Miracle-dz/UniFAR-FTUs huggingface dataset:
Autophagy in Negative-Strand RNA Virus Infection

Autophagy is a homoeostatic process by which cytoplasmic material is targeted for degradation by the cell. Viruses have learned to manipulate the autophagic pathway to ensure their own replication and survival. Although much progress has been achieved in dissecting the interplay between viruses and cellular autophagic machinery, it is not well understood how the cellular autophagic pathway is utilized by viruses and manipulated to their own advantage. In this review, we briefly introduce autophagy, viral xenophagy and the interaction among autophagy, virus and immune response, then focus on the interplay between NS-RNA viruses and autophagy during virus infection. We have selected some exemplary NS-RNA viruses and will describe how these NS-RNA viruses regulate autophagy and the role of autophagy in NS-RNA viral replication and in immune responses to virus infection. We also review recent advances in understanding how NS-RNA viral proteins perturb autophagy and how autophagy-related proteins contribute to NS-RNA virus replication, pathogenesis and antiviral immunity.
ASPIRE

Many vertex-centric graph algorithms can be expressed using asynchronous parallelism by relaxing certain read-after-write data dependences and allowing threads to compute vertex values using stale (i.e., not the most recent) values of their neighboring vertices. We observe that on distributed shared memory systems, by converting synchronous algorithms into their asynchronous counterparts, algorithms can be made tolerant to high inter-node communication latency. However, high inter-node communication latency can lead to excessive use of stale values causing an increase in the number of iterations required by the algorithms to converge. Although by using bounded staleness we can restrict the slowdown in the rate of convergence, this also restricts the ability to tolerate communication latency. In this paper we design a relaxed memory consistency model and consistency protocol that simultaneously tolerate communication latency and minimize the use of stale values. This is achieved via a coordinated use of best effort refresh policy and bounded staleness. We demonstrate that for a range of asynchronous graph algorithms and PDE solvers, on an average, our approach outperforms algorithms based upon: prior relaxed memory models that allow stale values by at least 2.27x; and Bulk Synchronous Parallel (BSP) model by 4.2x. We also show that our approach frequently outperforms GraphLab, a popular distributed graph processing framework.
An investigation of behavior and modeling of bond for reinforced concrete

An Investigation of Behavior and Modeling of Bond for Reinforced Concrete Jingjuan Li Chair of the Supervisory Committee: Associate Professor Laura N. Lowes Department of Civil & Environmental Engineering This research investigates bond between concrete and steel in reinforced concrete (RC) using X-Ray tomography image data and nonlinear analysis, with the objective of developing recommendations for modeling bond in RC structures. RC is a composite material that combines concrete, which is strong in compression and weak in tension, with reinforcing steel, which is strong is tension and buckles in compression. Bond is necessary to maintain the composite action and realize the full utility of the material. However, bond-zone response data are not easily collected and the mechanics of bond are not easily assessed using traditional experimental test methods, as traditional instrumentation may interfere with the bond mechanism and can not provide high-fidelity data. Recently, X-ray computed tomography (CT), which is non-invasive and provides high resolution data, has been used to monitor bond tests. In this study, state-of-the-art image processing techniques are applied to 3D X-ray images of bond-zone specimens to characterize bond behavior. Bond-zone response data generated from X-ray CT images are used to verify nonlinear high-resolution finite element (FE) modeling of bond-zone specimens. These FE models are used to further investigate bond-zone response and the impact of modeling parameters on predicted response. The results of this research provide high-fidelity data characterizing bond-zone response, improved understanding of bond-zone mechanisms and recommendations for design and modeling of bond behavior in RC structural components.
Respiratory signal prediction based on adaptive boosting and multi-layer perceptron neural network

To improve the prediction accuracy of respiratory signals using adaptive boosting and multi-layer perceptron neural network (ADMLP-NN) for gated treatment of moving target in radiation therapy. The respiratory signals acquired using a real-time position management (RPM) device from 138 previous 4DCT scans were retrospectively used in this study. The ADMLP-NN was composed of several artificial neural networks (ANNs) which were used as weaker predictors to compose a stronger predictor. The respiratory signal was initially smoothed using a Savitzky–Golay finite impulse response smoothing filter (S–G filter). Then, several similar multi-layer perceptron neural networks (MLP-NNs) were configured to estimate future respiratory signal position from its previous positions. Finally, an adaptive boosting (Adaboost) decision algorithm was used to set weights for each MLP-NN based on the sample prediction error of each MLP-NN. Two prediction methods, MLP-NN and ADMLP-NN (MLP-NN plus adaptive boosting), were evaluated by calculating correlation coefficient and root-mean-square-error between true and predicted signals. For predicting 500 ms ahead of prediction, average correlation coefficients were improved from 0.83 (MLP-NN method) to 0.89 (ADMLP-NN method). The average of root-mean-square-error (relative unit) for 500 ms ahead of prediction using ADMLP-NN were reduced by 27.9%, compared to those using MLP-NN. The preliminary results demonstrate that the ADMLP-NN respiratory prediction method is more accurate than the MLP-NN method and can improve the respiration prediction accuracy.
Performance analysis of channelized cellular systems with dynamic channel allocation

We present an analytical model to compute the blocking probability in channelized cellular systems with dynamic channel allocation. We model the channel occupancy in a cell by a two-dimensional (2D) Markov chain, which can be solved to obtain the blocking probability in each cell. We apply our analytical model to linear highway systems with and without lognormal shadowing and then extend it to 2D cellular systems with lognormal shadowing. We show that, for linear highway systems, distributed dynamic channel-allocation schemes perform similarly to the centralized dynamic channel-allocation schemes in terms of blocking probability. However, for 2D cellular systems, the improvement in the performance is significant and the reduction in the blocking probability in systems with distributed dynamic channel allocation is by almost one order of magnitude, when compared to that in systems with centralized dynamic channel allocation. In practice, our analysis of linear highway systems is applicable to Digital European Cordless Telephony (DECT) and that of 2D cellular systems is applicable to global systems for mobile communications (GSM).
Efficacy of prasugrel administration immediately after percutaneous coronary intervention in ST-elevation myocardial infarction

Summary Prasugrel, a potent thienopyridine, achieves stronger inhibition of platelet activation than clopidogrel. However, onset of inhibition is significantly delayed in patients with acute ST-elevation myocardial infarction (STEMI), as haemodynamic instability and morphine application seem to exhibit significant influence. Since rapid onset of effect was demonstrated in non-STEMI patients when prasugrel was administered only after percutaneous coronary intervention (PCI) without increasing cardiovascular event rates we assessed the efficacy of prasugrel loading immediately after PCI for STEMI instead of pre-loading before revascu-larisation. We investigated 50 consecutive patients with acute STEMI (mean age 56 ± 10 years) admitted for primary PCI. Prasugrel efficacy was assessed by platelet reactivity index (PRI; VASP assay) before, 1, 2, 4, 6, 12, and 24 hours following an oral loading dose of 60 mg immediately after PCI. High on-treatment platelet reactivity (HTPR) was de-fined as PRI>50 %. Prasugrel significantly and rapidly reduced platelet reactivity in acute STEMI patients (p<0.0001 at each time point vs control). Morphine application resulted in a significantly higher HTPR rate among patients having received morphine less than 1 hour before pra-sugrel loading (p<0.001) while concomitant metoclopramide (MCP) treatment did not significantly affect prasugrel efficacy. In conclusion, in contrast to previous reports describing a significant delay in onset of prasugrel-mediated P2Y12 inhibition in acute STEMI, we observed a rapid onset with low HTPR rates comparable to those observed in stable non-STEMI patients. Prasugrel administered directly after primary PCI might therefore be a useful therapeutic strategy in patients with STEMI to provide strong and effective P2Y12 inhibition.
Dynamic Optimization for Resource Allocation in Relay-Aided OFDMA Systems Under Multiservice

This paper investigates the dynamic resource allocation (RA) problem in cooperative OFDMA systems to maximize the average utility of all mobile stations (MSs) under different services. We propose a dynamic optimization framework for RA by considering three dynamic situations: time-varying fading channel, MSs' change of states, and relay stations (RSs)' change of states. Moreover, a dynamic RA algorithm based on discrete particle swarm optimization (DPSO) is proposed. The correlation between the adjacent frames is exploited to improve the performance of the dynamic RA algorithm. Simulation results show that the proposed dynamic algorithm achieves better performance at linear complexity, compared with the existing algorithms under different dynamic environments, while guaranteeing fairness to a proper level.
How Much Is Short-Term Glucose Prediction in Type 1 Diabetes Improved by Adding Insulin Delivery and Meal Content Information to CGM Data? A Proof-of-Concept Study

Background: In type 1 diabetes (T1D) management, short-term glucose prediction can allow to anticipate therapeutic decisions when hypo/hyperglycemia is imminent. Literature prediction methods mainly use past continuous glucose monitoring (CGM) readings. Sophisticated algorithms can use information on insulin delivered and meal carbohydrate (CHO) content. The quantification of how much insulin and CHO information improves glucose prediction is missing in the literature and is investigated, in an open-loop setting, in this proof-of-concept study. Methods: We adopted a versatile literature prediction methodology able to utilize a variety of inputs. We compared predictors that use (1) CGM; (2) CGM and insulin; (3) CGM and CHO; and (4) CGM, insulin, and CHO. Data of 15 T1D subjects in open-loop setup were used. Prediction was evaluated via absolute error and temporal gain focusing on meal/night periods. The relative importance of each individual input of the predictor was evaluated with a sensitivity analysis. Results: For a prediction horizon (PH) ≥ 30 minutes, insulin and CHO information improves prediction accuracy of 10% and double the temporal gain during the 2 hours following the meal. During the night the 4 methods did not give statistically different results. When PH ≥ 45 minutes, the influence of CHO information on prediction is 5-fold that of insulin. Conclusions: In an open-loop setting, with PH ≥ 30 minutes, information on CHO and insulin improves short-term glucose prediction in the 2-hour time window following a meal, but not during the night. CHO information improves prediction significantly more than insulin.
Voting and Peer Effects: Experimental Evidence from Mozambique

Voter education campaigns often aim to increase voter participation and political accountability. Randomized interventions were implemented nationwide during the 2009 Mozambican elections using leaflets, text messaging, and a free newspaper. We study the local peer effects triggered by the campaign. We investigate whether treatment effects are transmitted through social networks and geographical proximity at the village level. For individuals personally targeted by the campaign, we estimate the reinforcement effect of proximity to other individuals in our sample. For untargeted individuals, we estimate how the campaign diffuses as a function of proximity to others in the sample. We find evidence for both effects that are similar across treatments and proximity measures. The campaign raises the level of interest in the election through networks, in line with the average treatment effect. However, we find a negative network effect of the treatment on voter participation, implying that the positive effect of treatment on more central individuals is smaller. We interpret this result as consistent with free riding through pivotal reasoning and provide additional evidence to support this claim.
Returning to Work after Childbirth in Europe: Well-Being, Work-Life Balance, and the Interplay of Supervisor Support

Parents returning to work after the arrival of a new son or daughter is an important question for understanding the trajectory of people's lives and professional careers amid current debates about gender equality and work-life balance (WLB). Interestingly, current research concludes that general WLB practices at the workplace may be necessary in the specific case of women returning to work after childbirth because of the particular maternal and infant factors involved. However, WLB practices as a flexible arrangement may work against women because they may be viewed as a lack of organizational commitment. Therefore, research on this topic could benefit from considering supervisor support as a complement of such practices, but previous research has analyzed WLB and supervisor support separately and scarcely. To fill this gap in the literature, we use two sub-samples of 664 female employees and 749 male employees with children under the age of one from 27 European countries participating in the 6th European Working Conditions Survey (EWCS-2015) to study the impact of perceived WLB on European women's perceived well-being after childbirth, in contrast with previous literature. We also analyze the impact of perceived supervisor support (SS) and its interaction with perceived WLB on women's well-being after childbirth, and explore differences with men after childbirth, a collective underexplored by the literature. We find significant gender differences on the relative impact of WLB, SS, and their interaction on perceived job well-being. Our results have important implications for human resource practices in organizations. In particular, they suggest that gendered WLB practices should be encouraged, and stress the relevance of the human factor over human resource practices in addressing the difficulties that women returning to work face after childbirth.
ANTHRACIS AT ANTHRAX 1 CARCASSES 2 3 TITLE : Effects of experimental exclusion of scavengers from anthrax-infected 4 herbivore carcasses on Bacillus anthracis sporulation , survival and distribution 5 6

24 Scavenging of anthrax carcasses has long been hypothesized to play a critical role 25 in the production of the infectious spore-stage of Bacillus anthracis after host death, 26 though empirical studies assessing this are lacking. We compared B. anthracis spore 27 production, distribution and survival at naturally occurring anthrax herbivore carcasses 28 that were either experimentally caged to exclude vertebrate scavengers or unmanipulated. 29 We found no significant effect of scavengers on soil spore density (p > .05). Soil stained 30 by terminally hemorrhaged blood and by non-hemorrhagic fluids exhibited high levels of 31 B. anthracis spore contamination (ranging from 10-10 spores per gram) even in the 32 absence of vertebrate scavengers. At the majority of carcass sites, we also found that 33 spore density in samples taken from hemorrhagic-fluid stained soil continued to increase 34 for longer than 4 days after host death. We conclude that scavenging by vertebrates is not 35 a critical factor in the life cycle of B. anthracis and that anthrax control measures relying 36 on deterrence or exclusion of vertebrate scavengers to prevent sporulation are unlikely to 37 be effective. 38 39
A Phylogenetic, Biogeographic, and Taxonomic study of all Extant Species of Anolis (Squamata; Iguanidae)

&NA; Anolis lizards (anoles) are textbook study organisms in evolution and ecology. Although several topics in evolutionary biology have been elucidated by the study of anoles, progress in some areas has been hampered by limited phylogenetic information on this group. Here, we present a phylogenetic analysis of all 379 extant species of Anolis, with new phylogenetic data for 139 species including new DNA data for 101 species. We use the resulting estimates as a basis for defining anole clade names under the principles of phylogenetic nomenclature and to examine the biogeographic history of anoles. Our new taxonomic treatment achieves the supposed advantages of recent subdivisions of anoles that employed ranked Linnaean‐based nomenclature while avoiding the pitfalls of those approaches regarding artificial constraints imposed by ranks. Our biogeographic analyses demonstrate complexity in the dispersal history of anoles, including multiple crossings of the Isthmus of Panama, two invasions of the Caribbean, single invasions to Jamaica and Cuba, and a single evolutionary dispersal from the Caribbean to the mainland that resulted in substantial anole diversity. Our comprehensive phylogenetic estimate of anoles should prove useful for rigorous testing of many comparative evolutionary hypotheses. [Anoles; biogeography; lizards; Neotropics; phylogeny; taxonomy]
Two‐sample tests and one‐way MANOVA for multivariate biomarker data with nondetects

Testing whether the mean vector of a multivariate set of biomarkers differs between several populations is an increasingly common problem in medical research. Biomarker data is often left censored because some measurements fall below the laboratory's detection limit. We investigate how such censoring affects multivariate two‐sample and one‐way multivariate analysis of variance tests. Type I error rates, power and robustness to increasing censoring are studied, under both normality and non‐normality. Parametric tests are found to perform better than non‐parametric alternatives, indicating that the current recommendations for analysis of censored multivariate data may have to be revised. Copyright © 2016 John Wiley & Sons, Ltd.
Strength Characterization of Untreated and Cement-Treated Recycled Flex-Base Materials

Annually millions of tons of reclaimed asphalt pavement (RAP) was generated in the United States of America. The use of RAP and RAP-virgin aggregate mixes in pavement base and sub-base construction are now well acknowledged. Whereas, lack of laboratory and field evaluation is limiting the prospective use of RAP and other recycled material mixes, which may demonstrate more efficiency in terms of cost, depletion of resource, construction waste disposal, and environmental conservation. To illuminate this unfocused sphere, on the basis of laboratory experimental works, this paper describes the strength and stiffness response of different cement treated RAP-recycled crushed concrete aggregate (RCA) Grade 2 base material. Based on the test results of Grade 2, strength and elasticity modulus prediction models for different percentage of RAP were proposed in this study, regardless the amount of cement used. Also, two different design charts for compressive strength and modulus of elasticity were also prepared to facilitate the design of pavement construction in selecting the appropriate aggregate blend and cement content.
Age and sex differences in microRNAs expression during the process of thymus aging

The gender-biased thymus involution and the importance of microRNAs (miRNAs, miRs) expression in modulating the thymus development have been reported in many studies. However, how males and females differ in so many ways in thymus involution remains unclear. To address this question, we investigated the miRNA expression profiles in both untreated 3- and 12-month-old female and male mice thymuses. The results showed that 7 and 18 miRNAs were defined as the sex- and age-specific miRNAs, respectively. The expression of miR-181c-5p, miR-20b-5p, miR-98b-5p, miR-329-3p, miR-341-5p, and miR-2137 showed significant age-difference in mice thymus by quantitative polymerase chain reaction. High expression levels of miR-2137 were detected in mice thymic epithelial cells and gradually increased during the process of thymus aging. MiR-27b-3p and miR-378a-3p of the female-biased miRNAs were confirmed as the sex- and estrogen-responsive miRNAs in mice thymus in vivo. Their potential target genes and the pathway were identified by the online software. Possible regulation roles of sex- and age-specific miRNA expression during the process of thymus aging were discussed. Our results suggested that these miRNAs may be potential biomarkers for the study of sex- and age-specific thymus aging and involution.
Mulching impact on plant growth and production of rainfed fig orchards under drought conditions

Field experiments were conducted in Estahban Fig Research Station in Iran from 2009 to 2010 in order to investigate the effects of five different organic mulches (wheat straw, maize straw, apple wood chips, almond shell and sawdust) and four different inorganic mulches (transparent plastic, plastic netting, volcanic rock and small stone) on soil temperature at the depths of 5 and 15 cm, soil moisture at the depths of 15, 30, 45 and 60 cm, plant growth and yield of rainfed fig (Ficus carica cv. Sabz) orchards under drought conditions. Comparison of experimental results of trees on bare soil with trees on mulch-treated soil surfaces indicated that applying proper mulches had positive impacts on the number and width of leaves, length growth rate and diameter of shoots, and fruit quality. Considering the significantly positive results (P<0.05) and the availability of almond shell (AS) and wheat straw (WS) mulches in the region, these two materials are recommended to be used in Estahban fig orchards.
Tendon explant cultures to study the communication between adipose stem cells and native tendon niche

Poor clinical outcomes of tendon repair, together with limited regenerative capacity of the tissue, have triggered the search for alternative regenerative medicine strategies. Human adipose‐derived stem cells (hASCs) are being investigated as a promising cell source in contributing for tendon repopulation and reconstruction. However, the mechanisms involved in a potential beneficial effect in tendon regeneration are still to be uncovered. To gain further insights on the bi‐directional crosstalk occurring between stem cells and the native tendon niche, it was used an indirect (trans‐well) system for co‐culturing human tendon explants and hASCs. The maintenance of tissue architecture was studied up to 14 days by histological techniques. The secretion of MMPs was evaluated at day 3. The behavior of hASCs was assessed regarding cell elongation and extracellular matrix (ECM) production. The paracrine communication enhanced collagenolytic activity of MMPs in co‐cultures at day 3, in comparison to hASCs alone or tendon explants alone, suggesting that ECM remodeling is triggered early in culture. Moreover, hASCs were spontaneously more elongated in co‐cultures and the deposition of collagen type III and tenascin‐C by hASCs in co‐culture was observed at a lower extent after 7 days, in comparison to hASCs alone, being lately recovered at day 14. Overall, explant co‐cultures established herein may constitute a tool for replicating the first steps in tendon healing and help uncovering the bi‐directional communication occurring between hASCs and the native tendon niche.