Miracle-dz/UniFAR-FTUs huggingface dataset:
Increasing transposase abundance with ocean depth correlates with a particle-associated lifestyle

ABSTRACT Transposases are mobile genetic elements that move within and between genomes, promoting genomic plasticity in microorganisms. In marine microbial communities, the abundance of transposases increases with depth, but the reasons behind this trend remain unclear. Our analysis of metagenomes from the Tara Oceans and Malaspina Expeditions suggests that a particle-associated lifestyle is the main covariate for the high occurrence of transposases in the deep ocean, and this trend holds true for individual genomes as well as in a community-wide sense. We observed a strong and depth-independent correlation between transposase abundance and the presence of biofilm-associated genes, as well as the prevalence of secretory enzymes. This suggests that mobile genetic elements readily propagate among microbial communities within crowded biofilms. Furthermore, we show that particle association positively correlates with larger genome size, which is in turn associated with higher transposase abundance. Cassette sequences associated with transposons are enriched with genes related to defense mechanisms, which are more highly expressed in the deep sea. Thus, while transposons spread at the expense of their microbial hosts, they also introduce novel genes and potentially benefit the hosts in helping to compete for limited resources. Overall, our results suggest a new understanding of deep ocean particles as highways for gene sharing among defensively oriented microbial genomes. IMPORTANCE Genes can move within and between microbial genomes via mobile genetic elements, which include transposases and transposons. In the oceans, there is a puzzling increase in transposase abundance in microbial genomes as depth increases. To gain insight into this trend, we conducted an extensive analysis of marine microbial metagenomes and metatranscriptomes. We found a significant correlation between transposase abundance and a particle-associated lifestyle among marine microbes at both the metagenome and genome-resolved levels. We also observed a link between transposase abundance and genes related to defense mechanisms. These results suggest that as microbes become densely packed into crowded particles, mobile genes are more likely to spread and carry genetic material that provides a competitive advantage in crowded habitats. This may enable deep sea microbes to effectively compete in such environments.
Amino acid 138 in the HA of a H3N2 subtype influenza A virus increases affinity for the lower respiratory tract and alveolar macrophages in pigs

Influenza A virus (FLUAV) infects a wide range of hosts and human-to-swine spillover events are frequently reported. However, only a few of these human viruses have become established in pigs and the host barriers and molecular mechanisms driving adaptation to the swine host remain poorly understood. We previously found that infection of pigs with a 2:6 reassortant virus (hVIC/11) containing the hemagglutinin (HA) and neuraminidase (NA) gene segments from the human strain A/Victoria/361/2011 (H3N2) and internal gene segments of an endemic swine strain (sOH/04) resulted in a fixed amino acid substitution in the HA (A138S, mature H3 HA numbering). In silico analysis revealed that S138 became predominant among swine H3N2 virus sequences deposited in public databases, while 138A predominates in human isolates. To understand the role of the HA A138S substitution in the adaptation of a human-origin FLUAV HA to swine, we infected pigs with the hVIC/11A138S mutant and analyzed pathogenesis and transmission compared to hVIC/11 and sOH/04. Our results showed that the hVIC/11A138S virus had an intermediary pathogenesis between hVIC/11 and sOH/04. The hVIC/11A138S infected the upper respiratory tract, right caudal, and both cranial lobes while hVIC/11 was only detected in nose and trachea samples. Viruses induced a distinct expression pattern of various pro-inflammatory cytokines such as IL-8, TNF-α, and IFN-β. Flow cytometric analysis of lung samples revealed a significant reduction of porcine alveolar macrophages (PAMs) in hVIC/11A138S-infected pigs compared to hVIC/11 while a MHCIIlowCD163neg population was increased. The hVIC/11A138S showed a higher affinity for PAMs than hVIC/11, noted as an increase of infected PAMs in bronchoalveolar lavage fluid (BALF), and showed no differences in the percentage of HA-positive PAMs compared to sOH/04. This increased infection of PAMs led to an increase of granulocyte-monocyte colony-stimulating factor (GM-CSF) stimulation but a reduced expression of peroxisome proliferator-activated receptor gamma (PPARγ) in the sOH/04-infected group. Analysis using the PAM cell line 3D4/21 revealed that the A138S substitution improved replication and apoptosis induction in this cell type compared to hVIC/11 but at lower levels than sOH/04. Overall, our study indicates that adaptation of human viruses to the swine host involves an increased affinity for the lower respiratory tract and alveolar macrophages.
NATURAL AND ACCELERATED WEATHERING OF TWO COLOURED SICILIAN BUILDING STONES

Among many coloured stones employed as "marbles" in the rich baroque architecture in Sicily, the dark grey Breccia di Billiemi and the Rosso di Piana degli Albanesi are of widespread use. Nowadays they are also exported in Northern Europe and in Arabian countries. Both stones were employed outdoor and indoor as slabs and for structural elements, such as columns, but when ex- posed outdoor, they undergo significant alteration processes, affecting not only their chromatic aspect but also the state of aggregation. Aim of this expe- rimental work is to investigate some alteration processes induced by weather- ing in order to understand the mechanism of their evolution. The effects of ac- celerated weathering in laboratory are compared with natural ageing in the urban environment. The study of such stones includes the description of litho- facies, the characterisation by means of petrographic and physical-chemical techniques - optical and electronic microscopy, XRD - and finally accelerated weathering experiments on both lithotypes - UV radiation plus dew, thermal treatments, washout, exposition to both oxidative and acid environment.
Health and Quality of Life Outcomes

Background: Although there is a considerably high prevalence of developmental disorders in Turkey there are not many assessment tools related to evaluating the impact of these children on their family. The aim of this study was to determine the validity and reliability of the Turkish version of the Impact on Family Scale (IPFAM), a health related quality of life measurement to be utilized in clinical trials, health care services, research and evaluation. Methods: Caregivers of 85 children with developmental disabilities answered the questionnaire and 65 of them answered it twice with a one week interval. The reliability of the measurement was assessed by Cronbach's alpha coefficient, and with intraclass correlation coefficient (ICC) for testretest reliability. Construct validity was assessed by calculating the correlation between total impact score of IPFAM, WeeFIM and the physiotherapists' evaluation via Visual Analogue Scale (VAS) to determine the child's disability. Results: Test-retest reliability was found to be ICC = 0.953 for total impact, 0.843 for financial support, 0.940 for general impact, 0.871 for disruption of social relations and 0.787 for coping. Internal consistency was tested using Cronbach's alpha and was found to be 0.902 for total impact of IPFAM. For construct validity the correlation between total impact score of IPFAM and WeeFIM was r = -0,532 (p < 0.001) and the correlation between total impact score of IPFAM and the physiotherapist's evaluation was r = 0.519 (p < 0.001). Conclusion: The Turkish version of IPFAM was found to be a reliable and valid instrument for assessing the impact of developmental disorders of the child on the family. Background Within the cost conscious healthcare system, healthrelated quality of life measurement has become an important health outcome. This is most obvious in current multi-centered studies [1]. However, while assessing the quality of life amongst the disabled, the burden carried by their caregivers is usually not given adequate consideration. This is particularly true for the families of impaired children. Because the extent to which the family is burdened by the child's illness may also influence child's own quality of life. Chronic childhood illnesses have considerable consequences for the family system. Thus, the process of family adaptation to the presence of an ill member has been explored in the medical and sociological literature [2,3]. Published: 28 January 2009 Health and Quality of Life Outcomes 2009, 7:4 doi:10.1186/1477-7525-7-4 Received: 20 November 2007 Accepted: 28 January 2009 This article is available from: http://www.hqlo. com/content/7/1/4 © 2009 Bek et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
A Mixed-Methods Investigation of Coping, Adaptation and Health-Related Quality of Life in Individuals Experiencing Endometriosis

ObjectivesEndometriosis is associated with reduced health-related quality of life (HRQoL). Coping has been linked to HRQoL in this population but longitudinal research to establish the impact of coping on HRQoL over time is lacking. Additionally, limited research has examined coping and adaptation to endometriosis from an in-depth qualitative or mixed-methods perspective. Therefore, adopting a mixed-methods approach, the current research aimed to investigate how individuals experiencing endometriosis coped and adapted to their condition, and the extent to which coping predicted HRQoL over time. DesignA sequential, mixed-methods design incorporating a two-wave longitudinal survey and semi-structured interviews. Methods408 UK-based participants diagnosed with endometriosis completed the baseline survey, measuring demographics, clinical factors, and coping with 283 completing the follow-up survey assessing HRQoL a year later. Data was analysed through hierarchical regression analysis. Meanwhile, 30 semi-structured interviews were conducted and analysed using reflexive thematic analysis. Findings were integrated by considering points of convergence, divergence, and complementarity between the datasets. ResultsAnalysis of the quantitative data indicated an enduring impact of coping on HRQoL. Avoidant strategies and endometriosis-related information-seeking predicted reduced HRQoL, whilst trust in medical care exerted a protective function. Three themes were constructed from the qualitative data: disconnection from the body; balancing boundaries and self-care; and empowered adaptation. Integration of the datasets emphasised the significant impact of coping on HRQoL and wellbeing, revealing avoidance and positive adaptation as prominently employed coping strategies. ConclusionsThe results position coping as an important therapeutic target in endometriosis care, particularly through fostering empowerment and adaptation to support HRQoL.
Electrohydrodynamic flows inside a neutrally buoyant leaky dielectric drop

We present for the first time an experimental investigation of electrohydrodynamic (EHD) flows within a neutrally buoyant drop with initial radius of 2.25 mm. Utilizing particle image velocimetry (PIV) and high-speed shadowgraphy, we measure the internal circulation and reported velocity profiles in the bulk and at the interface of the drop. Two leaky dielectric liquids, Silicone and Castor oils, are employed as the drop and external phase, allowing for the analysis of two shape configurations: oblate and prolate. The strength of the applied uniform electric field, $E_o$, spans from 0.125 to 1.75 kV/cm, enabling the analysis covering the small-deformation limit, where the leaky dielectric model (LDM) is applicable. Drops with larger deformations, for which no analytical velocity field is available, are also investigated. Our measurements show a good agreement with the LDM theory for the small-deformation cases. The flows begin at the interface as a result of jump in the electric stresses, leading then to four counter-rotating vortices inside the drop. At permanent regime, the analytical solutions adequately predicts the radial and tangential velocity components both in the bulk and at the interface of the drop. However, a nuanced behavior is noticed for larger deformations, where the LDM theory underpredicts the internal circulation. Moreover, due to the increased deformation, a non-uniform azimuthal profile is observed for the velocity at the interface. Transient measurements of this velocity component enlighten the dynamic response of the EHD flows of the drop. Following the currently available analytical solutions, the dynamic response is governed by the time-scale of its deformation. We propose a critical value of electric capillary number of roughly 0.1 below which the LDM adequately describes the velocity field in both quasi steady-state and transitory regimes.
Galactic Diffuse Emission from Radio to Ultra-high-energy γ-Rays in Light of Up-to-date Cosmic-Ray Measurements

Cosmic rays (CRs) travel throughout the Galaxy, leaving traces from radio to ultra-high-energy γ-rays due to interactions with the interstellar gas, radiation field, and magnetic field. Therefore, it is necessary to utilize multiwavelength investigations on the Galactic diffuse emission to shed light on the physics of CR production and propagation. In this work, we present a spatially dependent propagation scenario, taking account of a local source contribution, while making allowances for an additional CR component freshly accelerated near their sources. In this picture, after reproducing the particle measurements at the solar system, we calculated the intensity and compared the spectral energy distribution to observations from Fermi-LAT and LHAASO-KM2A in the γ-ray band, and from WMAP and Planck among other radio surveys at lower energies. Multiband data considered in conjunction, the former comparison exhibits sufficiently good consistency in favor of our model, while the latter calls for improvement in data subtraction and processing. From this standpoint, there remains potential for advanced observations at energies from milli-eVs to MeVs toward the Galactic plane, in order to evaluate our model further and more comprehensively in the future.
The Brauer-Siegel ratio for prime cyclotomic fields

The Brauer-Siegel theorem concerns the size of the product of the class number and the regulator of a number field $K$. We derive bounds for this product in case $K$ is a prime cyclotomic field, distinguishing between whether there is a Siegel zero or not. In particular, we make a result of Tatuzawa (1953) more explicit. Our theoretical advancements are complemented by numerical illustrations that are consistent with our findings.
Higher-order fractional equations and related time-changed pseudo-processes

We study Cauchy problems of fractional differential equations in both space and time variables by expressing the solution in terms of ``stochastic composition"of the solutions to two simpler problems. These Cauchy sub-problems respectively concern the space and the time differential operator involved in the main equation. We provide some probabilistic and pseudo-probabilistic applications, where the solution can be interpreted as the pseudo-transition density of a time-changed pseudo-process. To extend our results to higher order time-fractional problems, we introduce pseudo-subordinators as well as its pseudo-inverse. Finally, we present our results in the case of more general differential operators and we interpret the results by means of a linear combination of pseudo-subordinators and its inverse.
Spectral selectors on lens spaces and applications to the geometry of the group of contactomorphisms

Using Givental's non-linear Maslov index we define a sequence of spectral selectors on the universal cover of the identity component of the contactomorphism group of any lens space. As applications, we prove that the standard Reeb flow is a geodesic for the discriminant and oscillation norms, and we define a stably unbounded conjugation invariant spectral pseudonorm.
Misalignment, Learning, and Ranking: Harnessing Users Limited Attention

In digital health and EdTech, recommendation systems face a significant challenge: users often choose impulsively, in ways that conflict with the platform's long-term payoffs. This misalignment makes it difficult to effectively learn to rank items, as it may hinder exploration of items with greater long-term payoffs. Our paper tackles this issue by utilizing users' limited attention spans. We propose a model where a platform presents items with unknown payoffs to the platform in a ranked list to $T$ users over time. Each user selects an item by first considering a prefix window of these ranked items and then picking the highest preferred item in that window (and the platform observes its payoff for this item). We study the design of online bandit algorithms that obtain vanishing regret against hindsight optimal benchmarks. We first consider adversarial window sizes and stochastic iid payoffs. We design an active-elimination-based algorithm that achieves an optimal instance-dependent regret bound of $O(\log(T))$, by showing matching regret upper and lower bounds. The key idea is using the combinatorial structure of the problem to either obtain a large payoff from each item or to explore by getting a sample from that item. This method systematically narrows down the item choices to enhance learning efficiency and payoff. Second, we consider adversarial payoffs and stochastic iid window sizes. We start from the full-information problem of finding the permutation that maximizes the expected payoff. By a novel combinatorial argument, we characterize the polytope of admissible item selection probabilities by a permutation and show it has a polynomial-size representation. Using this representation, we show how standard algorithms for adversarial online linear optimization in the space of admissible probabilities can be used to obtain a polynomial-time algorithm with $O(\sqrt{T})$ regret.
Near-Field Multiuser Beam-Training for Extremely Large-Scale MIMO Systems

Extremely large-scale multiple-input multiple-output (XL-MIMO) systems are capable of improving spectral efficiency by employing far more antennas than conventional massive MIMO at the base station (BS). However, beam training in multiuser XL-MIMO systems is challenging. To tackle these issues, we conceive a three-phase graph neural network (GNN)-based beam training scheme for multiuser XL-MIMO systems. In the first phase, only far-field wide beams have to be tested for each user and the GNN is utilized to map the beamforming gain information of the far-field wide beams to the optimal near-field beam for each user. In addition, the proposed GNN-based scheme can exploit the position-correlation between adjacent users for further improvement of the accuracy of beam training. In the second phase, a beam allocation scheme based on the probability vectors produced at the outputs of GNNs is proposed to address the above beam-direction conflicts between users. In the third phase, the hybrid TBF is designed for further reducing the inter-user interference. Our simulation results show that the proposed scheme improves the beam training performance of the benchmarks. Moreover, the performance of the proposed beam training scheme approaches that of an exhaustive search, despite requiring only about 7% of the pilot overhead.
Powerful Large-scale Inference in High Dimensional Mediation Analysis

In genome-wide epigenetic studies, exposures (e.g., Single Nucleotide Polymorphisms) affect outcomes (e.g., gene expression) through intermediate variables such as DNA methylation. Mediation analysis offers a way to study these intermediate variables and identify the presence or absence of causal mediation effects. Testing for mediation effects lead to a composite null hypothesis. Existing methods like the Sobel's test or the Max-P test are often underpowered because 1) statistical inference is often conducted based on distributions determined under a subset of the null and 2) they are not designed to shoulder the multiple testing burden. To tackle these issues, we introduce a technique called MLFDR (Mediation Analysis using Local False Discovery Rates) for high dimensional mediation analysis, which uses the local False Discovery Rates based on the coefficients of the structural equation model specifying the mediation relationship to construct a rejection region. We have shown theoretically as well as through simulation studies that in the high-dimensional setting, the new method of identifying the mediating variables controls the FDR asymptotically and performs better with respect to power than several existing methods such as DACT (Liu et al.)and JS-mixture (Dai et al).
Investigating the Histogram Loss in Regression

It is becoming increasingly common in regression to train neural networks that model the entire distribution even if only the mean is required for prediction. This additional modeling often comes with performance gain and the reasons behind the improvement are not fully known. This paper investigates a recent approach to regression, the Histogram Loss, which involves learning the conditional distribution of the target variable by minimizing the cross-entropy between a target distribution and a flexible histogram prediction. We design theoretical and empirical analyses to determine why and when this performance gain appears, and how different components of the loss contribute to it. Our results suggest that the benefits of learning distributions in this setup come from improvements in optimization rather than learning a better representation. We then demonstrate the viability of the Histogram Loss in common deep learning applications without a need for costly hyperparameter tuning.
Scene Prior Filtering for Depth Map Super-Resolution

Multi-modal fusion is vital to the success of super-resolution of depth maps. However, commonly used fusion strategies, such as addition and concatenation, fall short of effectively bridging the modal gap. As a result, guided image filtering methods have been introduced to mitigate this issue. Nevertheless, it is observed that their filter kernels usually encounter significant texture interference and edge inaccuracy. To tackle these two challenges, we introduce a Scene Prior Filtering network, SPFNet, which utilizes the priors surface normal and semantic map from large-scale models. Specifically, we design an All-in-one Prior Propagation that computes the similarity between multi-modal scene priors, i.e., RGB, normal, semantic, and depth, to reduce the texture interference. In addition, we present a One-to-one Prior Embedding that continuously embeds each single-modal prior into depth using Mutual Guided Filtering, further alleviating the texture interference while enhancing edges. Our SPFNet has been extensively evaluated on both real and synthetic datasets, achieving state-of-the-art performance.
Grounding from an AI and Cognitive Science Lens

Grounding is a challenging problem, requiring a formal definition and different levels of abstraction. This article explores grounding from both cognitive science and machine learning perspectives. It identifies the subtleties of grounding, its significance for collaborative agents, and similarities and differences in grounding approaches in both communities. The article examines the potential of neuro-symbolic approaches tailored for grounding tasks, showcasing how they can more comprehensively address grounding. Finally, we discuss areas for further exploration and development in grounding.