Miracle-dz/UniFAR-FTUs huggingface dataset:
Potato NPH3/RPT2-Like Protein StNRL1, Targeted by a Phytophthora infestans RXLR Effector, Is a Susceptibility Factor1[OPEN]

An effector from the potato late blight pathogen targets a host protein that negatively regulates immunity. Plant pathogens deliver effectors to manipulate host processes. We know little about how fungal and oomycete effectors target host proteins to promote susceptibility, yet such knowledge is vital to understand crop disease. We show that either transient expression in Nicotiana benthamiana, or stable transgenic expression in potato (Solanum tuberosum), of the Phytophthora infestans RXLR effector Pi02860 enhances leaf colonization by the pathogen. Expression of Pi02860 also attenuates cell death triggered by the P. infestans microbe-associated molecular pattern INF1, indicating that the effector suppresses pattern-triggered immunity. However, the effector does not attenuate cell death triggered by Cf4/Avr4 coexpression, showing that it does not suppress all cell death activated by cell surface receptors. Pi02860 interacts in yeast two-hybrid assays with potato NPH3/RPT2-LIKE1 (NRL1), a predicted CULLIN3-associated ubiquitin E3 ligase. Interaction of Pi02860 in planta was confirmed by coimmunoprecipitation and bimolecular fluorescence complementation assays. Virus-induced gene silencing of NRL1 in N. benthamiana resulted in reduced P. infestans colonization and accelerated INF1-mediated cell death, indicating that this host protein acts as a negative regulator of immunity. Moreover, whereas NRL1 virus-induced gene silencing had no effect on the ability of the P. infestans effector Avr3a to suppress INF1-mediated cell death, such suppression by Pi02860 was significantly attenuated, indicating that this activity of Pi02860 is mediated by NRL1. Transient overexpression of NRL1 resulted in the suppression of INF1-mediated cell death and enhanced P. infestans leaf colonization, demonstrating that NRL1 acts as a susceptibility factor to promote late blight disease.
Phantoms for diffuse optical imaging based on totally absorbing objects, part 2: experimental implementation

Abstract. We present the experimental implementation and validation of a phantom for diffuse optical imaging based on totally absorbing objects for which, in the previous paper [J. Biomed. Opt. 18(6), 066014, (2013)], we have provided the basic theory. Totally absorbing objects have been manufactured as black polyvinyl chloride (PVC) cylinders and the phantom is a water dilution of intralipid-20% as the diffusive medium and India ink as the absorber, filled into a black scattering cell made of PVC. By means of time-domain measurements and of Monte Carlo simulations, we have shown the reliability, the accuracy, and the robustness of such a phantom in mimicking typical absorbing perturbations of diffuse optical imaging. In particular, we show that such a phantom can be used to generate any absorption perturbation by changing the volume and position of the totally absorbing inclusion.
Links between apoptosis, proliferation and the cell cycle

Abstract Many physiological processes, including proper tissue development and homeostasis, require a balance between apoptosis and cell proliferation. All somatic cells proliferate via a mitotic process determined by progression through the cell cycle. Apoptosis (programmed cell death) occurs in a wide variety of physiological settings, where its role is to remove harmful, damaged or unwanted cells. Apoptosis and cell proliferation are linked by cell-cycle regulators and apoptotic stimuli that affect both processes. This review covers recent developments in the field and examines new evidence of the interconnection between apoptosis and cell proliferation.
On-chip implementation of Extended Kalman Filter for adaptive battery states monitoring

This paper reports the development and implementation of an adaptive lithium-ion battery monitoring system. The monitoring algorithm is based on the nonlinear Dual Extended Kalman Filter (DEKF), which allows for simultaneous states and parameters estimation. The hardware platform consists of an ARM cortex-M0 processor with six embedded analogue-to-digital converters (ADCs) for data acquisition. Two definitions for online state-of-health (SOH) characterisation are presented; one energy-based and one power-based. Moreover, a method for online estimation of battery's capacity, which is used in SOH characterisation is proposed. Two definitions for state-of-power (SOP) are adopted. Despite the presence of large sensor noise and incorrect filter initialisation, the DEKF algorithm poses excellent SOC and SOP tracking capabilities during a dynamic discharge test. The SOH prediction results are also in good agreement with actual measurements.
Microstructural characterization of asphalt mixtures containing recycled asphalt materials

AbstractMost studies addressing the use of recycled asphalt materials in asphalt paving mixtures are based on experimental tests and performance evaluation. Investigating the effect of adding recycled materials to the microstructure of asphalt mixtures has received little consideration. For example, higher-order microstructural information can be used in place of simple volumetric information as input in micromechanical models that can more accurately predict the effective properties of asphalt mixtures. In this paper, the influence of adding three different recycled materials, reclaimed asphalt pavement (RAP), manufacturer waste scrap shingles (MWSS), and tear-off scrap shingles (TOSS), on the microstructural distribution of the aggregate phase is investigated using digitally processed images of asphalt mixtures and numerical evaluations of two- and three-point correlation functions. No significant variations are found among the gradation curves, and minimal differences were observed for two- and three-p.
VIP: Joint traffic engineering and caching in Named Data Networks

Emerging information-centric networking architectures seek to optimally utilize both bandwidth and storage for efficient content distribution. This highlights the need for joint design of traffic engineering and caching strategies. We present a systematic framework for joint dynamic interest request forwarding and dynamic cache placement and eviction, within the context of the Named Data Networking (NDN) architecture. The framework employs a virtual control plane which operates on the user demand rate for data objects in the network, and an actual plane which handles Interest Packets and Data Packets. We develop distributed algorithms within the virtual plane to achieve network load balancing through dynamic forwarding and caching, thereby maximizing the user demand rate that the NDN network can satisfy. Numerical experiments demonstrate the superior performance of the resulting algorithms for the actual plane in terms of low user delay.
An Enhanced Non-Coherent Pre-Filter Design for Tracking Error Estimation in GNSS Receivers

Tracking error estimation is of great importance in global navigation satellite system (GNSS) receivers. Any inaccurate estimation for tracking error will decrease the signal tracking ability of signal tracking loops and the accuracies of position fixing, velocity determination, and timing. Tracking error estimation can be done by traditional discriminator, or Kalman filter-based pre-filter. The pre-filter can be divided into two categories: coherent and non-coherent. This paper focuses on the performance improvements of non-coherent pre-filter. Firstly, the signal characteristics of coherent and non-coherent integration—which are the basis of tracking error estimation—are analyzed in detail. After that, the probability distribution of estimation noise of four-quadrant arctangent (ATAN2) discriminator is derived according to the mathematical model of coherent integration. Secondly, the statistical property of observation noise of non-coherent pre-filter is studied through Monte Carlo simulation to set the observation noise variance matrix correctly. Thirdly, a simple fault detection and exclusion (FDE) structure is introduced to the non-coherent pre-filter design, and thus its effective working range for carrier phase error estimation extends from (−0.25 cycle, 0.25 cycle) to (−0.5 cycle, 0.5 cycle). Finally, the estimation accuracies of discriminator, coherent pre-filter, and the enhanced non-coherent pre-filter are evaluated comprehensively through the carefully designed experiment scenario. The pre-filter outperforms traditional discriminator in estimation accuracy. In a highly dynamic scenario, the enhanced non-coherent pre-filter provides accuracy improvements of 41.6%, 46.4%, and 50.36% for carrier phase error, carrier frequency error, and code phase error estimation, respectively, when compared with coherent pre-filter. The enhanced non-coherent pre-filter outperforms the coherent pre-filter in code phase error estimation when carrier-to-noise density ratio is less than 28.8 dB-Hz, in carrier frequency error estimation when carrier-to-noise density ratio is less than 20 dB-Hz, and in carrier phase error estimation when carrier-to-noise density belongs to (15, 23) dB-Hz ∪ (26, 50) dB-Hz.
Gremlin inhibits UV-induced skin cell damages via activating VEGFR2-Nrf2 signaling

Ultra Violet (UV) radiation induces reactive oxygen species (ROS) production, DNA oxidation and single strand breaks (SSBs), which will eventually lead to skin cell damages or even skin cancer. Here, we tested the potential activity of gremlin, a novel vascular endothelial growth factor (VEGF) receptor 2 (VEGFR2) agonist, against UV-induced skin cell damages. We show that gremlin activated VEGFR2 and significantly inhibited UV-induced death and apoptosis of skin keratinocytes and fibroblasts. Pharmacological inhibition or shRNA-mediated knockdown of VEGFR2 almost abolished gremlin-mediated cytoprotection against UV in the skin cells. Further studies showed that gremlin activated VEGFR2 downstream NF-E2-related factor 2 (Nrf2) signaling, which appeared required for subsequent skin cell protection. Nrf2 shRNA knockdown or S40T dominant negative mutation largely inhibited gremlin-mediated skin cell protection against UV. At last, we show that gremlin dramatically inhibited UV-induced ROS production and DNA SSB formation in skin keratinocytes and fibroblasts. We conclude that gremlin protects skin cells from UV damages via activating VEGFR2-Nrf2 signaling. Gremlin could be further tested as a novel anti-UV skin protectant.
Cellular and Humoral Mechanisms of Immune Tolerance in Immediate-Type Allergy Induced by Specific Immunotherapy

The management of immediate-type allergy (ITA) is based on allergen avoidance, symptomatic pharmacological therapy and specific immunotherapy (SIT). Among these, SIT presents the only curative treatment. The efficacy of SIT in the treatment of IgE-mediated ITA has been proven in numerous clinical studies and is well established. This review discusses the relevance of immunoregulative humoral and cellular mechanisms leading to immune tolerance in ITA. Special focus is placed on the role of antibodies potentially interfering with the IgE-mediated immune reaction and regulatory T (Treg) cells including their immunosuppressive cytokines, which play a critical role in shifting the T helper 2 cell-driven allergic immune response towards allergen tolerance. Distinct subsets of constitutive and inducible Treg cells have been identified inhibiting the activation of allergen-specific effector T cells via cell contact- or cytokine-dependent suppression. Current research suggests that both inducible interleukin-10-producing CD4+ Treg cells and naturally occurring CD4+CD25+ Treg cells actively control allergic responses and that the disturbance of their function or number may contribute to the development or progression of allergy. Thus, the fine balance between allergen-specific T helper 2 and Treg cells constitutes a critical factor for the successful treatment of ITA by SIT.
Learning structured reactive navigation plans from executing MDP navigation policies

Autonomous robots, such as robot office couriers, need navigation routines that support flexible task execution and effective action planning. This paper describes \xfl, a system that learns structured symbolic navigation plans. Given a navigation task, \xfl\ learns to structure continuous navigation behavior and represents the learned structure as compact and transparent plans. The structured plans are obtained by starting with monolithical default plans that are optimized for average performance and adding subplans to improve the navigation performance for the given task. Compactness is achieved by incorporating only subplans that achieve significant performance gains. The resulting plans support action planning and opportunistic task execution. \xfl\ is implemented and extensively evaluated on an autonomous mobile robot.
Inhibition of PDE5A1 guanosine cyclic monophosphate (cGMP) hydrolysing activity by sildenafil analogues that inhibit cellular cGMP efflux

To determine the ability of 11 sildenafil analogues to discriminate between cyclic nucleotide phosphodiesterases (cnPDEs) and to characterise their inhibitory potencies (Ki values) of PDE5A1‐dependent guanosine cyclic monophosphate (cGMP) hydrolysis.
An Improved Proportional Quasi-Resonant Control of Wind Power GCI under Unbalanced Grid Conditions

with conventional control strategy under unbalanced grid conditions, power fluctuations will be generated in the input active power and reactive power of the wind power Grid Connected Inverter (GCI). In this paper, a novel sequence extraction method is proposed in the voltage components decomposition. Based on second order generalized integrator (SOGI) with PLL, a decomposition module with an ability of frequency adaptation is built up, called FA-SOGI. To avoid the sequence extraction of grid current, a novel proportional quasi-resonant controller implemented also by FA-SOGI within αβ stationary coordinate system is introduced to improve innerloop current control performance. With two objectives of active power fluctuation suppression and reactive power fluctuation suppression, the proposed strategy is verified by simulation and experiment. The results show that the sequence decomposition module is correct and the power fluctuations can be obviously suppressed and DC-bus voltage can be steady. Key-Words: proportional quasi-resonant (PQR), power fluctuations, unbalanced grid, grid connected inverter (GCI), second order generalized integrator with frequency adaptation (FA-SOGI)
Corneal Endofhelial Function and Structure Following Cryo-lnjury in the Rabbit

Wide-field specular microscopy, fluorophotometry, pachymetry, and scanning electron microscopy are used to characterize a reproducible, in vivo model of corneal endothelial injury and recovery in the rabbit. Following an 8-mm central cryo-injury, the cornea remains thickened for as long as 3 weeks. Mean endothelial permeability to fluorescein is above normal for 10 days following injury, but by 14 days postinjury the endothelial permeability to fluorescein is not statistically significantly different from preinjury control values, thus indicating that endothelial permeability probably returns to normal by approximately 2 weeks postinjury. Cell morphology, as determined by scanning electron microscopy, is also essentially normal by 2 weeks postinjury. Endothelial permeability appears to recover before stromal thickness normalizes, suggesting a lag in recovery of endothelial pump function. Invest Ophthalmol Vis Sci 25:1416-1425, 1984
Proneness to Boredom and Risk Behaviors During Adolescents’ Free Time

As a clinical condition, boredom is an emotional state, widespread among young people, characterized by unpleasant feelings, lack of motivation, and low physiological arousal in which the level of stimulation is perceived as unsatisfactorily low. Boredom is an important emotional state due to its spread among young people. Recent research has mainly studied the complex connection between boredom and leisure-time experiences, which may be involved in adolescents’ risk-taking behaviors. The current study aims to investigate boredom proneness, conceived as a personality trait, in adolescents’ free time, and its involvement in more extreme behaviors, such as binge drinking and addictive Internet use, which may represent ways to cope with the search for additional stimuli. Data from a large sample of Italian adolescents (n = 478, aged between 14 years and 19 years, M = 16.31, SD = 1.47) revealed significant differences between low-boredom and high-boredom subjects. Both girls and boys with high boredom proneness used technology more, engaged less in hobbies and activities such as sports, more frequently consumed strong drinks and binge drank, and were more at risk of Internet addiction than non-bored adolescents. These findings suggest a hypothetical risk profile linked to boredom proneness in adolescence. The results are discussed in light of the literature from a psychosocial and clinical perspective.
NO-Mediated [Ca2+]cyt Increases Depend on ADP-Ribosyl Cyclase Activity in Arabidopsis1[OPEN]

ADP-ribosyl cyclase activity in Arabidopsis is up-regulated by nitric oxide to increase the cellular concentration of cyclic ADP ribose and free Ca2+. Cyclic ADP ribose (cADPR) is a Ca2+-mobilizing intracellular second messenger synthesized from NAD by ADP-ribosyl cyclases (ADPR cyclases). In animals, cADPR targets the ryanodine receptor present in the sarcoplasmic/endoplasmic reticulum to promote Ca2+ release from intracellular stores to increase the concentration of cytosolic free Ca2+ in Arabidopsis (Arabidopsis thaliana), and cADPR has been proposed to play a central role in signal transduction pathways evoked by the drought and stress hormone, abscisic acid, and the circadian clock. Despite evidence for the action of cADPR in Arabidopsis, no predicted proteins with significant similarity to the known ADPR cyclases have been reported in any plant genome database, suggesting either that there is a unique route for cADPR synthesis or that a homolog of ADPR cyclase with low similarity might exist in plants. We sought to determine whether the low levels of ADPR cyclase activity reported in Arabidopsis are indicative of a bona fide activity that can be associated with the regulation of Ca2+ signaling. We adapted two different fluorescence-based assays to measure ADPR cyclase activity in Arabidopsis and found that this activity has the characteristics of a nucleotide cyclase that is activated by nitric oxide to increase cADPR and mobilize Ca2+.
Iterative Knowledge-Based Scoring Functions Derived from Rigid and Flexible Decoy Structures: Evaluation with the 2013 and 2014 CSAR Benchmarks

In this study, we developed two iterative knowledge-based scoring functions, ITScore_pdbbind(rigid) and ITScore_pdbbind(flex), using rigid decoy structures and flexible decoy structures, respectively, that were generated from the protein-ligand complexes in the refined set of PDBbind 2012. These two scoring functions were evaluated using the 2013 and 2014 CSAR benchmarks. The results were compared with the results of two other scoring functions, the Vina scoring function and ITScore, the scoring function that we previously developed from rigid decoy structures for a smaller set of protein-ligand complexes. A graph-based method was developed to evaluate the root-mean-square deviation between two conformations of the same ligand with different atom names and orders due to different file preparations, and the program is freely available. Our study showed that the two new scoring functions developed from the larger training set yielded significantly improved performance in binding mode predictions. For binding affinity predictions, all four scoring functions showed protein-dependent performance. We suggest the development of protein-family-dependent scoring functions for accurate binding affinity prediction.
Common variants at 12 q 24 are associated with drinking behavior in Han Chinese 1 – 3

Background: Alcohol consumption is heritable, but genetic susceptibility to drinking behavior has not been investigated widely in genome-wide association studies. Objective: We aimed to identify susceptibility loci for drinking behavior (drinkers compared with nondrinkers) in Han Chinese. Design: We performed 2 genome-wide association studies including 1420 drinkers and 3590 nondrinkers in discovery, followed by a de novo replication analysis comprising 4896 drinkers and 13,293 nondrinkers. DNA samples of the subjects were collected
Large‐scale analysis of frequency modulation in birdsong data bases

Birdsong often contains large amounts of rapid frequency modulation (FM). It is believed that the use or otherwise of FM is adaptive to the acoustic environment and also that there are specific social uses of FM such as trills in aggressive territorial encounters. Yet temporal fine detail of FM is often absent or obscured in standard audio signal analysis methods such as Fourier analysis or linear prediction. Hence, it is important to consider high‐resolution signal processing techniques for analysis of FM in bird vocalizations. If such methods can be applied at big data scales, this offers a further advantage as large data sets become available. We introduce methods from the signal processing literature which can go beyond spectrogram representations to analyse the fine modulations present in a signal at very short time‐scales. Focusing primarily on the genus Phylloscopus, we investigate which of a set of four analysis methods most strongly captures the species signal encoded in birdsong. We evaluate this through a feature selection technique and an automatic classification experiment. In order to find tools useful in practical analysis of large data bases, we also study the computational time taken by the methods, and their robustness to additive noise and MP3 compression. We find three methods which can robustly represent species‐correlated FM attributes and can be applied to large data sets, and that the simplest method tested also appears to perform the best. We find that features representing the extremes of FM encode species identity supplementary to that captured in frequency features, whereas bandwidth features do not encode additional information. FM analysis can extract information useful for bioacoustic studies, in addition to measures more commonly used to characterize vocalizations. Further, it can be applied efficiently across very large data sets and archives.
Challenges and opportunities for meningococcal vaccination in the developing world

ABSTRACT Meningococcal disease continues to be a life threatening infection with high morbidity and mortality even in appropriately treated patients. Meningococcal vaccination plays a major role in the control of the disease; however, implementing vaccination remains problematic in the developing world. The objective of this review is to identify the challenges facing the use of meningococcal vaccines in the developing world in order to discuss the opportunities and available solutions to improve immunization in these countries. Inadequate epidemiologic information necessary to implement vaccination and financial challenges predominate. Multiple measures are needed to achieve the successful implementation of meningococcal conjugate vaccination programs that protect against circulating serogroups in developing countries including enhanced surveillance systems, financial support and aid through grants, product development partnerships that are the end result of effective collaboration and communication between different interdependent stakeholders to develop affordable vaccines, and demonstration of the cost-effectiveness of new meningococcal vaccines.