Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of the RNA Pseudoknot within the 3′ End of the Porcine Reproductive and Respiratory Syndrome Virus Genome as a Pathogen-Associated Molecular Pattern To Activate Antiviral Signaling via RIG-I and Toll-Like Receptor 3

ABSTRACT Once infected by viruses, cells can detect pathogen-associated molecular patterns (PAMPs) on viral nucleic acid by host pattern recognition receptors (PRRs) to initiate the antiviral response. Porcine reproductive and respiratory syndrome virus (PRRSV) is the causative agent of porcine reproductive and respiratory syndrome (PRRS), characterized by reproductive failure in sows and respiratory diseases in pigs of different ages. To date, the sensing mechanism of PRRSV has not been elucidated. Here, we reported that the pseudoknot region residing in the 3′ untranslated regions (UTR) of the PRRSV genome, which has been proposed to regulate RNA synthesis and virus replication, was sensed as nonself by retinoic acid-inducible gene I (RIG-I) and Toll-like receptor 3 (TLR3) and strongly induced type I interferons (IFNs) and interferon-stimulated genes (ISGs) in porcine alveolar macrophages (PAMs). The interaction between the two stem-loops inside the pseudoknot structure was sufficient for IFN induction, since disruption of the pseudoknot interaction powerfully dampened the IFN induction. Furthermore, transfection of the 3′ UTR pseudoknot transcripts in PAMs inhibited PRRSV replication in vitro. Importantly, the predicted similar structures of other arterivirus members, including equine arteritis virus (EAV), lactate dehydrogenase-elevating virus (LDV), and simian hemorrhagic fever virus (SHFV), also displayed strong IFN induction activities. Together, in this work we identified an innate recognition mechanism by which the PRRSV 3′ UTR pseudoknot region served as PAMPs of arteriviruses and activated innate immune signaling to produce IFNs that inhibit virus replication. All of these results provide novel insights into innate immune recognition during virus infection. IMPORTANCE PRRS is the most common viral disease in the pork industry. It is caused by PRRSV, a positive single-stranded RNA virus, whose infection often leads to persistent infection. To date, it is not yet clear how PRRSV is recognized by the host and what is the exact mechanism of IFN induction. Here, we investigated the nature of PAMPs on PRRSV and the associated PRRs. We found that the 3′ UTR pseudoknot region of PRRSV, which has been proposed to regulate viral RNA synthesis, could act as PAMPs recognized by RIG-I and TLR3 to induce type I IFN production to suppress PRRSV infection. This report is the first detailed description of pattern recognition for PRRSV, which is important in understanding the antiviral response of arteriviruses, especially PRRSV, and extends our knowledge on virus recognition.
Diapause Induction, Color Change, and Cold Tolerance Physiology of the Diapausing Larvae of the Chouioia cunea (Hymenoptera: Eulophidae)

Abstract The chalcid wasp Chouioia cunea Yang (Hymenoptera: Eulophidae) is one of the most dominant pupal parasitoids of Hyphantria cunea (Drury) (Lepidoptera: Arctiidae), an invasive pest of many forestry trees and agricultural crops. For mass rearing C. cunea for biological control purposes, the pupae of Antheraea pernyi (Guérin-Méneville) (Lepidoptera: Saturniidae) have been widely used as a substitute host in China. In this article, photoperiodic effect on diapause induction in C. cunea within the pupae of A. pernyi was investigated, and the differences in cold tolerance physiology including supercooling point, water content, and activities of three protective enzymes (Peroxidase [POD], Catalase [CAT], and Superoxide dismuase [SOD]) between diapause and nondiapause mature larvae were comparatively determined. Our results revealed that C. cunea possess a short-day induced larval diapause. The critical photoperiods for diapause induction in C. cunea were estimated to be between a photoperiod of 13:11 and 14:10 (L:D) h at 18°C, or between a photoperiod of 12:12 and 13:11 (L:D) h at 21°C or 24°C. We also found that the color of C. cunea diapausing larvae was taupe, while the normally developed (nondiapausing) individuals were light yellow. This body color change can be used as an indicator of diapause entry of C. cunea larave. The average supercooling point of diapausing mature larvae were lower than those of nondiapausing ones. There were significant differences in the activity of three protective enzymes (POD, CAT, and SOD) between diapausing and nondiapausing mature larvae.
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Mounting evidence shows that the gut microbiota, an important player within the gut-brain communication axis, can affect metabolism, inflammation, brain function and behavior. Interestingly, gut microbiota composition is known to be altered in patients with metabolic syndrome (MetS), who also often display neuropsychiatric symptoms. The use of prebiotics, which beneficially alters the microbiota, may therefore be a promising way to potentially improve physical and mental health in MetS patients. This hypothesis was tested in a mouse model of MetS, namely the obese and type-2 diabetic db/db mice, which display emotional and cognitive alterations associated with changes in gut microbiota composition and hippocampal inflammation compared to their lean db/+ littermates. We assessed the impact of chronic administration (8 weeks) of prebiotics (oligofructose) on both metabolic (body weight, food intake, glucose homeostasis) and behavioral (increased anxiety-like behavior and impaired spatial memory) alterations characterizing db/db mice, as well as related neurobiological correlates, with particular attention to neuroinflammatory processes. Prebiotic administration improved excessive food intake and glycemic dysregulations (glucose tolerance and insulin resistance) in db/db mice. This was accompanied by an increase of plasma antiinflammatory cytokine IL-10 levels and hypothalamic mRNA expression of the anorexigenic cytokine IL-1b, whereas unbalanced mRNA expression of hypothalamic orexigenic (NPY) and anorexigenic (CART, POMC) peptides was unchanged. We also detected signs of improved blood-brain-barrier integrity in the hypothalamus of oligofructose-treated db/db mice (normalized expression of tight junction proteins ZO-1 and occludin). On the contrary, prebiotic administration did not improve behavioral alterations and associated reduction of hippocampal neurogenesis displayed by db/db mice, despite normalization of increased hippocampal IL-6 mRNA expression. Of note, we found a relationship between the effect of treatment on dentate gyrus neurons and spatial memory. These findings may prove valuable for introducing novel approaches to treat some of the comorbidities associated with MetS. 2016 Elsevier Inc. All rights reserved.
Speed of saccade execution and inhibition associated with fractional anisotropy in distinct fronto‐frontal and fronto‐striatal white matter pathways

Fast cancellation or switching of action plans is a critical cognitive function. Rapid signal transmission is key for quickly executing and inhibiting responses, and the structural integrity of connections between brain regions plays a crucial role in signal transmission speed. In this study, we used the search‐step task, which has been used in nonhuman primates to measure dynamic alteration of saccade plans, in combination with functional and diffusion‐weighted MRI. Functional MRI results were used to identify brain regions involved in the reactive control of gaze. Probabilistic tractography was used to identify white matter pathways connecting these structures, and the integrity of these connections, as indicated by fractional anisotropy (FA), was correlated with search‐step task performance. Average FA from tracts between the right frontal eye field (FEF) and both right supplementary eye field (SEF) and the dorsal striatum were associated with faster saccade execution. Average FA of connections between the dorsal striatum and both right SEF and right inferior frontal cortex (IFC) as well as between SEF and IFC predicted the speed of inhibition. These relationships were largely behaviorally specific, despite the correlation between saccade execution and inhibition. Average FA of connections between the IFC and both SEF and the dorsal striatum specifically predicted the speed of inhibition, and connections between the FEF and SEF specifically predicted the speed of execution. In addition, these relationships were anatomically specific; correlations were observed after controlling for global FA. These data suggest that networks supporting saccade initiation and inhibition are at least partly dissociable. Hum Brain Mapp 37:2811–2822, 2016. © 2016 Wiley Periodicals, Inc.
A comparative evaluation of effect of modern-curing lights and curing modes on conventional and novel-resin monomers

Aim: The aim of this study is to compare and to evaluate effect of curing light and curing modes on the nanohybrid composite resins with conventional Bis-GMA and novel tricyclodecane (TCD) monomers. Methodology: Two nanohybrid composites, IPS empress direct and charisma diamond were used in this study. Light-emitting diode (LED)-curing unit and quartz-tungsten-halogen (QTH)-curing unit which were operated into two different modes: continuous and soft start. Based on the composite resin, curing lights, and mode of curing used, the samples were divided into 8 groups. After polymerization, the samples were stored for 48 h in complete darkness at 37°C and 100% humidity. The Vickers hardness (VK) of the surface was determined with Vickers indenter by the application of 200 g for 15 s. Three VK readings were recorded for each sample surface both on top and bottom surfaces. For all the specimens, the three hardness values for each surface were averaged and reported as a single value. The mean VK and hardness ratio were calculated. The depth of cure was assessed based on the hardness ratio. Results: Comparison of mean hardness values and hardness ratios was done using ANOVA with post hoc Tukey's test. Conclusion: Both QTH- and LED-curing units had shown the adequate depth of cure. Soft-start-curing mode in both QTH- and LED-curing lights had effectively increased microhardness than the continuous mode of curing. TCD monomer had shown higher hardness values compared with conventional Bis-GMA-containing resin.
Local Conditions, Not Regional Gradients, Drive Demographic Variation of Giant Ragweed (Ambrosia trifida) and Common Sunflower (Helianthus annuus) Across Northern U.S. Maize Belt

Abstract Knowledge of environmental factors influencing demography of weed species will improve understanding of current and future weed invasions. The objective of this study was to quantify regional-scale variation in vital rates of giant ragweed and common sunflower . To accomplish this objective, a common field experiment was conducted across seven sites between 2006 and 2008 throughout the north central U.S. maize belt. Demographic parameters of both weed species were measured in intra- and interspecific competitive environments, and environmental data were collected within site-years. Site was the strongest predictor of belowground vital rates (summer and winter seed survival and seedling recruitment), indicating sensitivity to local abiotic conditions. However, biotic factors influenced aboveground vital rates (seedling survival and fecundity). Partial least squares regression (PLSR) indicated that demography of both species was most strongly influenced by thermal time and precipitation. The first PLSR components, both characterized by thermal time, explained 63.2% and 77.0% of variation in the demography of giant ragweed and common sunflower, respectively; the second PLSR components, both characterized by precipitation, explained 18.3% and 8.5% of variation, respectively. The influence of temperature and precipitation is important in understanding the population dynamics and potential distribution of these species in response to climate change. Nomenclature: Giant ragweed, Ambrosia trifida L. AMBTR; common sunflower, Helianthus annuus L. HELAN; maize, Zea mays L. ; soybean, Glycine max (L.) Merr.
Effects of Non-Driving Related Task Modalities on Takeover Performance in Highly Automated Driving

Objective: Aim of the study was to evaluate the impact of different non-driving related tasks (NDR tasks) on takeover performance in highly automated driving. Background: During highly automated driving, it is allowed to engage in NDR tasks temporarily. However, drivers must be able to take over control when reaching a system limit. There is evidence that the type of NDR task has an impact on takeover performance, but little is known about the specific task characteristics that account for performance decrements. Method: Thirty participants drove in a simulator using a highly automated driving system. Each participant faced five critical takeover situations. Based on assumptions of Wickens’s multiple resource theory, stimulus and response modalities of a prototypical NDR task were systematically manipulated. Additionally, in one experimental group, the task was locked out simultaneously with the takeover request. Results: Task modalities had significant effects on several measures of takeover performance. A visual-manual texting task degraded performance the most, particularly when performed handheld. In contrast, takeover performance with an auditory-vocal task was comparable to a baseline without any task. Task lockout was associated with faster hands-on-wheel times but not altered brake response times. Conclusion: Results showed that NDR task modalities are relevant factors for takeover performance. An NDR task lockout was highly accepted by the drivers and showed moderate benefits for the first takeover reaction. Application: Knowledge about the impact of NDR task characteristics is an enabler for adaptive takeover concepts. In addition, it might help regulators to make decisions on allowed NDR tasks during automated driving.
The Intensification of Two-Dimensional Swirling Flows by Stochastic Asymmetric Forcing

Abstract The effects of stochastically excited asymmetric disturbances on two-dimensional vortices are investigated. These vortices are maintained by the radial inflow of fixed cylindrical deformation fields, which are chosen so that both one-celled and two-celled vortices may be studied. The linearized perturbation equations are reduced to the form of a linear dynamical system with stochastic forcing, that is, dx/dt = Ax + Fξ, where the columns of F are forcing functions and the elements of ξ are Gaussian white-noise processes. Through this formulation the stochastically maintained variance of the perturbations, the structures that dominate the response (the empirical orthogonal functions), and the forcing functions that contribute most to this response (the stochastic optimals) can be directly calculated. For all cases the structures that most effectively induce the transfer of energy from the mean flow to the perturbation field are close approximations to the global optimals (i.e., the initial perturba.
Insect Fauna Associated With Anacardium occidentale (Sapindales: Anacardiaceae) in Benin, West Africa

ABSTRACT. Cashew, Anacardium occidentale L. (Sapindales: Anacardiaceae), is an important cash crop in Benin. However, its production is threatened by several biotic factors, especially insects. In Benin, very few studies have focused on insects and just listed species commonly found on cashew worldwide. The present investigation fills this gap by presenting an exhaustive inventory of insect species associated with this crop in the country. The survey was carried out from September 2009 to August 2010 in 22 cashew orchards (5 young and 17 mature) distributed over three major agroecological zones where cashew is most produced in the country. Insects were collected using chemical knock-down technique and visual observation followed by capture with sweep net. In addition, infested plant organs were sampled and incubated to collect emerging insects. In total, 262 insect species were recorded and identified. Among them, the wood borer Apate terebrans Pallas, the leafminer Eteoryctis gemoniella Stainton, and the mirid bugs Helopeltis schoutedeni Reuter. , and Helopeltis anacardii Miller. , appeared as the most important insect species attacking cashew in Benin. Beneficial insects encountered included some predators, parasitoids, and pollinators. Few vertebrate predators were also recorded on the trees. Differences in agroecological conditions or in field cleanliness did not affect the number of insect species encountered in the cashew orchards. The results of this study represent an important baseline data for the design and implementation of strategies for cashew protection in Benin.
Hybrid Analog–Digital Transmit Beamforming for Spectrum Sharing Backhaul Networks

This paper deals with the problem of analog–digital transmit beamforming under spectrum sharing constraints for backhaul systems. In contrast to fully digital designs, where the spatial processing is done at baseband unit with all the flexible computational resources of digital processors, analog–digital beamforming schemes require that certain processing is done through analog components, such as phase-shifters or switches. These analog components do not have the same processing flexibility as the digital processor, but on the other hand, they can substantially reduce the cost and complexity of the beamforming solution. This paper presents the joint optimization of the analog and digital parts, which results in a nonconvex, NP-hard, and coupled problem. In order to solve it, an alternating optimization with a penalized convex–concave method is proposed. According to the simulation results, this novel iterative procedure is able to find a solution that behaves close to the fully digital beamforming upper bound scheme.
Relationship between Physicochemical Properties of Saliva and Dental Caries and Periodontal Status among Female Teachers Living in Central Iran

Objectives: There are inconsistent data about the association between saliva properties, dental caries, and periodontal status. In this study, we tried to examine the association between dental caries and periodontal status with salivary viscosity, flow rate, pH, and buffering capacity in adults. Methods: In the present cross-sectional study, 450 female teachers were randomly selected from schools located in Yazd, Iran. Oral examinations were conducted, and unstimulated saliva samples were collected. Salivary viscosity, flow rate, pH, and buffering capacity were assessed. The salivary physicochemical properties were compared among teachers with different types of oral health. Analyses were done using the Statistical Package for the Social Sciences version 16. Results: In total, 431 female teachers aged 40.45 ± 8.18 years were included in the study. Salivary flow rate, buffering capacity, pH, and viscosity, community periodontal index status were not significantly different in participants with and without tooth caries. There was a reverse linear association between salivary pH and flow rate with the decayed, missed, and filled teeth index (P < 0.05). The saliva buffering capacity was not significantly related to dental properties. Those with bleeding on probing had lower salivary pH, and buffering capacity compared to those with healthy gum. However, the salivary resting flow rate was not different in participants with bleeding on probing and healthy participants. Conclusion: Based on our results, saliva properties might be important predictors in oral health status. This means that any change in saliva combination might affect periodontal and dental diseases. Future prospective studies are recommended to confirm these results.
Laboratory investigation of hot mix asphalt containing waste materials

It has been recognised with growing concern that agricultural and industrial wastes are increasingly produced in large volume. In order to reduce environmental hazards and conserve natural resources, the use of waste materials in highway pavements would be extremely effective in terms of recycling waste materials. The main purpose of this study was to investigate the effects of waste materials as filler on the performance of hot mix asphalt (HMA) mixtures. HMA mixtures containing waste glass powder (WGP), waste brick powder (WBP), rice husk ash (RHA) and stone dust (control mixture) were fabricated and the optimum asphalt binder content was determined for each mixture. The properties of HMA mixtures were investigated by Marshall, indirect tensile stiffness modulus and indirect tensile fatigue tests. The results indicated that WGP and WBP mixtures exhibited higher fatigue life and better performance than other mixtures. In addition, it was determined that there was no considerable difference in the performance of RHA mixture and control mixture.
A new asymptotic enumeration technique: the Lovasz Local Lemma

Our previous paper applied a lopsided version of the Lovasz Local Lemma that allows negative dependency graphs to the space of random injections from an $m$-element set to an $n$-element set. Equivalently, the same story can be told about the space of random matchings in $K_{n,m}$. Now we show how the cited version of the Lovasz Local Lemma applies to the space of random matchings in $K_{2n}$. We also prove tight upper bounds that asymptotically match the lower bound given by the Lovasz Local Lemma. As a consequence, we give new proofs to results on the enumeration of $d$-regular graphs. The tight upper bounds can be modified to the space of matchings in $K_{n,m}$, where they yield as application asymptotic formulas for permutation and Latin rectangle enumeration problems. The strength of the method is shown by a new result: enumeration of graphs by degree sequence or bipartite degree sequence and girth. As another application, we provide a new proof to the classical probabilistic result of Erd\H os that showed the existence of graphs with arbitrary large girth and chromatic number. If the degree sequence satisfies some mild conditions, almost all graphs with this degree sequence and prescribed girth have high chromatic number.
Emotions Are Understood From Biological Motion Across Remote Cultures

Patterns of bodily movement can be used to signal a wide variety of information, including emotional states. Are these signals reliant on culturally learned cues or are they intelligible across individuals lacking exposure to a common culture? To find out, we traveled to a remote Kreung village in Ratanakiri, Cambodia. First, we recorded Kreung portrayals of 5 emotions through bodily movement. These videos were later shown to American participants, who matched the videos with appropriate emotional labels with above chance accuracy (Study 1). The Kreung also viewed Western point-light displays of emotions. After each display, they were asked to either freely describe what was being expressed (Study 2) or choose from 5 predetermined response options (Study 3). Across these studies, Kreung participants recognized Western point-light displays of anger, fear, happiness, sadness, and pride with above chance accuracy. Kreung raters were not above chance in deciphering an American point-light display depicting love, suggesting that recognizing love may rely, at least in part, on culturally specific cues or modalities other than bodily movement. In addition, multidimensional scaling of the patterns of nonverbal behavior associated with each emotion in each culture suggested that similar patterns of nonverbal behavior are used to convey the same emotions across cultures. The considerable cross-cultural intelligibility observed across these studies suggests that the communication of emotion through movement is largely shaped by aspects of physiology and the environment shared by all humans, irrespective of differences in cultural context.