxicity, and oxidative stress. It is believed that multifactorial complex interactions between diet, lifestyle, gut microbiota, and genetic background determine the development of NAFLD. Currently, the management of NAFLD is based on lifestyle modification, such as diet and physical activity, and pharmacological intervention. As the understanding of NAFLD pathophysiology furthers, some interesting novel approaches to treating NAFLD are emerging, such as antioxidants and probiotics. This review is focused on the pathogenesis of NAFLD and potential therapeutic approaches to treat the disease.
A Fixed Point Theorem for Three Pairs of Mappings Satisfying Contractive Condition of Integral Type in Dislocated Metric Space

The aim of this paper is to study a common fixed point theorem for three pairs of self-mappings satisfying a contractive condition of integral type in the setting of dislocated metric space. We notice that our established theorem generalizes the main result of Branciari (2002) in the context of dislocated metric space.
Early Quality-of-Life Changes in Mild Traumatic Brain Injury: A Prospective Study

BACKGROUND: Postinjury symptoms and decreased quality of life are common after mild traumatic brain injury. However, few studies have examined how soon, after injury, these changes dissipate. OBJECTIVES: This study aimed to compare changes in postconcussion symptoms, posttraumatic stress, and illness representations and identify predictors of health-related quality of life before and 1 month after hospital discharge for mild traumatic brain injury. METHODS: A prospective, multicenter, correlational design was used to measure postconcussion symptoms, posttraumatic stress, illness representations, and health-related quality of life. The survey was administered to 136 patients with mild traumatic brain injury between June 2020 and July 2021 at three hospitals in Indonesia. Data were collected at discharge and 1 month later. RESULTS: Compared with before hospital discharge, data collected 1 month after discharge showed that patients experienced reduced postconcussion symptoms, posttraumatic stress, better illness perceptions, and quality of life. Those with postconcussion symptoms (β =−.35, p < .001), more posttraumatic stress symptoms (β =−.12, p = .044), more identity symptoms (β = .11, p = .008), worsened personal control (β =−.18, p = .002), worsened treatment control (β =−.16, p = .001), and negative emotional representations (β =−.17, p = .007) were significantly related to worsened health-related quality of life. CONCLUSION: This study shows that within 1 month of hospital discharge, patients with mild traumatic brain injury had decreased postconcussion symptoms, posttraumatic stress, and improved illness perceptions. Efforts to impact mild brain injury quality of life should focus on inhospital care to optimize the transition to discharge.
Statistical characterization of blob turbulence across the separatrix in HL-2A tokamak

Blob statistical characteristics across the separatrix of HL-2A tokamak plasma have been studied using a reciprocating Langmuir five-probe array. The radial profile of inverse pressure gradient scale length has a maximum just inside the last closed flux surface (LCFS), where the skewness is close to zero. Conditional average reveals that the density holes and blobs are produced just inside the LCFS and they propagate in opposite directions. The poloidal velocity of blobs changes its sign when it is across the separatrix, which is consistent with E × B drift flow. The dramatic change in phase shift between density and potential fluctuations across the separatrix suggests the distinct properties of turbulence when the magnetic field line changes from a closed to an open one. The dependence of a weak three-wave interaction in terms of wavelet bicoherence on strong time-asymmetry blobs is observed for the first time. Moreover, the effective blob generation rate is estimated as 8.0 × 103 s−1 and the convective particle flux induced by the ejective blobs can lead to about 58% loss of radial particle flux.
Detailed comparisons of front‐capturing methods for turbulent two‐phase flow simulations

In the framework of numerical study of multiphase flows, different front‐capturing methods are compared. Two different approaches dealing with the incompressibility constraint will be compared, too. Then, every technique is tested on several relevant test cases in order to make a comparison. The surface tension treatment is evaluated for each method and every front‐capturing method is tested on a case where interface deformations have something in common with turbulent behaviour. Finally, every method is studied through a phase inversion problem, which is an unsteady test case. Front‐capturing methods are tested on physical cases where Navier–Stokes and advection equations are coupled in a non‐linear way. Copyright © 2008 John Wiley & Sons, Ltd.
EFFECTS OF RANDOM MATERIAL PROPERTIES ON BUCKLING OF COMPOSITE PLATES

Composites exhibit a considerable amount of variation in their material properties because their fabrication/manufacturing process involves a large number of parameters that cannot be controlled effectively. In the present study, the material properties have been modeled as random variables for better prediction of the system behavior. The classical laminate theory and first-order and higher-order shear deformation theories have been employed in deriving the governing equations for buckling of laminated rectangular plates. A mean-centered first-order perturbation technique has been used to find the second-order statistics of the buckling load. The approach has been validated by comparison with results of Monte Carlo simulation. Typical results have been presented for a plate with all edges simply supported. The effectiveness of the theories in predicting the buckling load dispersions has been examined. The sensitivity of buckling loads to change in the standard deviation of random material properties and .
Investigation of Secondary Flow Behavior in a Radial Turbine Nozzle

Fundamental investigation of secondary flow phenomena in a radial turbine nozzle are presented. L2F measurements have been used for validation of numerical CFD calculations. Having a good agreement by using the Reynolds stress turbulence model (RSM) the numerical results have been used further to analyse the structure of secondary vortices. Contour plots of the flow angle with typical isoline pattern as well as the vorticity have been evaluated. It is shown that the channel of the radial nozzle similar secondary vorticity systems generates as known from the axial turbine nozzles. The formation and the development of the horse-shoe vortex and the corner vortex are discussed. The well known passage vortex of the axial turbines could not been found because of the small curvature of the streamlines. Instead of these an additional single vortex can be observed, called the “inflow” vortex caused by the unsymmetrical flow into the radial cascade from the upstream scroll.Copyright © 2006 by ASME
Infrared spectra of obscuring dust tori around active galactic nuclei. I - Calculational method and basic trends

Using a new 2D radiative transfer algorithm, we have calculated the thermally reradiated infrared spectra of the compact dust tori which are thought to surround many AGN. These tori radiate anisotropically. Face-on tori may be from one-half to a few orders of magnitude brighter than edge-on tori throughout the infrared. Their spectra at nearly all viewing angles are basically 'bumps' which are about 50 percent wider than blackbodies and peak in the mid-infrared at a wavelength determined mainly by the flux of nuclear radiation on the inner edge of the torus. The infrared color temperatures are hotter for face-on tori than edge-on tori by about 100 K. The 10 micron silicate feature often associated with dust can appear in absorption, emission, or not at all. There is a rough tendency for absorption features to be more prominent for edge-on tori than for face-on tori.