Miracle-dz/UniFAR-FTUs huggingface dataset:
Appearances Can Be Deceptive: Revealing a Hidden Viral Infection with Deep Sequencing in a Plant Quarantine Context

Comprehensive inventories of plant viral diversity are essential for effective quarantine and sanitation efforts. The safety of regulated plant material exchanges presently relies heavily on techniques such as PCR or nucleic acid hybridisation, which are only suited to the detection and characterisation of specific, well characterised pathogens. Here, we demonstrate the utility of sequence-independent next generation sequencing (NGS) of both virus-derived small interfering RNAs (siRNAs) and virion-associated nucleic acids (VANA) for the detailed identification and characterisation of viruses infecting two quarantined sugarcane plants. Both plants originated from Egypt and were known to be infected with Sugarcane streak Egypt Virus (SSEV; Genus Mastrevirus, Family Geminiviridae), but were revealed by the NGS approaches to also be infected by a second highly divergent mastrevirus, here named Sugarcane white streak Virus (SWSV). This novel virus had escaped detection by all routine quarantine detection assays and was found to also be present in sugarcane plants originating from Sudan. Complete SWSV genomes were cloned and sequenced from six plants and all were found to share >91% genome-wide identity. With the exception of two SWSV variants, which potentially express unusually large RepA proteins, the SWSV isolates display genome characteristics very typical to those of all other previously described mastreviruses. An analysis of virus-derived siRNAs for SWSV and SSEV showed them to be strongly influenced by secondary structures within both genomic single stranded DNA and mRNA transcripts. In addition, the distribution of siRNA size frequencies indicates that these mastreviruses are likely subject to both transcriptional and post-transcriptional gene silencing. Our study stresses the potential advantages of NGS-based virus metagenomic screening in a plant quarantine setting and indicates that such techniques could dramatically reduce the numbers of non-intercepted virus pathogens passing through plant quarantine stations.
Nonlinear Motion Control of a Hydraulic Press Based on an Extended Disturbance Observer

This paper focuses on high-performance motion control of the electro-hydraulic system of hydraulic presses. A detailed mathematical model of the system was constructed. An electro-hydraulic system of hydraulic presses is a kind of nonlinear system with parametric uncertainties, uncertain nonlinearities, and external disturbances. To attenuate the above effects, a nonlinear robust motion controller based on an extended disturbance observer was developed. The outer position tracking loop was designed with a sliding mode control to compensate for disturbance estimation error, while the inner pressure control loop using the backstepping method can realize accurate output force control. The stability of the overall closed-loop system based on the Lyapunov approach can be proven to be effective. Both simulation and experiment results showed that the proposed controller has a good transient-response and provides accurate position tracking in the presence of parametric uncertainties, uncertain nonlinearities, and external disturbances.
PLANT COMPETITION UNDERGROUND

Belowground competition occurs when plants decrease the growth, survival, or fecundity of neighbors by reducing available soil resources. Competition belowground can be stronger and involve many more neighbors than aboveground competition. Physiological ecologists and population or community ecologists have traditionally studied belowground competition from different perspectives. Physiologically based studies often measure resource uptake without determining the integrated consequences for plant performance, while population or community level studies examine plant performance but fail to identify the resource intermediary or mechanism. Belowground competitive ability is correlated with such attributes as root density, surface area, and plasticity either in root growth or in the properties of enzymes involved in nutrient uptake. Unlike competition for light, in which larger plants have a disproportionate advantage by shading smaller ones, competition for soil resources is apparently more symmetric. Below.
Maternal dietary glycemic index and glycemic load in early pregnancy are associated with offspring adiposity in childhood: the Southampton Women's Survey.

BACKGROUND Maternal hyperglycemia in pregnancy is associated with greater adiposity in offspring. The glycemic index (GI) and glycemic load (GL) describe the glycemic response to carbohydrate ingestion. However, the influence of maternal dietary GI and GL in pregnancy on childhood adiposity is unknown. OBJECTIVE We examined relations of maternal dietary GI and GL in early and late pregnancy with offspring body composition. DESIGN A total of 906 mother-child pairs from the prospective cohort the Southampton Women's Survey were included. Children underwent dual-energy X-ray absorptiometry measurements of body composition at birth and 4 and 6 y of age. Log-transformed fat mass and lean mass were standardized with a mean (±SD) of 0 ± 1. Maternal dietary GI and GL were assessed at 11 and 34 wk of gestation by using an administered food-frequency questionnaire. RESULTS After control for potential confounders, both maternal dietary GI and GL in early pregnancy were positively associated with fat mass at 4 and 6 y of age [fat mass SDs per 10-unit GI increase: β = 0.43 (95% CI: 0.06, 0.80), P = 0.02 at 4 y of age; β = 0.40 (95% CI: 0.10, 0.70), P = 0.01 at 6 y of age; fat mass SDs per 50-unit GL increase: β = 0.43 (95% CI: 0.19, 0.67), P < 0.001 at 4 y of age; β = 0.27 (95% CI: 0.07, 0.47), P = 0.007 at 6 y of age]. In contrast, there were no associations between maternal dietary GI or GL in late pregnancy and offspring fat mass at these ages. Maternal dietary GI and GL were not associated with fat mass at birth or offspring lean mass at any of the ages studied. CONCLUSION Higher maternal dietary GI and GL in early pregnancy are associated with greater adiposity in childhood.
Time-Varying Nonlinear Causality Detection Using Regularized Orthogonal Least Squares and Multi-Wavelets With Applications to EEG

A new transient Granger causality detection method is proposed based on a time-varying parametric modeling framework, and is applied to the real EEG signals to reveal the causal information flow during motor imagery (MI) tasks. The time-varying parametric modeling approach employs a nonlinear autoregressive with external input model, whose parameters are approximated by a set of multi-wavelet basis functions. A regularized orthogonal least squares (ROLS) algorithm is then used to produce a parsimonious or sparse regression model and estimate the associated model parameters. The time-varying Granger causality between nonstationary signals can be detected accurately by making use of both the good approximation properties of multi-wavelets and the good generalization performance of the ROLS in the presence of high-level noise. Two simulation examples are presented to demonstrate the effectiveness of the proposed method for both linear and nonlinear causal detection respectively. The proposed method is then applied to real EEG signals of MI tasks. It follows that transient causal information flow over the time course between various sensorimotor related channels can be successfully revealed during the whole reaction processes. Experimental results from these case studies confirm the applicability of the proposed scheme and show its utility for the understanding of the associated neural mechanism and the potential significance for developing MI tasks based brain-computer interface systems.
Applications of the FIV Model to Study HIV Pathogenesis

Feline immunodeficiency virus (FIV) is a naturally-occurring retrovirus that infects domestic and non-domestic feline species, producing progressive immune depletion that results in an acquired immunodeficiency syndrome (AIDS). Much has been learned about FIV since it was first described in 1987, particularly in regard to its application as a model to study the closely related lentivirus, human immunodeficiency virus (HIV). In particular, FIV and HIV share remarkable structure and sequence organization, utilize parallel modes of receptor-mediated entry, and result in a similar spectrum of immunodeficiency-related diseases due to analogous modes of immune dysfunction. This review summarizes current knowledge of FIV infection kinetics and the mechanisms of immune dysfunction in relation to opportunistic disease, specifically in regard to studying HIV pathogenesis. Furthermore, we present data that highlight changes in the oral microbiota and oral immune system during FIV infection, and outline the potential for the feline model of oral AIDS manifestations to elucidate pathogenic mechanisms of HIV-induced oral disease. Finally, we discuss advances in molecular biology, vaccine development, neurologic dysfunction, and the ability to apply pharmacologic interventions and sophisticated imaging technologies to study experimental and naturally occurring FIV, which provide an excellent, but often overlooked, resource for advancing therapies and the management of HIV/AIDS.
Multiscale Modelling of Hydrogen Transport and Segregation in Polycrystalline Steels

A key issue in understanding and effectively managing hydrogen embrittlement in complex alloys is identifying and exploiting the critical role of the various defects involved. A chemo-mechanical model for hydrogen diffusion is developed taking into account stress gradients in the material, as well as microstructural trapping sites such as grain boundaries and dislocations. In particular, the energetic parameters used in this coupled approach are determined from ab initio calculations. Complementary experimental investigations that are presented show that a numerical approach capable of massive scale-bridging up to the macroscale is required. Due to the wide range of length scales accounted for, we apply homogenisation schemes for the hydrogen concentration to reach simulation dimensions comparable to metallurgical process scales. Via a representative volume element approach, an ab initio based scale bridging description of dislocation-induced hydrogen aggregation is easily accessible. When we extend the representative volume approach to also include an analytical approximation for the ab initio based description of grain boundaries, we find conceptual limitations that hinder a quantitative comparison to experimental data in the current stage. Based on this understanding, the development of improved strategies for further efficient scale bridging approaches is foreseen.
Designing for social interaction in open-ended play environments

Interactive technology is becoming more strongly integrated in innovative play solutions. As play is often a social experience, understanding the dynamic social context in which such play takes place is an essential step in designing new interactive play environments. In this paper, we explore the notion of social interaction in the context of open-ended play environments. We present an integrated model of interaction and transitions over time. Next, we describe two design case studies of open-ended, interactive play environments, GlowSteps and Wobble, discussing how these designs support social interaction over time. Results show that social interaction changes over time, starting with solitary play and moving towards more complex social play later on. These results are translated into implications for design, which guide designers in achieving a better understanding of how to design for the social context of their design proposals.
Sintering strategies for inkjet printed metallic traces in 3D printed electronics

Emerging from 2D printed electronics, 3D printed electronics promise a break-through in additive manufacturing and prototyping of electronics. However, transferring the know-how from 2D flexible electronics to 3D parts with complex structures (e.g. internal vias and external interconnects) might not be a straightforward approach. As an example, the variation of light intensity with respect to the distance and angle of incidence casts doubt on the efficiency of the intense pulsed laser (IPL) as a robust sintering method for metallic traces in 3D printed bulk structures, whereas IPL is currently by far the most prevailing sintering technique for 2D printed flexible electronics. Sintering of metallic traces in 3D printed parts can be executed either as a sequential layer-by-layer printing and processing step (LP) or as a bulk post-processing step (BP). In the current study, a survey on the most common sintering strategies for inkjet printed silver nanoparticles was conducted, while the compatibility to 3D printed structures was brought into the focal point. To discover the capabilities and limitations of six sintering methods (i. e. IPL, ohmic curing, thermal heating, laser, atmospheric plasma and microwave sintering) for 3D printed electronics, a comparative study utilizing the same materials and diagnostic methods was pursued. The results revealed that for 3D functional parts, some of the sintering techniques can be considered as complementary methods for each other, whereas a few showed readily the potential to be adapted in 3D printed electronics production.
The Church-Turing Thesis : Its Nature and Status

happens next in a Turing machine or a polycellular automation has a strictly local character . Now it is time for me to come down off the fence-on both sides . 1 . I think it conceivable that in fifty or a hundred years time there will be machines of the tenth or twentieth generation which in some areas of mathematics will be regarded by first-rate mathematicians as valuable colleagues (not merely assistants) . The machines will write papers, argue back when criticized, and will take part in discussion on how best to tackle a new problem. This is an updated version of the Turing Test . The conception raises an important point . In his book Penrose asserts forcefully that consciousness is essential to rational thought; I do not quite understand what he means by consciousness . But machines of the kind I am imagining would display the effects of consciousness-the ability to concentrate attention on a particular part or aspect of their input, the ability to reflect on and to alter the behaviour of subsystems in their hierarchic structure, the ability to produce a range of alternatives, and even, in a very restricted way, an ability to adapt their social behaviour . I remember a long time ago asking Donald MacKay what sort of evidence or knowledge he thought would be required to attribute consciousness to a computer ; he replied that it would not primarily be a matter of using evidence and knowledge, but a matter of having the nerve . If my fantasy becomes fact, people will have the nerve . z . Now for the other side of the fence . Even if machines of that kind are built, discussions about them, explanations of their working, proposals for their improvement will (when not concerned only with the lowest levels of this hierarchical structure) be carried on not in terms of algorithms but in the same sort of terms as we use-as I used-in discussing human intelligence and rational thought . At a sophisticated level it is not practical, nor useful, nor sensible to discuss intelligent behaviour solely in terms of algorithms or machine programs; and this would remain true even if there were some master program producing the behaviour . g
Single-phase bidirectional three-level T-type inverter

This paper proposes a single-phase bidirectional three-level T-type inverter. The proposed inverter has a T-type switching leg and a half-bridge switching leg. The T-type switching leg operates at high switching frequency with sinusoidal pulse width modulation. The half-bridge switching leg operates at the grid frequency according to the voltage polarity of the grid. Due to the three-level switching operation of the proposed inverter, it provides the advantages of low voltage stress, reduced switching loss, and low harmonic components for the single-phase gird-tied applications. The proposed inverter is introduced by describing its circuit configuration, switching technique, operation modes, and control scheme. A 1.0 kW prototype has been designed and experimentally tested to verify the performance of the proposed inverter.
A General Stock Model for Fuzzy Markets

This paper presents a general stock model for fuzzy markets based on a class of fuzzy process known as Liu process. Firstly, a brief history of stock models and some methodologies used in stochastic stock models are reviewed. Next, some useful concepts and properties about fuzzy process are presented. Then, a general stock model for fuzzy markets is formulated by the way of fuzzy dierential equation. This basic single-factor model leads quite naturally to multi-factor extensions. Some option pricing formulas on the proposed fuzzy stock model are investigated. Finally, some remarks are made in the concluding section. c 2008 World Academic Press, UK. All rights reserved.
A Soft Computing Approach for Data Routing in Hospital Area Networks (HAN)

This paper proposes an alternative model to deliver vital signs of patients in a hospital indoor environment where a large number of patients exist and the traffic generated rapidly changes over time using Body Area Network (BAN). The methodology for finding an optimal path includes a meta-heuristic that combines ANT Colony Optimization (ACO). The authors propose an ACO based framework for monitoring data originating from a BAN to improve network life, energy and load balancing of the overall network. Since the traffic generated by BANs on the network changes with time, finding a shortest path is important for Hospital Area Network. In this paper, the authors implemented an ACO based method and have carried out simulations using OMNeT++ to prove that the proposed method can find a better solution than conventional methods.
Analysis of the Relationship between Alternative Respiration and Sterigmatocystin Formation in Aspergillus nidulans

Aspergillus nidulans has one gene for alternative oxidase (EC 1.10.3.11). To investigate the relationship between this mitochondrial terminal oxidase and the formation of the mycotoxin sterigmatocystin, the encoding aodA gene was both deleted and overexpressed. Relative to the wild-type, the cyanide-resistant fraction of respiration in the late stationary stage—when sterigmatocystin production occurs—doubled in the overexpressing mutant carrying three aodA gene copies, but decreased to 10% in the deletant. Essentially identical results were obtained regardless whether the cultures were illuminated or protected from light. In contrast, sterigmatocystin yield in the aodA deletant was about half of that in the control when grown in the dark, while aodA overexpression resulted in up to 70% more sterigmatocystin formed, the yield increasing with alternative oxidase activity. Results were quite different when cultures were illuminated: under those conditions, sterigmatocystin volumetric yields were considerably lower, and statistically unvarying, regardless of the presence, absence, or the copy number of aodA. We conclude that the copy number of aodA, and hence, the balance between alternative- and cytochrome C-mediated respiration, appears to correlate with sterigmatocystin production in A. nidulans, albeit only in the absence of light.
Beyond Smartphone Overuse: Identifying Addictive Mobile Apps

Current research on smartphone addiction has mainly focused on addiction at the device level. This motivated us to explore more specifically on app addiction. We investigate smartphone usage for college students using surveys, logged data, and interviews. Specifically, we adapted existing smartphone addiction assessment instruments to measure app addiction. The analysis of our data shows that social and communication apps are the top 2 most addictive categories among participants. Female and male participants show no significant difference in terms of smartphone addiction. However, female participants tend to report that they are addicted to more apps. The psychological factors associated with app addiction are different between app categories. For example, compared to communication apps, participants report that it is easier to withdraw from social apps, but more difficult to control time spent on them. Correlation analysis between app usage features and app addictiveness scores reveals that compulsive open times, usage duration, and regularity of usage are good indicators of app addiction, though response time to notifications has limited predictive power.
Tranquil spaces in a metropolitan area

The literature points to the importance of quiet areas, green spaces and natural surroundings in relieving stress and improving feelings of well being. Such tranquil landscapes and soundscapes are potentially well suited to the needs of citizens of metropolitan areas because the stress of everyday city life can often involve intense periods of ‘directed attention’ over many hours, leading to stress and mental fatigue. At the University of Bradford in the UK research has provided a unique engineering tool for predicting the perceived tranquillity of open spaces in towns, cities and countryside. The tool has initially been used to carry out a pilot tranquillity audit of 3 open spaces [1] and has now been extended to all 4 major parks in a metropolitan area. The dominant noise source in each case results from traffic on roads close to the boundaries. The results provide useful insights into the levels of tranquillity that can be achieved in such urban conditions and the effects of moderating factors are discussed based on recent research results. Suggestions are made for improving the levels of tranquillity. The paper describes the results of the survey and discusses the trends found if the area of the parks and open spaces is considered.
The Versatility of Paramyxovirus RNA Polymerase Stuttering

ABSTRACT Paramyxoviruses cotranscriptionally edit their P gene mRNAs by expanding the number of Gs of a conserved AnGnrun. Different viruses insert different distributions of guanylates, e.g., Sendai virus inserts a single G, whereas parainfluenza virus type 3 inserts one to six Gs. The sequences conserved at the editing site, as well as the experimental evidence, suggest that the insertions occur by a stuttering process, i.e., by pseudotemplated transcription. The number of times the polymerase “stutters” at the editing site before continuing strictly templated elongation is directed by acis-acting sequence found upstream of the insertions. We have examined the stuttering process during natural virus infections by constructing recombinant Sendai viruses with mutations in theircis-acting sequences. We found that the template stutter site is precisely determined (C1052) and that a relatively short region (∼6 nucleotides) just upstream of the AnGn run can modulate the overall frequency of mRNA editing as well as the distribution of the nucleotide insertions. The positions more proximal to the 5′ AnGn run are the most important in this respect. We also provide evidence that the stability of the mRNA/template hybrid plays a determining role in the overall frequency and range of mRNA editing. When the template U run is extended all the way to the stutter site, adenylates rather than guanylates are added at the editing site and their distribution begins to resemble the polyadenylation associated with mRNA 3′ end formation by the viral polymerase. Our data suggest how paramyxovirus mRNA editing and polyadenylation are related mechanistically and how editing sites may have evolved from poly(A)-termination sites or vice versa.