Miracle-dz/UniFAR-FTUs huggingface dataset:
Two-dimensional photonic MXene nanomedicine

Abstract Two-dimensional (2D) transition metal carbides and nitrides (MXenes) with fascinating physicochemical properties, ultrathin lamellar structure, high specific surface area, and excellent biocompatibility have been extensively explored in biomedical applications over the past decade. Photonic MXene nanomedicine and materdicine, as one of the most burgeoning emerging treatment modalities, are of great research interest owing to their photon utilization ability and high therapeutic efficiency. This review aims to summarize and discuss the very-recent advances in engineering 2D MXenes for photonic theranostic applications. We initially concentrate on the synthesis methods, surface modification, and functionalization with respect to MXenes. Furthermore, the photonic biological applications including photonic antibacteria, photonic bioimaging, photonic therapy, and photonic theranostics are highlighted in detail with the selected paradigms. Finally, the current challenges and future directions for 2D MXene biomaterials in regard to their photonic biomedicines are discussed in depth, aiming to drive the speed of their practical applications in clinic.
Foundational Development of an Occupation Ontology

The classification of occupations, key to policy development regarding the economy, education, research, organizational infrastructure, as well as health and safety analysis, has received considerable attention and development over the last half century. However, international and national standardized taxonomies, while very well executed, are dissimilar, dated and could benefit from a new organization employing ontological methods. This paper builds the case for the development of an Occupation Ontology, showing an approach that employs successful methods of the Open Biological and Biomedical (OBO) Foundry. The importance of occupations and their characterization is described, and four popular taxonomies available in English are presented and compared. We selected and transformed the US Bureau of Labor Statistics Standard Occupational Classification into a prototype OBO compliant ontology, designated OccO, to illustrate the presentation of occupational information as an ontology. OccO is then compared to the representation of occupations in the fastest growing semantic web knowledge base, Wikidata, where occupations are organized neither in compliance with any standard taxonomy nor with a consistent upper level ontological framework. We then present the benefits of developing an ontology-driven occupational framework. This development is at the alpha stage, with the hope that the concept of an occupation ontology will gain the support of research organizations who could cooperate to formulate and demonstrate the utility of a well-designed and widely used ontology for occupations.
A New Framework for Data Streams Classification

Mining data streams has recently become an important and challenging task for a wide range of services, including credit card fraud detection, sensor networks and web applications. In these applications data do not typically take the form of persistent relations, but tend to arrive in multiple, continuous, rapid and timevarying data streams. Hence, conventional knowledge discovery tools cannot manage this overwhelming volume of streaming data. The nature of data streams requires the use of algorithms, which involve at most one pass over the data, and try to keep track of time-evolving features, also known as concept drifting. In the literature, several techniques for the efficient computation of compact space representations of massive data have been proposed to improve model reliability, including methods to cope with concept drifting. The challenges of these methods are that they are allowed to use small space and time to process a single item, while they must provide an accurate representation of some relevant characteristics of data streams. Based on the above considerations, our approach attempts to solve the problem of data streams classification, presenting a framework based on two main components. First, an on-line component is used to compute and manage some statistical aggregates information about data streams. The latter are viewed as divided into chunks, and an aggregate representation, called snapshot, is defined and built out of each stream chunk. All the statistics produced are stored in a summary structure called frame, using different levels of granularity. Second, a mining component is employed to extract a classifier from all the snapshots produced. In order to maximize the number of elements from which the model is extracted, this component employs snapshots with different levels of granularity, while only most recent data are used in the presence of concept drifting. We argue that the proposed approach avoids the continuous update of the same mining model, i.e. new models are continually extracted from scratch, while the system constantly updates summarized data structures. Furthermore, this approach employs a selective ensemble classifier combining the predictive power of the models extracted with different and increasingly larger data chunks representing different portions of data streams. Since both the performance and the accuracy of the whole system are based on single model evaluation, it is necessary to check the set of actually activatable models to classify new instances,
Determination of the Hyperfine Structure of N2D+

We present new high spectral resolution observations of the N2D+ J = 2 → 1 and J = 3 → 2 as well as N2H+ J = 3 → 2 lines toward dense molecular cores. The hyperfine structure of the N2H+ and N2D+ transitions is clearly resolved in these sources, in excellent agreement with quantum mechanical calculations. Optical depths are determined from the observed spectra, leading to D/H values on the order of 10%-30% for the N2D+/N2H+ system. There are a large number of hyperfine components, and in addition to providing satellites, they contribute to the broadening and asymmetric shapes of the N2H+ and N2D+ line profiles. It is therefore important to take into account the detailed hyperfine structure of the transitions when deducing astrophysical parameters from observed data.
Dynamics and Formation of the Near-resonant K2-24 System: Insights from Transit-timing Variations and Radial Velocities

While planets between the size of Uranus and Saturn are absent within the solar system, the star K2-24 hosts two such planets, K2-24b and c, with radii equal to 5.4 and 7.5 , respectively. The two planets have orbital periods of 20.9 days and 42.4 days, residing only 1% outside the nominal 2:1 mean-motion resonance. In this work, we present results from a coordinated observing campaign to measure planet masses and eccentricities that combines radial velocity measurements from Keck/HIRES and transit-timing measurements from K2 and Spitzer. K2-24b and c have low, but nonzero, eccentricities of . The low observed eccentricities provide clues to the formation and dynamical evolution of K2-24b and K2-24c, suggesting that they could be the result of stochastic gravitational interactions with a turbulent protoplanetary disk, among other mechanisms. K2-24b and c are and , respectively; K2-24c is 20% less massive than K2-24b, despite being 40% larger. Their large sizes and low masses imply large envelope fractions, which we estimate at % and %. In particular, K2-24c’s large envelope presents an intriguing challenge to the standard model of core-nucleated accretion that predicts the onset of runaway accretion when ≈ 50%.
Mechanical Vibration: Analysis, Uncertainties, and Control

Introduction and Background. Some Mathematics. Single Degree of Freedom Vibration: An Introduction to Discrete Models. Single Degree of Freedom Vibration: Discrete Models with Damping. Single Degree of Freedom Vibration: Advanced Topics. Single Degree of Freedom Vibration: Probabilistic Forces. Vibration Control. Variational Principles. Multi Degree of Freedom Vibration. Multi Degree of Freedom Vibration: Advanced Topics. Continuous Models for Vibration. Continuous Models for Vibration: Advanced Models. Nonlinear Oscillation. Index.
Long-range DNA end resection supports homologous recombination by checkpoint activation rather than extensive homology generation

Homologous recombination (HR), the error-free mechanism for double-strand break (DSB) repair, relies on DNA end resection by nucleolytic degradation of the 5′-terminated ends. However, the role of long-range resection mediated by Exo1 and/or Sgs1-Dna2 in HR is not fully understood. Here, we show that Exo1 and Sgs1 are dispensable for recombination between closely-linked repeats but are required for interchromosomal repeat recombination in Saccharomyces cerevisiae. This requirement for long-range resection is coupled to DNA damage checkpoint activation and the need for checkpoint proteins. Furthermore, artificial activation of the checkpoint partially restores interchromosomal recombination to exo1Δ sgs1Δ cells. However, cell cycle delay is insufficient to rescue the interchromosomal recombination defect of exo1Δ sgs1Δ cells, suggesting an additional role for the checkpoint. Given that the checkpoint is necessary for DNA damage-induced chromosome mobility, we propose that the importance of the checkpoint, and therefore long-range resection, in interchromosomal recombination is due to a need to increase chromosome mobility to facilitate pairing of distant sites. The need for long-range resection is circumvented when the DSB and its repair template are in close proximity.
Occurrence and classification of T-shaped interactions between nucleobases in RNA structures

Understanding the frequency and structural context of discrete noncovalent interactions between nucleotides is of pivotal significance in establishing the rules that govern RNA structure and dynamics. Although T-shaped contacts (i.e., perpendicular stacking contacts) between aromatic amino acids and nucleobases at the nucleic acid–protein interface have recently garnered attention, the analogous contacts within the nucleic acid structures have not been discussed. In this work, we have developed an automated method for identifying and unambiguously classifying T-shaped interactions between nucleobases. Using this method, we identified a total of 3262 instances of T-shaped (perpendicular stacking) contacts between two nucleobases in an array of RNA structures from an up-to-date dataset of high-resolution crystal structures deposited in the Protein Databank. These analyses add to the understanding of the physicochemical forces that are responsible for structure and dynamics of RNA.
High-resolution methylome analysis in the clonal Populus nigra cv. ‘Italica’ reveals environmentally sensitive hotspots and drought-responsive TE superfamilies

DNA methylation is environment-sensitive and can mediate plant stress responses. In long-lived trees, changing environments might cumulatively shape the methylome landscape over their lifetime. However, because high-resolution methylome studies usually focus on single environments, it remains unclear to what extent the methylation responses are generic or stress-specific, and how this relates to their long-term stability. Here, we studied the methylome plasticity of a single poplar genotype, Populus nigra cv. ‘Italica’. Adult poplar trees with diverse environmental histories were clonally propagated, and the ramets exposed to experimental cold, heat, drought, herbivory, rust infection and salicylic acid treatments. Then, we identified and compared stress-induced vs. naturally occurring DNA methylation changes using whole genome bisulfite sequencing data. Methylation changes mainly targeted transposable elements and when occurring in CG/CHG contexts, the same regions were often affected by multiple stresses, indicating a generic response. Drought triggered a unique CHH hypermethylation response in transposable elements, affecting entire superfamilies and often occurring near drought-responsive genes. Stress-induced methylation variation in CG/CHG contexts showed striking overlap with methylation differences observed between trees from distinct geographical locations. Altogether, our results indicate that generic methylome stress responses can persist as epialleles in nature while some environments trigger more transient but large and specific responses, with possible functional consequences.
Approximate Relaxation Function for Concrete

Presented is an approximate algebraic formula for calculating the relaxation function for aging concrete. The formula is general; it applies to any form of the creep function. Compared to the previously used effective modulus method, the formula reduces the error from up to 37% to within 2% relative to the exact solution according to the superpositon principle. Calculation of long-time relaxation does not require knowledge of the elastic modulus and of the creep function for load duration below one day. The formula enables direct calculation of the age-adjusted effective modulus from the creep function, and thus it allows dispensing with the table of the aging coefficient. This is particularly useful in case of a more sophisticated creep model which reflects the fact that the creep functions for different humidities and sizes have different (nonproportional) shapes.
Nanoscale Dynamics of Streptococcal Adhesion to AGE-Modified Collagen

The adhesion of initial colonizers such as Streptococcus mutans to collagen is critical for dentinal and root caries progression. One of the most described pathological and aging-associated changes in collagen—including dentinal collagen—is the generation of advanced glycation end-products (AGEs) such as methylglyoxal (MGO)–derived AGEs. Despite previous reports suggesting that AGEs alter bacterial adhesion to collagen, the biophysics driving oral streptococcal attachment to MGO-modified collagen remains largely understudied. Thus, the aim of this work was to unravel the dynamics of the initial adhesion of S. mutans to type I collagen in the presence and absence of MGO-derived AGEs by employing bacterial cell force spectroscopy with atomic force microscopy (AFM). Type I collagen gels were treated with 10 mM MGO to induce AGE formation, which was characterized with microscopy and enzyme-linked immunosorbent assay. Subsequently, AFM cantilevers were functionalized with living S. mutans UA 159 or Streptococcus sanguinis SK 36 cells and probed against collagen surfaces to obtain force curves displaying bacterial attachment in real time, from which the adhesion force, number of events, Poisson analysis, and contour and rupture lengths for each individual detachment event were computed. Furthermore, in silico computer simulation docking studies between the relevant S. mutans UA 159 collagen-binding protein SpaP and collagen were computed, in the presence and absence of MGO. Overall, results showed that MGO modification increased both the number and adhesion force of single-unbinding events between S. mutans and collagen, without altering the contour or rupture lengths. Both experimental and in silico simulations suggest that this effect is due to increased specific and nonspecific forces and interactions between S. mutans UA 159 and MGO-modified collagen substrates. In summary, these results suggest that collagen alterations due to aging and glycation may play a role in early bacterial adherence to oral tissues, associated with conditions such as aging or chronic hyperglycemia, among others.
Progressive decline in the levels of six miRNAs from parents to children in autism

The growing burden of a gradual increase in births of children with autism has placed it at the center of the concerns of major laboratories. We have previously detected a decrease in the levels of six miRNAs (miR-19a-3p, miR-361-5p, miR-3613-3p, miR-150-5p, miR-126-3p, and miR-499a-5p) in parents and their children inherited at a lower level. Here, we suggest that down-regulation of each of these six miRNAs inherited from parents contributes to the development of children with autism. We compare their levels of distribution in each family between the autistic child and siblings. We find that the distribution of levels of these miRNAs in siblings (undiagnosed as autism) is not always higher than in autistic children, but it is at varying levels. These data support a model in which autistic behavior relies on low levels of the six miRNAs expressed in children potentially associated with autistic syndrome (ASD). The intimate link between miRNAs levels and behavioral characteristics suggests possibilities for understanding the basic circuitry involved in autism and thus advancing partial knowledge of brain functions. An early diagnosis of autism helps provide children an environment conducive to their development. Graphical abstract
Short-range interactions between fibrocytes and CD8+ T cells in COPD bronchial inflammatory response

Bronchi of chronic obstructive pulmonary disease (COPD) are the site of extensive cell infiltration, allowing persistent contacts between resident cells and immune cells. Tissue fibrocytes interaction with CD8+ T cells and its consequences were investigated using a combination of in situ, in vitro experiments and mathematical modeling. We show that fibrocytes and CD8+ T cells are found in vicinity in distal airways and that potential interactions are more frequent in tissues from COPD patients compared to those of control subjects. Increased proximity and clusterization between CD8+ T cells and fibrocytes are associated with altered lung function. Tissular CD8+ T cells from COPD patients promote fibrocyte chemotaxis via the CXCL8-CXCR1/2 axis. Live imaging shows that CD8+ T cells establish short-term interactions with fibrocytes, that trigger CD8+ T cell proliferation in a CD54– and CD86-dependent manner, pro-inflammatory cytokines production, CD8+ T cell cytotoxic activity against bronchial epithelial cells and fibrocyte immunomodulatory properties. We defined a computational model describing these intercellular interactions and calibrated the parameters based on our experimental measurements. We show the model’s ability to reproduce histological ex vivo characteristics, and observe an important contribution of fibrocyte-mediated CD8+ T cell proliferation in COPD development. Using the model to test therapeutic scenarios, we predict a recovery time of several years, and the failure of targeting chemotaxis or interacting processes. Altogether, our study reveals that local interactions between fibrocytes and CD8+ T cells could jeopardize the balance between protective immunity and chronic inflammation in bronchi of COPD patients.
Charge dynamics in transparent single-walled carbon nanotube films from optical transmission measurements

We report the transmission over a wide frequency range (far infrared–visible) of pristine and hole-doped, free-standing carbon nanotube films at temperatures between 50 K and 300 K. Optical constants are estimated by Kramers-Kronig analysis of transmittance. We see evidence in the far infrared for a gap below 10 meV. Hole doping causes a shift of spectral weight from the first interband transition into the far infrared. Temperature dependence in both the doped and undoped samples is restricted to the far-infrared region. PACS numbers: 73.63Fg, 78.67. Ch, 81.07De
LRBA balances antigen presentation and T-cell responses by facilitating autophagy through the binding to PIK3R4 and FYCO1

Patients with lipopolysaccharide responsive beige-like anchor protein (LRBA) deficiency have an exacerbated T-cell activation and a defective B-cell response. Previously, we suggested reduced autophagy as the biological cause of the aberrant humoral response; however, the exact molecular mechanism of LRBA in autophagy and its impact on T-cell responses remain unknown. We screened for LRBA-interacting proteins, finding that LRBA interacts with the phosphoinositide 3-kinase regulatory subunit 4 (PIK3R4) and with the FYVE And Coiled-Coil Domain Autophagy Adaptor 1 (FYCO1). Interestingly, both proteins play essential roles at different stages of autophagy. Specifically, PIK3R4 facilitates the production of phosphatidylinositol-3 phosphate (PI(3)P) required for the recruitment of PI(3)P-binding adaptor proteins allowing autophagosome formation and autophagosome-lysosome fusion, whereas FYCO1 allows autophagosome movement. LRBA-KO cells showed an impaired production of PI(3)P, a delayed autophagosome-lysosome fusion, an accumulation of abnormal autophagosomes and an atypical lysosomal positioning. These observations explain the decreased cargo material degradation and the overall defective autophagy flux in LRBA-KO cells. Abnormal autophagosomes in LRBA-KO cells are associated with prolonged antigen presentation to T cells, resulting in a higher production of proinflammatory cytokines, as autophagy is a major intracellular degradation system for major histocompatibility class II complex (MHCII) loading. Taken together, our data suggest that i) LRBA forms different protein complexes serving at different stages of autophagy, and ii) loss of LRBA impacts the targeting of cytosolic antigens for autophagy degradation, enhancing antigen presentation. The latter could contribute to the exacerbated T-cell immune dysregulation observed in LRBA-deficient patients. Key points LRBA is required for the different steps of autophagy from autophagosome formation to cargo degradation through the interaction with PIK3R4 and FYCO1. Loss of LRBA enhances T-cell driven proinflammatory response as a consequence of increased antigen presentation.
Multigenerational effect of heat stress on the Drosophila melanogaster sperm proteome

The notion that genes are the sole units of heredity and that a barrier exists between soma and germline has been a major hurdle in elucidating the heritability of traits that were observed to follow a non-Mendelian inheritance pattern. It was only after the conception of epigenetics by Conrad Waddington that the effect of parental environment on subsequent generations via non-DNA sequence-based mechanisms, such as DNA methylation, chromatin modifications, non-coding RNAs and proteins, could be established, now referred to as multigenerational epigenetic inheritance. Despite growing evidence, the male gamete-derived epigenetic factors that mediate the transmission of such phenotypes are seldom explored, particularly in the model organism Drosophila melanogaster. Using the heat stress-induced multigenerational epigenetic inheritance paradigm in a widely used position-effect variegation line of Drosophila, named white-mottled, we have dissected the effect of heat stress on the sperm proteome in the current study. We demonstrate that multiple successive generations of heat stress at the early embryonic stage results in a significant downregulation of proteins associated with a diverse set of functions, such as translation, chromatin organization, microtubule-based processes, and generation of metabolites and energy, in the sperms. Based on our findings, we propose chromatin-based epigenetic mechanisms, a well-established mechanism for multigenerational effects, as a plausible way of transmitting heat stress memory via the male germline in this case. Moreover, we show that despite these heat stress-induced changes, the life-history traits, such as reproductive fitness and stress tolerance of the subsequent generations, are unaffected, probing the evolutionary relevance of multigenerational epigenetic effects.