Miracle-dz/UniFAR-FTUs huggingface dataset:
Spectrum Inference in Cognitive Radio Networks: Algorithms and Applications

Spectrum inference, also known as spectrum prediction in the literature, is a promising technique of inferring the occupied/free state of radio spectrum from already known/measured spectrum occupancy statistics by effectively exploiting the inherent correlations among them. In the past few years, spectrum inference has gained increasing attention owing to its wide applications in cognitive radio networks (CRNs), ranging from adaptive spectrum sensing, and predictive spectrum mobility, to dynamic spectrum access and smart topology control, to name just a few. In this paper, we provide a comprehensive survey and tutorial on the recent advances in spectrum inference. Specifically, we first present the preliminaries of spectrum inference, including the sources of spectrum occupancy statistics, the models of spectrum usage, and characterize the predictability of spectrum state evolution. By introducing the taxonomy of spectrum inference from a time-frequency-space perspective, we offer an in-depth tutorial on the existing algorithms. Furthermore, we provide a comparative analysis of various spectrum inference algorithms and discuss the metrics of evaluating the efficiency of spectrum inference. We also portray the various potential applications of spectrum inference in CRNs and beyond, with an outlook to the fifth-generation mobile communications and next generation high frequency communications systems. Last but not least, we highlight the critical research challenges and open issues ahead.
Load the Edges You Need: A Generic I/O Optimization for Disk-based Graph Processing

Single-PC, disk-based processing of big graphs has recently gained much popularity. At the core of an efficient disk-based system is a well-designed partition structure that can minimize random disk accesses. All existing systems use static partitions that are created before processing starts. These partitions have static layouts and are loaded entirely into memory in every single iteration even though much of the edge data is not changed across many iterations, causing these unchanged edges to have zero new impact on the computation of vertex values. This work provides a general optimization that removes this I/O inefficiency by employing dynamic partitions whose layouts are dynamically adjustable. Our implementation of this optimization in GraphChi -- a representative out-of-core vertex-centric graph system -- yielded speedups of 1.5-2.8× on six large graphs. Our idea is generally applicable to other systems as well.
Dormant origins and fork protection mechanisms rescue sister forks arrested by transcription

Abstract The yeast RNA/DNA helicase Sen1, Senataxin in human, preserves the integrity of replication forks encountering transcription by removing RNA-DNA hybrids. Here we show that, in sen1 mutants, when a replication fork clashes head-on with transcription is arrested and, as a consequence, the progression of the sister fork moving in the opposite direction within the same replicon is also impaired. Therefore, sister forks remain coupled when one of the two forks is arrested by transcription, a fate different from that experienced by forks encountering Double Strand Breaks. We also show that dormant origins of replication are activated to ensure DNA synthesis in the proximity to the forks arrested by transcription. Dormant origin firing is not inhibited by the replication checkpoint, rather dormant origins are fired if they cannot be timely inactivated by passive replication. In sen1 mutants, the Mre11 and Mrc1–Ctf4 complexes protect the forks arrested by transcription from processing mediated by the Exo1 nuclease. Thus, a harmless head-on replication-transcription clash resolution requires the fine-tuning of origin firing and coordination among Sen1, Exo1, Mre11 and Mrc1–Ctf4 complexes.
Patient Engagement Is Related to Impairment Reduction During Digital Game-Based Therapy in Stroke.

OBJECTIVE Upper limb impairment in the chronic phase of stroke recovery is persistent, disabling, and difficult to treat. The objectives of this study were to determine whether therapeutic enjoyment is related to clinical improvement after upper limb rehabilitation and to assess the feasibility of a therapy gaming system. MATERIALS AND METHODS Ten chronic stroke survivors with persistent upper limb impairment were enrolled in the study. Upper limb impairment was evaluated by using the Fugl-Meyer Assessment of Upper Extremity Function (FMA-UE). The Physical Activity Enjoyment Scale (PACES) assessed the level of therapy enjoyment, and the System Usability Scale (SUS) measured the ease of operation of the game. Upper limb therapy involved 30 minutes of novel digital gaming therapy, three times per week, for 6 weeks. RESULTS The average improvement in the FMA-UE after the digital gaming therapy was 2.8 (±2.1) points. Participants scored the digital gaming system as having good usability (SUS: 72 ± 7.9), and the physical activity as enjoyable (PACES: 65.8 ± 10.6). There was a strong positive correlation between improvement in the FMA-UE score and the PACES (Spearman's Rho = 0.84; P < 0.002). CONCLUSION This pilot study demonstrates the feasibility and potential for improvements in upper limb motor function by using digital gaming in the chronic stroke patient population. The positive correlation found between therapy enjoyment and clinical gains highlights the importance of engagement in therapy to optimize outcomes in chronic stroke survivors.
Differential Role of Cathepsins S and B In Hepatic APC-Mediated NKT Cell Activation and Cytokine Secretion

Natural killer T (NKT) cells exhibit a specific tissue distribution, displaying the liver the highest NKT/conventional T cell ratio. Upon antigen stimulation, NKT cells secrete Th1 cytokines, including interferon γ (IFNγ), and Th2 cytokines, including IL-4 that recruit and activate other innate immune cells to exacerbate inflammatory responses in the liver. Cysteine cathepsins control hepatic inflammation by regulating κB-dependent gene expression. However, the contribution of cysteine cathepsins other than Cathepsin S to NKT cell activation has remained largely unexplored. Here we report that cysteine cathepsins, cathepsin B (CTSB) and cathepsin S (CTSS), regulate different aspects of NKT cell activation. Inhibition of CTSB or CTSS reduced hepatic NKT cell expansion in a mouse model after LPS challenge. By contrast, only CTSS inhibition reduced IFNγ and IL-4 secretion after in vivo α-GalCer administration. Accordingly, in vitro studies reveal that only CTSS was able to control α-GalCer-dependent loading in antigen-presenting cells (APCs), probably due to altered endolysosomal protein degradation. In summary, our study discloses the participation of cysteine cathepsins, CTSB and CTSS, in the activation of NKT cells in vivo and in vitro.
Prevention of cardiotoxicity among survivors of childhood cancer

This article is part of a joint Themed section with the British Journal of Pharmacology on Cardiotoxicity. The rest of the Themed section will appear in a future issue of BJP and will be available at http://onlinelibrary.wiley. com/journal/10.1111/(ISSN)1476‐5381
Racial Dynamics and Cultural Competence Training in Medical and Pharmacy Education

Using the Self-Assessment of Perceived Level of Cultural Competence (SAPLCC) questionnaire, frequencies, means, and ANOVAS were determined to create medical and pharmacy student profiles of cultural competence. Profiles were used to identify needs for training and underscore critical issues that should be given priority in the curriculum. Significant differences were found in several domains of cultural competence (knowledge, skills, attitudes, and abilities); they may be explained by differences in the implementation of a pilot curriculum, the racial composition of students in both programs, and other characteristics. However, in the awareness domain, the main differences found may be explained only by respondents’ attitudes and their personal experiences. Results confirm the importance of examining the racial dynamics factor and the need to address this sensitive topic early in the academic programs so students are prepared more fully to have sincere and meaningful encounters with their patients during the clinical years and as health care providers.
Impact of Nutritional Intervention on Length of Hospital Stay and Mortality among Hospitalized Patients with Malnutrition: A Clinical Randomized Controlled Trial

ABSTRACT Objective: The objective of this study was to evaluate the impact of a nutritional intervention on hospital stay and mortality among hospitalized patients with malnutrition. Methods: Hospitalized patients with a diagnosis of malnutrition were enrolled and randomly allocated to either an intervention or control group. Participants in the intervention group received an individualized nutrition plan according to energy and protein (1.0–1.5 g/kg) intake requirements as well as dietary advice based on face-to-face interviews with patients and their caregivers or family members. Individuals in the control group received standard nutritional management according to the Hospital Nutrition Department. Nutritional status and disease severity were assessed using nutritional risk screening. Length of hospital stay was defined by the number of days of hospitalization from hospital admission to medical discharge. Reference to another service or death were criteria for study withdrawal. To evaluate mortality, individuals were followed up for 6 months after hospital discharge. Hospital stay and mortality were the intention-to-treat analysis. Results: A total of 55 patients with an average age of 57.1 ± 20.7 years were included into intervention (n = 28) and control (n = 27) groups, respectively. At basal condition, nutritional status, measured by nutritional risk screening score, was similar between the study groups (4.1 ± 0.8 vs 4.2 ± 1.2, p = 0.6). The average hospital stay was lower in the intervention group compared to the control group (6.4 ± 3.0 vs 8.4 ± 4.0 days, p = 0.03). Finally, the mortality rate at 6 months of follow-up was similar in both groups (hazard ratio [HR] = 0.85; 95% confidence interval [CI], 0.17–4.21). Conclusions: Results of this study suggest that, in hospitalized patients with malnutrition, nutritional intervention and dietary advice decrease hospital stay but not mortality.
Separability and Sum-Rate Maximization in MIMO Interfering Networks

MIMO systems in the lower part of the millimetre-wave spectrum band (i.e., below 28 GHz) do not exhibit enough directivity and selectively, as their counterparts in higher bands of the spectrum (i.e., above 60 GHz), and thus still suffer from the detrimental effect of interference, on the system sum-rate. As such systems exhibit large numbers of antennas and short coherence times for the channel, traditional methods of distributed coordination are ill-suited, and the resulting communication overhead would offset the gains of coordination. In this work, we propose algorithms for tackling the sum-rate maximization problem, that are designed to address the above limitations. We derive a lower bound on the sum-rate, a so-called DLT bound (i.e., a difference of log and trace), shed light on its tightness, and highlight its decoupled nature at both the transmitters and receivers. Moreover, we derive the solution to each of the subproblems, that we dub non-homogeneous waterfilling (a variation on the MIMO waterfilling solution), and underline an inherent desirable feature: its ability to turn-off streams exhibiting low-SINR, and contribute to greatly speeding up the convergence of the proposed algorithm. We then show the convergence of the resulting algorithm, max-DLT, to a stationary point of the DLT bound. Finally, we rely on extensive simulations of various network configurations, to establish the fast-converging nature of our proposed schemes, and thus their suitability for addressing the short coherence interval, as well as the increased system dimensions, arising when managing interference in lower bands of the millimeter wave spectrum. Moreover, our results also suggest that interference management still brings about significant performance gains, especially in dense deployments.
Proteins P24 and P41 Function in the Regulation of Terminal-Organelle Development and Gliding Motility in Mycoplasma pneumoniae

ABSTRACT Mycoplasma pneumoniae is a major cause of bronchitis and atypical pneumonia in humans. This cell wall-less bacterium has a complex terminal organelle that functions in cytadherence and gliding motility. The gliding mechanism is unknown but is coordinated with terminal-organelle development during cell division. Disruption of M. pneumoniae open reading frame MPN311 results in loss of protein P41 and downstream gene product P24. P41 localizes to the base of the terminal organelle and is required to anchor the terminal organelle to the cell body, but during cell division, MPN311 insertion mutants also fail to properly regulate nascent terminal-organelle development spatially or gliding activity temporally. We measured gliding velocity and frequency and used fluorescent protein fusions and time-lapse imaging to assess the roles of P41 and P24 individually in terminal-organelle development and gliding function. P41 was necessary for normal gliding velocity and proper spatial positioning of new terminal organelles, while P24 was required for gliding frequency and new terminal-organelle formation at wild-type rates. However, P41 was essential for P24 function, and in the absence of P41, P24 exhibited a dynamic localization pattern. Finally, protein P28 requires P41 for stability, but analysis of a P28− mutant established that the MPN311 mutant phenotype was not a function of loss of P28.
The structure of FIV reverse transcriptase and its implications for non-nucleoside inhibitor resistance

Reverse transcriptase (RT) is the target for the majority of anti-HIV-1 drugs. As with all anti-AIDS treatments, continued success of RT inhibitors is persistently disrupted by the occurrence of resistance mutations. To explore latent resistance mechanisms potentially accessible to therapeutically challenged HIV-1 viruses, we examined RT from the related feline immunodeficiency virus (FIV). FIV closely parallels HIV-1 in its replication and pathogenicity, however, is resistant to all non-nucleoside inhibitors (NNRTI). The intrinsic resistance of FIV RT is particularly interesting since FIV harbors the Y181 and Y188 sensitivity residues absent in both HIV-2 and SIV. Unlike RT from HIV-2 or SIV, previous efforts have failed to make FIV RT susceptible to NNRTIs concluding that the structure or flexibility of the feline enzyme must be profoundly different. We report the first crystal structure of FIV RT and, being the first structure of an RT from a non-primate lentivirus, enrich the structural and species repertoires available for RT. The structure demonstrates that while the NNRTI binding pocket is conserved, minor subtleties at the entryway can render the FIV RT pocket more restricted and unfavorable for effective NNRTI binding. Measuring NNRTI binding affinity to FIV RT shows that the “closed” pocket configuration inhibits NNRTI binding. Mutating the loop residues rimming the entryway of FIV RT pocket allows for NNRTI binding, however, it does not confer sensitivity to these inhibitors. This reveals a further layer of resistance caused by inherent FIV RT variances that could have enhanced the dissociation of bound inhibitors, or, perhaps, modulated protein plasticity to overcome inhibitory effects of bound NNRTIs. The more “closed” conformation of FIV RT pocket can provide a template for the development of innovative drugs that could unlock the constrained pocket, and the resilient mutant version of the enzyme can offer a fresh model for the study of NNRTI-resistance mechanisms overlooked in HIV-1.
Microstructure Development in Bulk Niobium Following Severe Plastic Deformation and Annealing

Niobium (Nb) finds application in the fabrication of Nb3Sn superconducting wires for superconducting magnet applications, and SRF cavity applications. These applications need a favorable starting microstructure in precursor Nb to increase manufacturing reliability, reduce costs, and advance technology. The main problem with traditional Nb processing is that pure Nb is obtained by electron beam melting (EBM), which produces initial polycrystals tens to hundreds of centimeters in width/length, and can be comparable to the dimensions of the initial ingot. Breakdown of these initial cast microstructures, and to obtain consistent, fine grain microstructures in bulk product is a processing challenge. Generally, pure Nb, traditional thermo-mechanical processing methodologies such as: rolling, swaging, forging have been unable to effectively breakdown initial cast structures. An objective of the thesis is to develop thermo-mechanical processing strategies involving severe plastic deformation (SPD) by Equal Channel Angular Extrusion (ECAE) for bulk Nb. ECAE enables grain refinement without appreciable crossectional area changes to the workpiece, which is a hallmark of ECAE. The microstructure refinement process by ECAE is not well understood for the breakdown of large grain Nb. We have shown that ECAE produces continuous orientation splitting, and hence grain refinement even when processed under a strain path that is perceived to be structure conserving (route 2C). Initial bi-crystal results indicate that significant convergence in microstructure is possible within two ECAE passes for extremely large grain Nb. Processing strategies have been developed for effective control of grain size and texture in polycrystalline microstructures. The main results include effective grain
Recombinant cells in the lung increase with age via de novo recombination events and clonal expansion

Homologous recombination (HR) is a critical DNA repair pathway, which is usually error‐free, but can sometimes lead to cancer‐promoting mutations. Despite the importance of HR as a driver of mutations, the spontaneous frequency of such mutations has proven difficult to study. To gain insight to location, cell type, and subsequent proliferation of mutated cells, we used the Rosa26 Direct Repeat (RaDR) mice for in situ detection and quantification of recombinant cells in the lung. We developed a method for automated enumeration of recombinant cells in lung tissue using the Metafer 4 slide‐scanning platform. The mean spontaneous HR frequencies of the lung tissue in young and aged mice were 2 × 10−6 and 30 × 10−6, respectively, which is consistent with our previous reports that mutated cells accumulate with age. In addition, by using the capability of Metafer 4 to mark the position of fluorescent cells, we found that recombinant cells from the aged mice formed clusters in the lung tissue, likely due to clonal expansion of a single mutant cell. The recombinant cells primarily consisted of alveolar epithelial type II or club (previously known as Clara) cells, both of which have the potential to give rise to cancer. This approach to tissue image analysis reveals the location and cell types that have undergone HR. Being able to quantify mutant cells in situ within lung tissue opens doors to studies of exposure‐induced mutations and clonal expansion, giving rise to new opportunities for understanding how genetic and environmental factors cause tumorigenic mutations. Environ. Mol. Mutagen. 58:135–145, 2017. © 2017 Wiley Periodicals, Inc.
Asymmetric overlap and hysteresis current control of zero-current switched alternate arm converter

The alternate arm converter (AAC) is a multilevel converter of the same family as the modular multilevel converter (MMC). Contrary to the MMC, the AAC offers dc-fault tolerant capabilities but requires complex submodule (SM) capacitor voltage/energy regulation and circulating current control. Such control is also limited due to the small overlap period where both arms conduct and energy between the arms can be exchanged. This paper develops a double-band hysteresis-based circulating current control strategy by introducing an asymmetric overlap period control of the director switches (DSs). The proposed controller ensures zero-current switching operation of the DSs, and increases the flexibility of SM capacitor voltage regulation owing to the asymmetric overlap period. It improves the performance of current control and energy regulation for the AAC at both near sweet-spot and non sweet-spot operation without disturbing the output voltages and currents. The performance and effectiveness of the proposed controller are illustrated through simulations on MATLAB-Simulink and PLECS.
On meta‐ and mega‐analyses for gene–environment interactions

Gene‐by‐environment (G × E) interactions are important in explaining the missing heritability and understanding the causation of complex diseases, but a single, moderately sized study often has limited statistical power to detect such interactions. With the increasing need for integrating data and reporting results from multiple collaborative studies or sites, debate over choice between mega‐ versus meta‐analysis continues. In principle, data from different sites can be integrated at the individual level into a “mega” data set, which can be fit by a joint “mega‐analysis. ” Alternatively, analyses can be done at each site, and results across sites can be combined through a “meta‐analysis” procedure without integrating individual level data across sites. Although mega‐analysis has been advocated in several recent initiatives, meta‐analysis has the advantages of simplicity and feasibility, and has recently led to several important findings in identifying main genetic effects. In this paper, we conducted empirical and simulation studies, using data from a G × E study of lung cancer, to compare the mega‐ and meta‐analyses in four commonly used G × E analyses under the scenario that the number of studies is small and sample sizes of individual studies are relatively large. We compared the two data integration approaches in the context of fixed effect models and random effects models separately. Our investigations provide valuable insights in understanding the differences between mega‐ and meta‐analyses in practice of combining small number of studies in identifying G × E interactions.
Impact of anthropogenic pressure on the formation of population structure and genetic diversity of raccoon dog Nyctereutes procyonoides

Abstract The raccoon dog Nyctereutes procyonoides experienced an active introduction and acclimatization in the European part of Russia followed by its migration to and colonization in the neighboring countries. Eventually, it has spread rapidly into many European countries. N. procyonoides probably invaded Lithuania from the neighboring countries of Belarus and Latvia where the species was introduced. However, the data on genetic diversity and population structure of the raccoon dogs in the recently invaded territories are still scarce. The objectives of this study were to investigate genetic diversity of N. procyonoides in Lithuania after acclimatization, and to assess the impact of anthropogenic pressure on the formation of population structure. A total of 147 N. procyonoides individuals collected from different regions of Lithuania were genotyped using 17 microsatellite markers. The microsatellite analysis of raccoon dogs indicated high levels of genetic diversity within the population. The Bayesian clustering analysis in STRUCTURE identified 4 genetic clusters among sampled raccoon dogs that could not reveal a clear separation between subpopulations. The widespread distribution of raccoon dogs in Lithuania, high level of genetic variation observed within subpopulations, and low level of variation portioned among subpopulations suggest migration and gene flow among locations. The significant correlation between genetic and geographic distances indicated isolation that reflected the distance between locations. The fencing of highways and very intensive traffic could be barriers to gene flow between the western and eastern sampling areas of raccoon dogs.