Miracle-dz/UniFAR-FTUs huggingface dataset:
The ND10 Component Promyelocytic Leukemia Protein Acts as an E3 Ligase for SUMOylation of the Major Immediate Early Protein IE1 of Human Cytomegalovirus

ABSTRACT Previous studies identified the nuclear domain 10 (ND10) components promyelocytic leukemia protein (PML), hDaxx, and Sp100 as factors of an intrinsic immune response against human cytomegalovirus (HCMV). This antiviral function of ND10, however, is antagonized by viral effector proteins like IE1p72, which induces dispersal of ND10. Furthermore, we have shown that both major immediate early proteins of HCMV, IE1p72 and IE2p86, transiently colocalize with ND10 subnuclear structures and undergo modification by the covalent attachment of SUMO. Since recent reports indicate that PML acts as a SUMO E3 ligase, we asked whether the SUMOylation of IE1p72 and IE2p86 is regulated by PML. To address this, PML-depleted fibroblasts, as well as cells overexpressing individual PML isoforms, were infected with HCMV. Western blot experiments revealed a clear correlation between the degree of IE1p72 SUMO conjugation and the abundance of PML. On the other hand, the SUMOylation of IE2p86 was not affected by PML. By performing in vitro SUMOylation assays, we were able to provide direct evidence that IE1p72 is a substrate for PML-mediated SUMOylation. Interestingly, disruption of the RING finger domain of PML, which is proposed to confer SUMO E3 ligase activity, abolished PML-induced SUMOylation of IE1p72. In contrast, IE1p72 was still efficiently SUMO modified by a SUMOylation-defective PML mutant, indicating that intact ND10 bodies are not necessary for this effect. Thus, this is the first report that the E3 ligase PML is capable of stimulating the SUMOylation of a viral protein which is supposed to serve as a cellular mechanism to compromise specific functions of IE1p72. IMPORTANCE The major immediate early proteins of human cytomegalovirus, termed IE1p72 and IE2p86, have previously been shown to undergo posttranslational modification by covalent coupling to SUMO moieties at specific lysine residues. However, the enzymatic activities that are responsible for this modification have not been identified. Here, we demonstrate that the PML protein, which mediates an intrinsic immune response against HCMV, specifically serves as an E3 ligase for SUMO modification of IE1p72. Since SUMO modification of IE1p72 has previously been shown to interfere with STAT factor binding, thus compromising the interferon-antagonistic function of this viral effector protein, our finding highlights an additional mechanism through which PML is able to restrict viral infections.
Evaluation of GMI and PMI diffeomorphic‐based demons algorithms for aligning PET and CT Images

Fusion of anatomic information in computed tomography (CT) and functional information in F18‐FDG positron emission tomography (PET) is crucial for accurate differentiation of tumor from benign masses, designing radiotherapy treatment plan and staging of cancer. Although current PET and CT images can be acquired from combined F18‐FDG PET/CT scanner, the two acquisitions are scanned separately and take a long time, which may induce potential positional errors in global and local caused by respiratory motion or organ peristalsis. So registration (alignment) of whole‐body PET and CT images is a prerequisite for their meaningful fusion. The purpose of this study was to assess the performance of two multimodal registration algorithms for aligning PET and CT images. The proposed gradient of mutual information (GMI)‐based demons algorithm, which incorporated the GMI between two images as an external force to facilitate the alignment, was compared with the point‐wise mutual information (PMI) diffeomorphic‐based demons algorithm whose external force was modified by replacing the image intensity difference in diffeomorphic demons algorithm with the PMI to make it appropriate for multimodal image registration. Eight patients with esophageal cancer(s) were enrolled in this IRB‐approved study. Whole‐body PET and CT images were acquired from a combined F18‐FDG PET/CT scanner for each patient. The modified Hausdorff distance (dMH) was used to evaluate the registration accuracy of the two algorithms. Of all patients, the mean values and standard deviations (SDs) of dMH were 6.65 (± 1.90) voxels and 6.01 (± 1.90) after the GMI‐based demons and the PMI diffeomorphic‐based demons registration algorithms respectively. Preliminary results on oncological patients showed that the respiratory motion and organ peristalsis in PET/CT esophageal images could not be neglected, although a combined F18‐FDG PET/CT scanner was used for image acquisition. The PMI diffeomorphic‐based demons algorithm was more accurate than the GMI‐based demons algorithm in registering PET/CT esophageal images. PACS numbers: 87.57. nj, 87.57. Q‐, 87.57. uk
The Stability of Third Generation Solar Cells

In the lasts fifty years the tremendous evolution of modern technologies has gradually unbalanced the equilibrium between the production and the consumption of energy. Traditional energy resources, like coal, oil and natural gases, are no longer sufficient to satisfy the demand of energy without spoiling earth environment. Renewable energies have attracted a lot of attention because they are potential solution to this important problem. In particular photovoltaic solar cells are considered the most promising technology for a low-cost and environmentally friendly energy production. However, in order to exploit these technologies in real world applications, the complete physics of solar cells must be understood. Stability is one of the fundamental aspects and is related to the processes that regulate the energy conversion, both in long-term degradation as well in electrical stability. In this work the stability of two emerging categories of solar cells is thoroughly addressed: organic photovoltaics and organometal-halide perovskite. In organic photovoltaics understanding the stability and degradation mechanisms of photoactive blends is required to achieve long device lifetimes. Recent reports on organic solar cells presenting power conversion efficiencies exceeding 10% have made the need to improve the device stability compelling. In general, instability is caused by the combination of light and atmospheric agents, with major roles of oxygen and water. The detrimental effects are electron trapping and photo-oxidation that break polymer conjugation and bleach the absorption. However, so far, no effective solution preserving low cost and flexibility has been achieved. The reason is that the degradation mechanisms are still unknown. Solution-processable hybrid perovskite semiconductors have risen to the forefront of photovoltaics research, offering the potential to combine low-cost fabrication with high-power conversion efficiency (PCE). Originally used in dye-sensitized solar cell technology, the first architectures saw the use of TiO2, both in the form of mesoporous and compact films, as an electron extracting layer. Further development has been driven by empirical optimization strategies and testing of a variety of different architectures. These devices are divided in two categories: standard and inverted. Standard uses TiO2 (compact or mesoporous) to collect the electrons and a small molecule or polymer organic semiconductor for the holes, with record efficiencies of 21% and an open circuit voltage above 1 V; it must be noted that these devices exhibit a kind of electrical instability manifested as slow transient and hysteretic effects that severely affect the final efficiency. The inverted configuration is more similar to organic photovoltaics, exploiting similar materials for the extraction of photogenerated charges. These devices report lower efficiencies respect to standard device but a higher electrical stability which is manifest with stabilized efficiencies and apparently hysteresis-free behaviour.
Intensity- and Duration-Adaptive Functional Electrical Stimulation Using Fuzzy Logic Control and a Linear Model for Dropfoot Correction

Functional electrical stimulation (FES) is important in gait rehabilitation for patients with dropfoot. Since there are time-varying velocities during FES-assisted walking, it is difficult to achieve a good movement performance during walking. To account for the time-varying walking velocities, seven poststroke subjects were recruited and fuzzy logic control and a linear model were applied in FES-assisted walking to enable intensity- and duration-adaptive stimulation (IDAS) for poststroke subjects with dropfoot. In this study, the performance of IDAS was evaluated using kinematic data, and was compared with the performance under no stimulation (NS), FES-assisted walking triggered by heel-off stimulation (HOS), and speed-adaptive stimulation. A larger maximum ankle dorsiflexion angle in the IDAS condition than those in other conditions was observed. The ankle plantar flexion angle in the IDAS condition was similar to that of normal walking. Improvement in the maximum ankle dorsiflexion and plantar flexion angles in the IDAS condition could be attributed to having the appropriate stimulation intensity and duration. In summary, the intensity- and duration-adaptive controller can attain better movement performance and may have great potential in future clinical applications.
Øpass: Zero-storage Password Management Based on Password Reminders

A plethora of Internet services and applications require user authentication. Although many alternatives have been proposed, and despite the significant advancement in attackers' capabilities to perform password cracking, the most attractive authentication technology today, is still text-based passwords. The last years, there is a rapid increase in the number of web services a user accesses in their everyday life. Most of these services (e.g., online shops, OSNs, chat clients, etc.) require their very own password, thus increasing the burden of password management on the user side. In this paper, we propose Øpass, a novel system that combines ideas from existing authentication methods, to offer a user-friendly mechanism to securely maintain accounts. Øpass works as a password manager, but it requires zero storage for the passwords: no password will ever get stored either in the user's device, or in a third-party database. We implement Øpass as an extension for the popular Google Chrome browser, and we evaluate it by using the popular business-oriented social networking service LinkedIn. Early results from our performance tests show that Øpass, using a proactive strategy, can achieve more than 2 orders of magnitude better performance than the current state-of-the-art authentication mechanism.
Ubiquitination-dependent control of sexual differentiation in fission yeast

In fission yeast, meiosis-specific transcripts are selectively eliminated during vegetative growth by the combined action of the YTH-family RNA-binding protein Mmi1 and the nuclear exosome. Upon nutritional starvation, the master regulator of meiosis Mei2 inactivates Mmi1, thereby allowing expression of the meiotic program. Here, we show that the E3 ubiquitin ligase subunit Not4/Mot2 of the evolutionarily conserved Ccr4-Not complex, which associates with Mmi1, promotes suppression of meiotic transcripts expression in mitotic cells. Our analyses suggest that Mot2 directs ubiquitination of Mei2 to preserve the activity of Mmi1 during vegetative growth. Importantly, Mot2 is not involved in the constitutive pathway of Mei2 turnover, but rather plays a regulatory role to limit its accumulation or inhibit its function. We propose that Mmi1 recruits the Ccr4-Not complex to counteract its own inhibitor Mei2, thereby locking the system in a stable state that ensures the repression of the meiotic program by Mmi1.
Characterizing Interconnections and Linguistic Patterns in Twitter

Social media is considered a democratic space in which people connect and interact with each other regardless of their gender, race, or any other demographic aspect. Despite numerous efforts that explore demographic aspects in social media, it is still unclear whether social media perpetuates old inequalities from the offline world. In this dissertation, we attempt to identify gender and race of Twitter users located in the United States using advanced image processing algorithms from Face++. We investigate how different demographic groups connect with each other and differentiate them regarding linguistic styles and also their interests. We quantify to what extent one group follows and interacts with each other and the extent to which these connections and interactions reflect in inequalities in Twitter. We also extract linguistic features from six categories (affective attributes, cognitive attributes, lexical density and awareness, temporal references, social and personal concerns, and interpersonal focus) in order to identify the similarities and the differences in the messages they share in Twitter. Furthermore, we extract the absolute ranking difference of top phrases between demographic groups. As a dimension of diversity, we use the topics of interest that we retrieve from each user. Our analysis shows that users identified as white and male tend to attain higher positions, in terms of the number of followers and number of times in another user's lists, in Twitter. There are clear differences in the way of writing across different demographic groups in both gender and race domains as well as in the topic of interest. We hope our effort can stimulate the development of new theories of demographic information in the online space. Finally, we developed a Web-based system that leverages the demographic aspects of users to provide transparency to the Twitter trending topics system.
Enhanced thermal conductivity of rheologically percolated carbon nanofiber reinforced polypropylene composites

Three different types of carbon nanofibers (CNF) were incorporated in the same polypropylene (PP) matrix by twin-screw extrusion. The rheological and thermal properties were investigated. The rheological characterization of CNFs/PP composites as function of their volume fraction shows different microstructures: percolated and non-percolated behaviors of their CNF's networks. In this work, the laser flash technique is employed in the experimental determination of the thermal diffusivity and conductivity of composites at room temperature. The ultimate aim is to correlate microstructure described by rheological analysis with final thermal properties. The results show that thermal diffusivity and conductivity are clearly higher for rheologically percolated composites suggesting that above certain critical content of nanofibers thermal transport is mainly controlled by percolated structures caused by interconnected CNFs' networks. Finally, thermal conductivity results are described by means of percolation theory from which an intrinsic thermal conductivity for the CNFs' network of approximately 6.5 W/m K, i.e. close to three times lower than some values reported in literature for SWCNTs' networks, was calculated. Copyright © 2015 John Wiley & Sons, Ltd.
Ifit2 Is a Restriction Factor in Rabies Virus Pathogenicity

ABSTRACT Understanding the interactions between rabies virus (RABV) and individual host cell proteins is critical for the development of targeted therapies. Here we report that interferon-induced protein with tetratricopeptide repeats 2 (Ifit2), an interferon-stimulated gene (ISG) with possible RNA-binding capacity, is an important restriction factor for rabies virus. When Ifit2 was depleted, RABV grew more quickly in mouse neuroblastoma cells in vitro. This effect was replicated in vivo, where Ifit2 knockout mice displayed a dramatically more severe disease phenotype than wild-type mice after intranasal inoculation of RABV. This increase in pathogenicity correlated to an increase in RABV mRNA and live viral load in the brain, as well as to an accelerated spread to brain regions normally affected by this RABV model. These results suggest that Ifit2 exerts its antiviral effect mainly at the level of viral replication, as opposed to functioning as a mechanism that restricts viral entry/egress or transports RABV particles through axons. IMPORTANCE Rabies is a fatal zoonotic disease with a nearly 100% case fatality rate. Although there are effective vaccines for rabies, this disease still takes the lives of about 50,000 people each year. Victims tend to be children living in regions without comprehensive medical infrastructure who present to health care workers too late for postexposure prophylaxis. The protein discussed in our report, Ifit2, is found to be an important restriction factor for rabies virus, acting directly or indirectly against viral replication. A more nuanced understanding of this interaction may reveal a step of a pathway or site at which the system could be exploited for the development of a targeted therapy.
Multi-excitonic complexes in single InGaN quantum dots

Cathodoluminescence spectra employing a shadow mask technique of InGaN layers grown by metalorganic chemical vapor deposition on Si(111) substrates are reported. Sharp lines originating from InGaN quantum dots are observed. Temperature dependent measurements reveal thermally induced carrier redistribution between the quantum dots. Spectral diffusion is observed and was used as a tool to correlate up to three lines that originate from the same quantum dot. Variation of excitation density leads to identification of exciton and biexciton. Binding and anti-binding complexes are discovered.
Distributed Demand-Aware Channel-Slot Selection for Multi-UAV Networks: A Game-Theoretic Learning Approach

Over the past decades, the unmanned aerial vehicle (UAV) has received unprecedented surge of scientific and military interest worldwide. This paper investigates the problem of opportunistic spectrum access for multi-UAV networks from a game-theoretic perspective. Due to the topology of the multi-UAV networks, the interference may be classified into two parts, i.e., the intra-cluster and the inter-cluster interference. Moreover, since the UAVs in the network have different tasks, the communication demand of each UAV should be taken into account. First, we formulate the demand-aware joint channel-slot selection problem as a weighted interference mitigation game, and then, design the utility function considering features of multi-UAV network, e.g., some rewards due to the channel and slots selection. We prove that the formulated game is an exact potential game with at least one pure-strategy Nash equilibrium. Next, we apply the distributed log-linear algorithm to achieve the desired optimization and overcome the constraint of dynamic communication demand of each UAV. To speed up the convergence, we also propose a low-complexity and realistic channel and slot initialization scheme for UAVs. Finally, the simulation results validate the effectiveness of the formulated game.
The influence of conduction band location on the leakage current level of a glass insulator

This paper discusses the influence of conduction band location on the leakage current level of a glass insulator. A sodium chloride solution has been used as a pollutant forming the conduction band. The solution concentration has been changed by using five variations of salt mass which was dissolved into 250 ml of water. The salt mass variation is proportional to its related mole equivalent of sodium chloride solution concentration. The experiment results indicate that the position of the conduction band on the insulator surface affects the surface resistivity. The largest resistivity occurs when the conduction band is located near the ground side, whereas the smallest one occurs when the band is in the middle between the ground side and the HV side. The value of the surface resistance for the band located on the HV side is between that near the ground side and that in the middle location. The level of the leakage current on the glass surface rises with the increase in the applied AC voltage. The leakage current increase is relatively linear up to around 20 kV, beyond which the leakage current starts to decrease. This decrease is related to the formation of dry bands which will increase the overall resistance of the glass insulator surface. The largest power and annual energy losses being caused by the leakage current are found when the conduction band is located in the middle part of the surface, whereas the smallest ones are obtained when the conduction band is located on the ground side. The power and annual energy losses increase even greater when the applied voltage is higher.
CONTROLLING CELL MORPHOLOGY ON ION BEAM TEXTURED POLYMERIC SURFACES

Objectives: Nano and micro sized textures on surfaces are generally useful biomaterials. Although the importance of roughness degree has been reported for cell morphology, texture morphology can be more determining for cell adhesion and proliferation. Biodegradable polymers are extensively used as scaffolds as well as implant materials in the human body. The aim of this study was to investigate the effect of ion beam bombardment on cell morphology. Methods: Gold and carbon ion implantation was made on biodegradable polymers polyglycolic acid, polycaprolactone and polylactic-co-glycolic-acid. Roughness data were obtained from atomic force microscopy. After surface modification with ion beam, B35 neural cells were evaluated on surfaces for cell compatibility. Morphology and cell surface interaction were analyzed with scanning electron microscopy. Results: We observed improved cell adhesion after ion beam surface modification. Cell adhesion was greater on gold implanted surfaces compared to the carbon implanted. Neural cells attached to lamellar wrinkles, spread by taking the shape of the pattern and exhibited high aspect ratios and axon extension. In contrast, cells that attached on the untreated surfaces remained rounded with low spreading. Conclusion: The findings of this study are important for development of ion beam modified cell cultures and scaffold systems to understand texture-based cell adhesion mechanisms. Keywords: cell culture; ion implantation; polylactic-co-glycolic acid; surface treatment; topography; wettability
Next Generation High-Rate Telemetry

Recent investigations show that high-rate telemetry systems, based on the CCSDS 131.2-B-1 standard and employed in Earth observation missions, do not fully exploit the available capacity. Thus, we propose and discuss possible ways to improve the data return of these systems that can be considered for a revision of the current standard. Some of them are represented by a revision and/or an extension of the currently adopted modulation and coding formats. The remaining techniques are related to an enhancement of the transceiver architecture. Different bandwidth allocation strategies are also considered. The benefits of the proposed techniques are assessed by means of computer simulations with reference to a realistic scenario where a real non-linear amplifier, real filters, and real impairments are considered.
The Mayhem Cyber Reasoning System

Mayhem is one of the first generation of autonomous computer security bots that finds and fixes vulnerabilities without any human intervention. Mayhem won the DARPA Cyber Grand Challenge (CGC) contest and $2,000,000 in August 2016 against six other finalists. The contest was the result of a two-year DARPA program, but the R&D necessary to compete stands on the shoulders of decades of basic academic and industry scientific research in program analysis, verification, and self-healing systems. The Mayhem system alone was developed over a decade of research in academia, which was spun out to a company called ForAllSecure. Mayhem is now being commercialized by ForAllSecure to autonomously check and protect the world’s software from exploitable bugs. In this article, we look back and give our story in creating Mayhem, and also look forward to a vision where autonomous security bots like Mayhem will radically improve the security of computer systems.