Miracle-dz/UniFAR-FTUs huggingface dataset:
On the generation and evolution of internal gravity waves

In order to study the tidal generation and evolution of internal waves, both experimentally and theoretically, a two-dimensional two-layer model has been developed. The laboratory model consists of two immiscible fluid layers in a long wave tank, where time-dependent flow can be created by towing a suitably shaped obstacle with a sinusoidal motion. The effects of changing the Froude number and the ratio of the depths of the two fluid layers on the shape of the interface are studied. The first theoretical model considers the motion to be quasi-steady, allowing only a balance between buoyancy and inertial forces, and is in reasonable agreement with the experimental results for very slow motions and the initial phase of the tidal cycle only. A more complete numerical solution is based on the vortex-point method in which the interface is modelled by a set of discrete vortices, while the rigid boundaries, which include the obstacle, are modelled by a source distribution. The resulting governing equations are expressed in Lagrangian form, and the baroclinic generation of vorticity is related to the generation of source density, through two simultaneous integrodifferential equations. For small Froude numbers, the experimental and numerical results are in good quantitative agreement. At large Froude numbers, the numerical solution, which does not consider mixing between the two layers nor boundary-layer separation from the obstacle, gives a slight difference in the position of the maximum interface displacement from that found in the experiment.
On a Model for Bivariate Left Censored Data

The lifetimes of subjects which are left-censored lie below a threshold value or a limit of detection. A popular tool used to handle left-censored data is the reversed hazard rate. In this work, we study the properties and develop characterizations of a class of distributions based on proportional reversed hazard rates used for analyzing left censored data. These characterizations are applied to simulate samples as well as analyze real data using distributions belonging to this class.
Digital Security -- A Question of Perspective. A Large-Scale Telephone Survey with Four At-Risk User Groups

This paper investigates the digital security experiences of four at-risk user groups in Germany, including older adults (70+), teenagers (14-17), people with migration backgrounds, and people with low formal education. Using computer-assisted telephone interviews, we sampled 250 participants per group, representative of region, gender, and partly age distributions. We examine their device usage, concerns, prior negative incidents, perceptions of potential attackers, and information sources. Our study provides the first quantitative and nationally representative insights into the digital security experiences of these four at-risk groups in Germany. Our findings show that participants with migration backgrounds used the most devices, sought more security information, and reported more experiences with cybercrime incidents than other groups. Older adults used the fewest devices and were least affected by cybercrimes. All groups relied on friends and family and online news as their primary sources of security information, with little concern about their social circles being potential attackers. We highlight the nuanced differences between the four at-risk groups and compare them to the broader German population when possible. We conclude by presenting recommendations for education, policy, and future research aimed at addressing the digital security needs of these at-risk user groups.
Your diffusion model secretly knows the dimension of the data manifold

In this work, we propose a novel framework for estimating the dimension of the data manifold using a trained diffusion model. A diffusion model approximates the score function i.e. the gradient of the log density of a noise-corrupted version of the target distribution for varying levels of corruption. We prove that, if the data concentrates around a manifold embedded in the high-dimensional ambient space, then as the level of corruption decreases, the score function points towards the manifold, as this direction becomes the direction of maximal likelihood increase. Therefore, for small levels of corruption, the diffusion model provides us with access to an approximation of the normal bundle of the data manifold. This allows us to estimate the dimension of the tangent space, thus, the intrinsic dimension of the data manifold. To the best of our knowledge, our method is the first estimator of the data manifold dimension based on diffusion models and it outperforms well established statistical estimators in controlled experiments on both Euclidean and image data.
TextBox 2.0: A Text Generation Library with Pre-trained Language Models

To facilitate research on text generation, this paper presents a comprehensive and unified library, TextBox 2.0, focusing on the use of pre-trained language models (PLMs). To be comprehensive, our library covers $13$ common text generation tasks and their corresponding $83$ datasets and further incorporates $45$ PLMs covering general, translation, Chinese, dialogue, controllable, distilled, prompting, and lightweight PLMs. We also implement $4$ efficient training strategies and provide $4$ generation objectives for pre-training new PLMs from scratch. To be unified, we design the interfaces to support the entire research pipeline (from data loading to training and evaluation), ensuring that each step can be fulfilled in a unified way. Despite the rich functionality, it is easy to use our library, either through the friendly Python API or command line. To validate the effectiveness of our library, we conduct extensive experiments and exemplify four types of research scenarios. The project is released at the link: https://github.com/RUCAIBox/TextBox.
Gamow shell model description of the radiative capture reaction $^8$B$(p,\gamma)$$^9$C

In low metallicity supermassive stars, the hot $pp$ chain can serve as an alternative way to produce the CNO nuclei. In the astrophysical environment of high temperature, the proton capture of $^8$B can be faster than its beta decay, thus $^8$B$(p,\gamma)$$^9$C reaction plays an important role in the hot $pp$ chain. Due to the unstable nature of $^8$B and the lack of the $^8$B beam, the measurement of $^8$B$(p,\gamma)$$^9$C reaction can only be achieved by the indirect method, and large uncertainties exist. The Gamow shell model in the coupled-channel representation (GSM-CC) is applied to study the proton radiative capture reaction $^8$B$(p,\gamma)$$^9$C. For the calculation of the $^8$B$(p,\gamma)$$^9$C astrophysical factors, all E1, M1, and E2 transitions from the initial continuum states to the final bound states ${3/2}_1^-$of $^9$C are considered. The resonant capture to the first resonant state ${1/2}_1^-$ of $^{9}$C is also calculated. The experimental low-energy levels and the proton emission threshold in $^9$C are reproduced by the GSM-CC. The calculated astrophysical factors agrees with the existed experimental data from the indirect measurements. The reaction rates from the direct capture and resonant capture are calculated for the temperature range of astrophysical interest. The calculated total astrophysical $S$ factor is dominated by the E1 transition to the ground state of $^9$C. The GSM-CC calculations suggest that $S$ first increase with the energy of the center of mass $E_{\rm c.m. }$, and then decrease with the energy. This agrees with the existing data, which has smaller values at around zero energy and larger value in the energy range of 0.2 MeV $\leq E_{\rm c.m. } \leq$ 0.6 MeV.
Spatiotemporal mode decomposition of ultrashort pulses propagating in graded-index multimode fibers

We develop a spatiotemporal mode decomposition technique to study the mode power distribution of ultrashort pulses emerging from long spans of graded-index multimode fiber, for different input laser conditions. We find that beam mode power content in the dispersive pulse propagation regime can be described by the Bose-Einstein law, as a result of the process of power diffusion from linear and nonlinear mode coupling among nondegenerate mode groups. In the soliton regime, the output mode power distribution approaches the Rayleigh-Jeans law
Nonnegative Matrix Factorization Based on Node Centrality for Community Detection

Community detection is an important topic in network analysis, and recently many community detection methods have been developed on top of the Nonnegative Matrix Factorization (NMF) technique. Most NMF-based community detection methods only utilize the first-order proximity information in the adjacency matrix, which has some limitations. Besides, many NMF-based community detection methods involve sparse regularizations to promote clearer community memberships. However, in most of these regularizations, different nodes are treated equally, which seems unreasonable. To dismiss the above limitations, this article proposes a community detection method based on node centrality under the framework of NMF. Specifically, we design a new similarity measure which considers the proximity of higher-order neighbors to form a more informative graph regularization mechanism, so as to better refine the detected communities. Besides, we introduce the node centrality and Gini impurity to measure the importance of nodes and sparseness of the community memberships, respectively. Then, we propose a novel sparse regularization mechanism which forces nodes with higher node centrality to have smaller Gini impurity. Extensive experimental results on a variety of real-world networks show the superior performance of the proposed method over thirteen state-of-the-art methods.
Staphylococcus aureus adaptive evolution: Recent insights on how immune evasion, immunometabolic subversion and host genetics impact vaccine development

Despite meritorious attempts, a S. aureus vaccine that prevents infection or mitigates severity has not yet achieved efficacy endpoints in prospective, randomized clinical trials. This experience underscores the complexity of host-S. aureus interactions, which appear to be greater than many other bacterial pathogens against which successful vaccines have been developed. It is increasingly evident that S. aureus employs strategic countermeasures to evade or exploit human immune responses. From entering host cells to persist in stealthy intracellular reservoirs, to sensing the environmental milieu and leveraging bacterial or host metabolic products to reprogram host immune responses, S. aureus poses considerable challenges for the development of effective vaccines. The fact that this pathogen causes distinct types of infections and can undergo transient genetic, transcriptional or metabolic adaptations in vivo that do not occur in vitro compounds challenges in vaccine development. Notably, the metabolic versatility of both bacterial and host immune cells as they compete for available substrates within specific tissues inevitably impacts the variable repertoire of gene products that may or may not be vaccine antigens. In this respect, S. aureus has chameleon phenotypes that have alluded vaccine strategies thus far. Nonetheless, a number of recent studies have also revealed important new insights into pathogenesis vulnerabilities of S. aureus. A more detailed understanding of host protective immune defenses versus S. aureus adaptive immune evasion mechanisms may offer breakthroughs in the development of effective vaccines, but at present this goal remains a very high bar. Coupled with the recent advances in human genetics and epigenetics, newer vaccine technologies may enable such a goal. If so, future vaccines that protect against or mitigate the severity of S. aureus infections are likely to emerge at the intersection of precision and personalized medicine. For now, the development of S. aureus vaccines or alternative therapies that reduce mortality and morbidity must continue to be pursued.
Structure of nanocrystalline Re-Si thin film composites and their unusual thermoelectric properties

The structure of nanocrystalline rhenium–silicon composite ReSix films with 1.4<x<2.2 has been studied as a function of the time by means of high temperature x-ray diffraction and transmission electron microscopy. Simultaneously, the thermoelectric transport properties were measured during the heat treatment. The nanocrystallization was achieved by annealing of amorphous films deposited onto oxidized Si wafers by magnetron cosputtering. The crystallization process is characterized by a decreasing average crystallite size in the range between 7 and 19 nm. An unknown mechanism limits the grain growth after reaching a maximum size, which decreases with increasing Si content. In the final state the films contain only two phases: the amorphous phase and the nanocrystalline ReSi1.75 phase. The electrical conductivity and the thermoelectric power of these thin film composites show nonmonotonic dependence on the volume fraction of the nanocrystalline phase and depend on different parameters, which suggests a way .
History-dependent muscle resistance to stretch remains high after small, posturally-relevant pre-movements

The contributions of intrinsic muscle fiber resistance during mechanical perturbations to standing and other postural behaviors are unclear. Muscle stiffness, a traditional metric for estimating muscle’s intrinsic resistance to stretch, is known to vary depending on the current level and history of the muscle’s activation, as well as the muscle’s recent movement history; this property has been referred to as history dependence or muscle thixotropy. However, we currently lack sufficient data about the degree to which muscle stiffness is modulated across posturally-relevant characteristics of muscle stretch and activation. Here, we characterized the history dependence of muscle’s resistance to stretch in single, permeabilized, activated, muscle fibers in posturally-relevant stretch conditions and activation levels. We used a classic paired muscle stretch paradigm, varying the amplitude of a “conditioning” triangular stretch-shorten cycle followed by a “test” ramp-and-hold imposed after a variable inter-stretch interval. We tested low (<15%), intermediate (15-50%) and high (>50%) muscle fiber activation levels, evaluating short-range stiffness and total impulse in the test stretch. Muscle fiber resistance to stretch remained high at conditioning amplitudes of <1% L0 and inter-stretch intervals of >1 s, characteristic of healthy standing postural sway. A ~70% attenuation of muscle resistance to stretch was reached at conditioning amplitudes of >3% L0 and inter-stretch intervals of <0.1s, characteristic of larger, faster postural sway in balance-impaired individuals. Overall, amplitude and inter-stretch interval interact to disrupt myofilaments such that intrinsic resistance to stretch is attenuated if the stretch is large enough and/or frequent enough. Summary Statement Intrinsic muscle fiber resistance to stretch is preserved after small, slow pre-movements based on healthy postural sway, but markedly reduced as pre-movements increase to emulate abnormal postural sway.
voyAGEr: free web interface for the analysis of age-related gene expression alterations in human tissues

We herein introduce voyAGEr, an online graphical interface to explore age-related gene expression alterations in 49 human tissues. voyAGEr offers a visualisation and statistical toolkit for the finding and functional exploration of sex– and tissue-specific transcriptomic changes with age. In its conception, we developed a novel bioinformatics pipeline leveraging RNA sequencing data, from the GTEx project, encompassing more than 900 individuals. voyAGEr reveals transcriptomic signatures of the known asynchronous ageing between tissues, allowing the observation of tissue-specific age-periods of major transcriptional changes, associated with alterations in different biological pathways, cellular composition, and disease conditions. Notably, voyAGEr was created to assist researchers with no expertise in bioinformatics, providing a supportive framework for elaborating, testing and refining their hypotheses on the molecular nature of human ageing and its association with pathologies, thereby also aiding in the discovery of novel therapeutic targets. voyAGEr is freely available at https://compbio.imm. medicina.ulisboa. pt/app/voyAGEr.
IFSAR phase unwrapping in the presence of Dirichlet boundary conditions

Phase unwrapping is one of the key computational elements in digital elevation model generation from interferometric SAR. In this paper we present a reformulation of the weighted least squares phase unwrapping approach that incorporates Dirichlet boundary conditions. The application of this formulation to the incorporation of control points into the solution as well as for unwrapping the interferogram in stages is discussed. The ability of the weighted least squares approach to fully unwrap an interferogram can be very dependent on the weight matrix used. This has led us to develop an adaptive approach to updating the weight matrix to be used in conjunction with our weighted least squares approach. Examples along the preliminary results based on ERS data will be presented.
Native adiponectin plays a role in the adipocyte-mediated conversion of fibroblasts to myofibroblasts

Adipocytes regulate tissues through production of adipokines that can act both locally and systemically. Adipocytes also have been found to play a critical role in regulating the healing process. To better understand this role, we developed a 3D human adipocyte spheroid system that has an adipokine profile similar to in vivo adipose tissues. Previously, we found that conditioned medium from these spheroids induces human dermal fibroblast conversion into highly contractile, collagen producing myofibroblasts through a transforming growth factor beta-1 (TGF-β1) independent pathway. Here, we sought to identify how mature adipocytes signal to dermal fibroblasts through adipokines to induce myofibroblast conversion. By using molecular weight fractionation, heat inactivation, and lipid depletion, we determined mature adipocytes secrete a factor that is 30-100 kDa, heat labile, and lipid associated that induces myofibroblast conversion. We also show that depletion of the adipokine adiponectin, which fits those physiochemical parameters, eliminates the ability of adipocyte conditioned media to induce fibroblast to myofibroblast conversion. Interestingly, native adiponectin secreted by cultured adipocytes consistently elicited a stronger level of α-SMA expression than exogenously added adiponectin. Thus, adiponectin secreted by mature adipocytes induces fibroblast to myofibroblast conversion and may lead to a phenotype of myofibroblasts distinct from TGF-β1 induced myofibroblasts.
Transcutaneous electrical nerve stimulation acutely impacts motor unit firing activity during isometric contractions

A low intensity electrical current delivered transcutaneously at a high frequency over a muscle can acutely recruit motor units in a physiological order by activating peripheral sensory pathways. This method has been used in patients to reduce tremor or supplement motor function, leading to the development of therapies and products. We aimed to better understand how the stimulation of the median nerve, the contralateral first dorsal interosseus muscle (FDI), and the combination of these two paradigms impact the motor unit activity from the FDI muscle. We identified and tracked the same motor units across the conditions and compared the electromyographic amplitude, motor unit discharge rates, and the degree of correlation between fast and slow oscillations of motor unit discharge rates. We found that the stimulation of the FDI muscle can acutely increase the electromyographic amplitude of the homonymous muscle on the contralateral side (F = 20.4; p < 0.001) while the discharge rate of motor units did not differ between the control and the stimulation condition (F = 0.2; p = 0.806). We did not observe any significant effect of the stimulation on the ratio of pairs of motor units with a significant correlation, showing that the stimulation barely impacted the distribution of correlated inputs to the pool of motor units. We did not observe short-term effects of the stimulation once it was discontinued. Overall, these results showed that the specific stimulation of peripheral sensory pathways can acutely impact motor unit firing activity without disturbing the neural control of force. New & Noteworthy We identified and tracked the same motor units across stimulation and control conditions using high-density electromyography. We found that the specific stimulation of peripherial sensory pathways can acutely impact motor unit firing activity, likely due to the recruitment of additional motor units. At the same time, the degree of correlation between fast and slow oscillations of motor unit discharge rates was stable, limiting the disturbance of the neural control of force.
Generalised interrelations among mutation rates drive the genomic compliance of Chargaff's second parity rule

Chargaff’s second parity rule (PR-2), where the complementary base and k-mer contents are matching within the same strand of a double stranded DNA (dsDNA), is a phenomenon that invited many explanations. The strict compliance of nearly all nuclear dsDNA to PR-2 implies that the explanation should also be similarly adamant. In this work, we revisited the possibility of mutation rates driving PR-2 compliance. Starting from the assumption-free approach, we constructed kinetic equations for unconstrained simulations. The results were analysed for their PR-2 compliance by employing symbolic regression and machine learning techniques. We arrived to a generalised set of mutation rate interrelations in place in most species that allow for their full PR-2 compliance. Importantly, our constraints explain PR-2 in genomes out of the scope of the prior explanations based on the equilibration under mutation rates with simpler no-strand-bias constraints. We thus reinstate the role of mutation rates in PR-2 through its molecular core, now shown, under our formulation, to be tolerant to previously noted strand biases and incomplete compositional equilibration. We further investigate the time for any genome to reach PR-2, showing that it is generally earlier than the compositional equilibrium, and well within the age of life on Earth.