Miracle-dz/UniFAR-FTUs huggingface dataset:
TRIM family proteins: roles in proteostasis and neurodegenerative diseases

Neurodegenerative diseases (NDs) are a diverse group of disorders characterized by the progressive degeneration of the structure and function of the central or peripheral nervous systems. One of the major features of NDs, such as Alzheimer's disease (AD), Parkinson's disease (PD) and Huntington's disease (HD), is the aggregation of specific misfolded proteins, which induces cellular dysfunction, neuronal death, loss of synaptic connections and eventually brain damage. By far, a great amount of evidence has suggested that TRIM family proteins play crucial roles in the turnover of normal regulatory and misfolded proteins. To maintain cellular protein quality control, cells rely on two major classes of proteostasis: molecular chaperones and the degradative systems, the latter includes the ubiquitin-proteasome system (UPS) and autophagy; and their dysfunction has been established to result in various physiological disorders including NDs. Emerging evidence has shown that TRIM proteins are key players in facilitating the clearance of misfolded protein aggregates associated with neurodegenerative disorders. Understanding the different pathways these TRIM proteins employ during episodes of neurodegenerative disorder represents a promising therapeutic target. In this review, we elucidated and summarized the diverse roles with underlying mechanisms of members of the TRIM family proteins in NDs.
Nuclear-specific gene expression in heterokaryons of the filamentous ascomycete Neurospora tetrasperma

Heterokaryosis is a system in which genetically distinct nuclei coexist within the same cytoplasm. While heterokaryosis dominates the life cycle of many fungal species, the transcriptomic changes associated with the transition from homokaryosis to heterokaryosis is not well understood. Here, we analyse gene expression profiles of homokaryons and heterokaryons from three phylogenetically and reproductively isolated lineages of the filamentous ascomycete Neurospora tetrasperma. We show that heterokaryons are transcriptionally distinct from homokaryons in the sexual stage of development, but not in the vegetative stage, suggesting that the phenotypic switch to fertility in heterokaryons is associated with major changes in gene expression. Heterokaryon expression is predominantly defined by additive effects of its two nuclear components. Furthermore, allele-specific expression analysis of heterokaryons with varying nuclear ratios show patterns of expression ratios strongly dependent on nuclear ratios in the vegetative stage. By contrast, in the sexual stage, strong deviations of expression ratios indicate a co-regulation of nuclear gene expression in all three lineages. Taken together, our results show two levels of expression control: additive effects suggest a nuclear level of expression, whereas co-regulation of gene expression indicate a heterokaryon level of control.
Application of machine learning in predicting blood flow and red cell distribution in capillary vessel networks

Capillary blood vessels in the body partake in the exchange of gas and nutrients with tissues. They are interconnected via multiple vascular junctions forming the microvascular network. Distributions of blood flow and red cells (RBCs) in such networks are spatially uneven and vary in time. Since they dictate the pathophysiology of tissues, their knowledge is important. Theoretical models used to obtain flow and RBC distribution in large networks have limitations as they treat each vessel as a one-dimensional segment and do not explicitly consider cell–cell and cell–vessel interactions. High-fidelity computational models that accurately model each individual RBC are computationally too expensive to predict haemodynamics in large vascular networks and over a long time. Here we investigate the applicability of machine learning (ML) techniques to predict blood flow and RBC distributions in physiologically realistic vascular networks. We acquire data from high-fidelity simulations of deformable RBC suspension flowing in the networks. With the flow and haematocrit specified at an inlet of vasculature, the ML models predict the time-averaged flow rate and RBC distributions in the entire network, time-dependent flow rate and haematocrit in each vessel and vascular bifurcation in isolation over a long time, and finally, simultaneous spatially and temporally evolving quantities through the vessel hierarchy in the networks.
Further aspects of Stochastic Cooperative Beamforming

The Stochastic Cooperative Beamforming (SCB) concept is analyzed from the point of view of maximum simplicity of implementation. The mismatches of the motes’ clocks after synchronization and their effect on the signal phase shift are analyzed. The dispersion of the clock errors with deviations of the order of a hundred nanoseconds introduce random shifts that allow the signal to be sent in several directions randomly. This multi-directional pointing multi-CB is achieved with a gain that is lower than the maximum expected for an optimal delay distribution. However, although with a low probability, high transmission gains of up to 50% of the maximum theoretical gain are achieved. It is observed that the gain conforms to a Rayleigh distribution function, and that the SCB transmission procedure allows sending to distant receivers in any direction. In SCB transmission a percentage of packets would be lost, and this would result in a higher number of transmissions, with the consequent energy consumption and decrease in effective transmission speed.
Analyzing Wireless Coverage for Industry 4.0 using a low-cost IoT System: A Case Study

Industry 4.0 is currently viewed as the future era in which a new generation of wireless communications will enable the widespread connectivity between machines, objects, and users, promising significant advancements in industrial automation. Industrial scenarios are highly dynamic environments that require the ability to adapt to changes in operating conditions. Reliable wireless communications can be challenging in industrial environments, where the communications signal is often blocked due to the presence of industrial machinery, with possible intermittent and/or unpredictable blockages. This paper analyzes the wireless coverage provided by a low-cost IoT system in an industrial environment. A measurement campaign in different points of an industrial warehouse were carried out, showing substantial differences in terms of coverage between a totally empty area and an area with machinery and workers. The results show that the IoT system is able to provide enough coverage around the whole area, even with mobility or blockages.
Low-cost clusters on big data - A systematic study

The growing gap between users and the Big Data analytics requires innovative tools that address the challenges faced by big data such as volume, variety, and velocity. Therefore, it becomes computationally inefficient to analyze this massive volume of data. Moreover, advancements in the field of Big Data applications and data science poses additional challenges, where High-Performance Computing (HPC) solution has become a key issue and has attracted attention in recent years. Because of the high costs to obtain a HPC, the researchers are looking for a solution that copes with the increasing demand on processing power due to the expanding amount of the data produced. Eventually, they have been trying to implement big data clusters based on low-cost and low-energy hardware. The goal of this paper is to identify how is possible to develop a big data cluster using hardware structures of low cost, exposing the studies found in literature. In order to fulfill this, a Systematic Literature Mapping (SLM) was realized, resulting in several relevant papers which are able to response three research questions. The SLM identified Single Board Computers (SBC) as hardware structure most used, being the Raspberry PI with major citations, and Apache Hadoop and Apache Spark as big data platforms used in these clusters. The validation of these clusters it was done with some popular algorithms, where the algorithms K-Means and Map-Reduce were the most quoted in the selected studies, this last based on its original approach, unlike the approach from Hadoop Map-Reduce.
Asymptotic expansions for laminar forced-convection heat and mass transfer

A method is presented in this article for deriving higher-order correction terms to the well-known asymptotic results for laminar forced-convection heat and mass transfer, and a formula is obtained for computing under fairly general conditions the first correction term to the asymptotic Nusselt number at large Péclet numbers for flows with small or moderate Reynolds numbers. This result is then applied to the problem of heat transfer from a solid, isothermal sphere in Stokes flow, to yield the asymptotic expression for the average Nusselt number, $\overline{Nu} = (Pe)^{1/3}[0\cdot 6245 + 0 \cdot 461(Pe)^{-1/3} + O(Re) + o(Pe^{-1/3})]$ for Pe→ ∞, Re→ 0, where $\overline{Nu}$ and Pe are based on the radius of the sphere.
VIRTUAL HERITAGE FOR THE DISSEMINATION OF THE BARATTI IN 3D PROJECT

Abstract. The paper describes the final step of the Baratti in 3D project, aimed at the dissemination of the important archaeological heritage of the Etruscan city of Populonia (Tuscany, Italy). The chain of “data metrical surveying – 2D and 3D representation – communication” has been applied on the “Princes's tombs” of the monumental necropolis of San Cerbone and its finds to provide a detailed description of their context, workmanship, morphological characteristics and materials to realize the virtual recreation. The preservation of the finds from the excavations in two different museums far from the archaeological area (the Museo Archeologico Nazionale di Firenze and the Museo Archeologico del Territorio di Populonia, in Piombino) makes the understanding of the original context very difficult for visitors. Thus the “Baratti in 3D Project” has been conceived in order to document the tombs, their finds and produce the “virtual match” showing in its entirety the environmental and architectural provenance and material ritual context and in order to display in innovative visual approach this archaeological heritage. To complement the interactive platform, as a physical fallout of this project has been realized “A museum in every sense”, a permanent exhibition in the Museo Archeologico del Territorio di Populonia.
Damage detection of simply supported reinforced concrete beam by S transform

Signal processing is the key component of vibration-based structural damage detection. The S transform is variable window of short time Fourier transform (STFT) or an extension of wavelet transform (WT). The goal of using S transform is to extract subtle changes in the vibration signals in order to detect and quantify the damage in the structure. This paper presents the concentrated load is applied to the simply supported reinforced concrete beam and adopting the stepwise loading method, the vibration signals of each loading and unloading state is obtained by using the hammer impact. Then the vibration data of the reinforced concrete beam pre-damage and post-damage is analysed by S transform. Experimental result shows the potential ability of S transform in identifying peak energy changes and multiple reflections with different loading force state.
Huygens’ Metadevices for Parametric Waves

Huygens' metasurfaces have demonstrated almost arbitrary control over the shape of a scattered beam, however, its spatial profile is typically fixed at fabrication time. Dynamic reconfiguration of this beam profile with tunable elements remains challenging, due to the need to maintain the Huygens' condition across the tuning range. In this work, we experimentally demonstrate that a time-varying metadevice which performs frequency conversion can steer transmitted or reflected beams in an almost arbitrary manner, with fully dynamic control. Our time-varying Huygens' metadevice is made of both electric and magnetic meta-atoms with independently controlled modulation, and the phase of this modulation is imprinted on the scattered parametric waves, controlling their shapes and directions. We develop a theory which shows how the scattering directionality, phase and conversion efficiency of sidebands can be manipulated almost arbitrarily. We demonstrate novel effects including all-angle beam steering and frequency-multiplexed functionalities at microwave frequencies around 4 GHz, using varactor diodes as tunable elements. We believe that the concept can be extended to other frequency bands, enabling metasurfaces with arbitrary phase pattern that can be dynamically tuned over the complete 2\pi range.
Error propagation in traffic modeling: solutions for the mesoscopic LWR model

ABSTRACT Traffic flow models are a valuable tool to design road networks, assess the effectiveness of traffic controls and provide real-time information for traffic management centers and users. When integrating data, they become the cornerstone for traffic monitoring and forecasting. However, these models are based on a simplified representation of the traffic, subject to uncertainties and with parameters likely to be refined. The paper proposes the formulation of a new traffic flow modeling framework that accounts for error propagation. It is based on the mesoscopic approach of the Lighthill-Whitham-Richards model, with traffic variables represented as Gaussian-Mixture probability density functions. Sensitivity for the error propagation model is analyzed regarding: the network topology, traffic flow parameters and parameterization of the error model. Applications for traffic indicators associated to their errors/uncertainties are illustrated. Novel indicators and decision-support tools can be built for advanced traffic modeling solutions based on the proposed model.
The reliability and validity of gait analysis system using 3D markerless pose estimation algorithms

Quantifying kinematic gait for elderly people is a key factor for consideration in evaluating their overall health. However, gait analysis is often performed in the laboratory using optical sensors combined with reflective markers, which may delay the detection of health problems. This study aims to develop a 3D markerless pose estimation system using OpenPose and 3DPoseNet algorithms. Moreover, 30 participants performed a walking task. Sample entropy was adopted to study dynamic signal irregularity degree for gait parameters. Paired-sample t-test and intra-class correlation coefficients were used to assess validity and reliability. Furthermore, the agreement between the data obtained by markerless and marker-based measurements was assessed by Bland–Altman analysis. ICC (C, 1) indicated the test–retest reliability within systems was in almost complete agreement. There were no significant differences between the sample entropy of knee angle and joint angles of the sagittal plane by the comparisons of joint angle results extracted from different systems (p > 0.05). ICC (A, 1) indicated the validity was substantial. This is supported by the Bland–Altman plot of the joint angles at maximum flexion. Optical motion capture and single-camera sensors were collected simultaneously, making it feasible to capture stride-to-stride variability. In addition, the sample entropy of angles was close to the ground_truth in the sagittal plane, indicating that our video analysis could be used as a quantitative assessment of gait, making outdoor applications feasible.
Intergenerational relationship quality, sense of loneliness, and attitude toward later life among aging Chinese adults in Hong Kong

A positive attitude toward later life is crucial for wellbeing among older adults. Maintaining a healthy relationship with adult children can help reduce older parents’ sense of loneliness and nurture a positive life attitude. This study aimed to investigate the associations between multidimensional intergenerational relationship quality and attitudes toward later life among aging Chinese adults in Hong Kong and examine the mediating effects of a sense of loneliness. Representative survey data were collected from 801 participants (aged 50 years and over) with at least one adult child. Multiple linear regression was employed to investigate the associations between overall intergenerational relationship quality with a sense of loneliness as well as the attitude toward later life. To examine the mediating effects of a sense of loneliness, causal mediational analyses were performed. Results demonstrated that overall intergenerational relationship quality was positively associated with aging parents’ attitude toward later life, and this relationship could be partially mediated by a sense of loneliness. Among the four subdomains of intergenerational relationship quality, the influences of structural-associational solidarity and intergenerational conflict on attitude toward later life were almost fully mediated by a sense of loneliness, whereas the influences of consensual-normative solidarity and affectual closeness were partially mediated. These findings contributed to an improved understanding of the relationship between intergenerational relationship quality, sense of loneliness, and attitude toward later life, and could inform future policies and service programs that promote aging adults’ social integration and positive aging.
Targeting regulation of stem cell exosomes: Exploring novel strategies for aseptic loosening of joint prosthesis

Periprosthetic osteolysis is a major long-term complication of total joint replacement. A series of biological reactions caused by the interaction of wear particles at the prosthesis bone interface and surrounding bone tissue cells after artificial joint replacement are vital reasons for aseptic loosening. Disorder of bone metabolism and aseptic inflammation induced by wear particles are involved in the occurrence and development of aseptic loosening of the prosthesis. Promoting osteogenesis and angiogenesis and mediating osteoclasts and inflammation may be beneficial in preventing the aseptic loosening of the prosthesis. Current research about the prevention and treatment of aseptic loosening of the prosthesis focuses on drug, gene, and stem cell therapy and has not yet achieved satisfactory clinical efficacy or has not been used in clinical practice. Exosomes are a kind of typical extracellular vehicle. In recent years, stem cell exosomes (Exos) have been widely used to regulate bone metabolism, block inflammation, and have broad application prospects in tissue repair and cell therapy.
The divergence between T cell and innate lymphoid cell fates controlled by E and Id proteins

T cells develop in the thymus from lymphoid primed multipotent progenitors or common lymphoid progenitors into αβ and γδ subsets. The basic helix-loop-helix transcription factors, E proteins, play pivotal roles at multiple stages from T cell commitment to maturation. Inhibitors of E proteins, Id2 and Id3, also regulate T cell development while promoting ILC differentiation. Recent findings suggest that the thymus can also produce innate lymphoid cells (ILCs). In this review, we present current findings that suggest the balance between E and Id proteins is likely to be critical for controlling the bifurcation of T cell and ILC fates at early stages of T cell development.
β-elemene Isopropanolamine Derivative LXX-8250 Induces Apoptosis Through Impairing Autophagic Flux via PFKFB4 Repression in Melanoma Cells

Melanoma is a highly aggressive skin cancer and accounts for most of the skin cancer-related deaths. The efficacy of current therapies for melanoma remains to be improved. The isopropanolamine derivative of β-elemene LXX-8250 was reported to present better water solubility and stronger toxicity to tumor cells than β-elemene. Herein, LXX-8250 treatment showed 4-5-fold more toxicity to melanoma cells than the well-known anti-melanoma drug, Dacarbazine. LXX-8250 treatment induced apoptosis remarkably, which was caused by the impairment of autophagic flux. To clarify the molecular mechanism, microarray analyses were conducted, and PFKFB4 expression was found to be suppressed by LXX-8250 treatment. The cells overexpressed with PFKFB4 exhibited resistance to apoptosis induction and autophagic flux inhibition by LXX-8250 treatment. Moreover, LXX-8250 treatment suppressed glycolysis, to which the cells overexpressed with PFKFB4 were tolerant. LXX-8250 treatment inhibited the growth of melanoma xenografts and suppressed PFKFB4 expression and glycolysis in vivo. Taken together, LXX-8250 treatment induced apoptosis through inhibiting autophagic flux and glycolysis in melanoma cells, which was mediated by suppression of PFKFB4 expression. The study provides a novel strategy to melanoma treatment.
Structural insight into ASH1L PHD finger recognizing methylated histone H3K4 and promoting cell growth in prostate cancer

ASH1L is a member of the Trithorax-group protein and acts as a histone methyltransferase for gene transcription activation. It is known that ASH1L modulates H3K4me3 and H3K36me2/3 at its gene targets, but its specific mechanism of histone recognition is insufficiently understood. In this study, we found that the ASH1L plant homeodomain (PHD) finger interacts with mono-, di-, and trimethylated states of H3K4 peptides with comparable affinities, indicating that ASH1L PHD non-selectively binds to all three methylation states of H3K4. We solved nuclear magnetic resonance structures picturing the ASH1L PHD finger binding to the dimethylated H3K4 peptide and found that a narrow binding groove and residue composition in the methylated-lysine binding pocket restricts the necessary interaction with the dimethyl-ammonium moiety of K4. In addition, we found that the ASH1L protein is overexpressed in castrate-resistant prostate cancer (PCa) PC3 and DU145 cells in comparison to PCa LNCaP cells. The knockdown of ASH1L modulated gene expression and cellular pathways involved in apoptosis and cell cycle regulation and consequently induced cell cycle arrest, cell apoptosis, and reduced colony-forming abilities in PC3 and DU145 cells. The overexpression of the C-terminal core of ASH1L but not the PHD deletion mutant increased the overall H3K36me2 level but had no effect on the H3K4me2/3 level. Overall, our study identifies the ASH1L PHD finger as the first native reader that non-selectively recognizes the three methylation states of H3K4. Additionally, ASH1L is required for the deregulation of cell cycle and survival in PCas.