Miracle-dz/UniFAR-FTUs huggingface dataset:
Peer-to-peer video-on-demand in future internet

The advance in broadband access technology is improving at the proverbial lightning fast speed. As a consequence, in the near future, we can expect to have 40G/100G bandwidth and Ultra High Definition Television (UHDTV) with a resolution of 4320p in contrast with today's 1080p technologies. In this chapter, we describe the recent trends of multimedia, especially video distribution techniques. Also, we point out the urgent need for some of the current content distribution protocols to be reviewed and revised in order to address and accommodate the latest improvements in content distribution technologies. We highlight that the Peer-to-Peer (P2P) protocol is one of the most popular techniques for downloading data, viewing online channels, and/or watching Video-on-Demand (VoD) movies. The chapter specifically addresses the use of P2P protocol in streaming a large volume of VoD data, which is corresponding to the future trends of video quality. Directions are presented toward how to improve P2P based VoD schemes in an effective fashion.
Mutation Scanning Using MUT-MAP, a High-Throughput, Microfluidic Chip-Based, Multi-Analyte Panel

Targeted anticancer therapies rely on the identification of patient subgroups most likely to respond to treatment. Predictive biomarkers play a key role in patient selection, while diagnostic and prognostic biomarkers expand our understanding of tumor biology, suggest treatment combinations, and facilitate discovery of novel drug targets. We have developed a high-throughput microfluidics method for mutation detection (MUT-MAP, mutation multi-analyte panel) based on TaqMan or allele-specific PCR (AS-PCR) assays. We analyzed a set of 71 mutations across six genes of therapeutic interest. The six-gene mutation panel was designed to detect the most common mutations in the EGFR, KRAS, PIK3CA, NRAS, BRAF, and AKT1 oncogenes. The DNA was preamplified using custom-designed primer sets before the TaqMan/AS-PCR assays were carried out using the Biomark microfluidics system (Fluidigm; South San Francisco, CA). A cross-reactivity analysis enabled the generation of a robust automated mutation-calling algorithm which was then validated in a series of 51 cell lines and 33 FFPE clinical samples. All detected mutations were confirmed by other means. Sample input titrations confirmed the assay sensitivity with as little as 2 ng gDNA, and demonstrated excellent inter- and intra-chip reproducibility. Parallel analysis of 92 clinical trial samples was carried out using 2–100 ng genomic DNA (gDNA), allowing the simultaneous detection of multiple mutations. DNA prepared from both fresh frozen and formalin-fixed, paraffin-embedded (FFPE) samples were used, and the analysis was routinely completed in 2–3 days: traditional assays require 0.5–1 µg high-quality DNA, and take significantly longer to analyze. This assay can detect a wide range of mutations in therapeutically relevant genes from very small amounts of sample DNA. As such, the mutation assay developed is a valuable tool for high-throughput biomarker discovery and validation in personalized medicine and cancer drug development.
Aging Does Not Affect Axon Initial Segment Structure and Somatic Localization of Tau Protein in Hippocampal Neurons of Fischer 344 Rats

Abstract Little is known about the specific contributions of aging to the neuron dysfunction and death in Alzheimer’s disease (AD). AD is characterized by the pathological accumulation of abnormal tau (a microtubule-associated protein), and the mislocalization of tau from the axon to the somatodendritic compartment is thought to play an important role in disease pathogenesis. The axon initial segment (AIS) is thought to play a role in the selective localization of tau in the axonal compartment. Thus, disruption in the AIS barrier may allow tau to diffuse freely back into the somatodendritic compartment and potentially lead to neurotoxicity. Here, we analyzed AISs using stereological methods and protein immunoblotting, and the localization of tau was assessed with immunofluorescence optical density measurements and protein immunoblotting. None of the outcome measurements assessed, including AIS structure, AIS protein levels, the distribution of tau in neurons of the hippocampus (HP), and total tau or phospho-tau protein levels were different in young, middle-, and old-age Fischer 344 rats. The outcome measurements assessed, including AIS structure, AIS protein levels, the distribution of tau in neurons of the HP, and total tau or phospho-tau protein levels were not different in young, middle-, and old-age Fischer 344 rats, with the exception of a small reduction in AIS volume and diameter in the CA2 region of aged animals. These data suggest that aging largely has no effect on these properties of the AIS or tau distribution, and thus, may not contribute directly to tau mislocalization.
Small Interfering RNA Pathway Modulates Initial Viral Infection in Midgut Epithelium of Insect after Ingestion of Virus

ABSTRACT Numerous viruses are transmitted in a persistent manner by insect vectors. Persistent viruses establish their initial infection in the midgut epithelium, from where they disseminate to the midgut visceral muscles. Although propagation of viruses in insect vectors can be controlled by the small interfering RNA (siRNA) antiviral pathway, whether the siRNA pathway can control viral dissemination from the midgut epithelium is unknown. Infection by a rice virus (Southern rice black streaked dwarf virus [SRBSDV]) of its incompetent vector (the small brown planthopper [SBPH]) is restricted to the midgut epithelium. Here, we show that the siRNA pathway is triggered by SRBSDV infection in continuously cultured cells derived from the SBPH and in the midgut of the intact insect. Knockdown of the expression of the core component Dicer-2 of the siRNA pathway by RNA interference strongly increased the ability of SRBSDV to propagate in continuously cultured SBPH cells and in the midgut epithelium, allowing viral titers in the midgut epithelium to reach the threshold (1.99 × 109 copies of the SRBSDV P10 gene/μg of midgut RNA) needed for viral dissemination into the SBPH midgut muscles. Our results thus represent the first elucidation of the threshold for viral dissemination from the insect midgut epithelium. Silencing of Dicer-2 further facilitated the transmission of SRBSDV into rice plants by SBPHs. Taken together, our results reveal the new finding that the siRNA pathway can control the initial infection of the insect midgut epithelium by a virus, which finally affects the competence of the virus's vector. IMPORTANCE Many viral pathogens that cause significant global health and agricultural problems are transmitted via insect vectors. The first bottleneck in viral infection, the midgut epithelium, is a principal determinant of the ability of an insect species to transmit a virus. Southern rice black streaked dwarf virus (SRBSDV) is restricted exclusively to the midgut epithelium of an incompetent vector, the small brown planthopper (SBPH). Here, we show that silencing of the core component Dicer-2 of the small interfering RNA (siRNA) pathway increases viral titers in the midgut epithelium past the threshold (1.99 × 109 copies of the SRBSDV P10 gene/μg of midgut RNA) for viral dissemination into the midgut muscles and then into the salivary glands, allowing the SBPH to become a competent vector of SRBSDV. This result is the first evidence that the siRNA antiviral pathway has a direct role in the control of viral dissemination from the midgut epithelium and that it affects the competence of the virus's vector.
Pore structure of cement pastes through NAD and MIP analysis

Two cement pastes (water to cement ratio, w/c = 0·5, 0·3) were investigated through mercury intrusion porosimetry (MIP) and nitrogen adsorption/desorption (NAD) methods at different hardening ages. The pore structure is characterised by specific surface area, pore volume and pore size distribution. The results show that: (a) the pore structure has strong scale dependence and NAD–MIP joint measurement helps to identify the different pore structure patterns; (b) MIP total pore volume captures the global process of the hydrates filling process with curing age, the mesopore (2–70 nm) volume is dominated by hydrates filling for w/c = 0·5 but countered by high-density calcium-silicate-hydrate growth for w/c = 0·3; (c) specific surface area is sensitive to calcium-silicate-hydrate growth and specific surface area values are likely to confirm that high w/c (0·5) favours low-density calcium-silicate-hydrate growth whereas low w/c (0·3) facilitates high-density calcium-silicate-hydrate formation.
Numerical streamline path planning based on log-space harmonic potential function: A simulation study

This paper presents a simulation validation of streamline-based path planning by log-space harmonic potential function method proposed in [1] for the numerical solution of a boundary value problem for Laplace equation associated with Dirichlet or Neumann boundary conditions in a closed region. Log-space iterative method resolves the precision problem of numerically computing the gradient of harmonic potential, or the streamline path to be followed. We begin with properties of harmonic functions and then summarize three basic numerical methods of Jacobi iteration, Gauss-Seidel iteration and SOR iteration used to solve the linear equations resulting from finite difference approximation to Laplace equation. For real-time mobile robot navigation, the iterative method is an anytime smooth path planning method that allows parallel implementation on GPU and incorporations of acceleration techniques and ordering/reordering of grids. A specific scheme implemented in this paper is a parallelized log-space Jacobi method to provide anytime and numerical-precision valid gradient of harmonic potential field for smooth path generation. Concrete numerical examples of smooth path planning in an experiment environment are presented to compare the paths generated via Laplace equation with Dirichlet or Neumann boundary conditions using log-space Jacobi method and the path generated by analytical potentials to show the advantages of iteration methods.
Identification of common immunodominant antigens of Eimeria tenella, Eimeria acervulina and Eimeria maxima by immunoproteomic analysis

Clinical chicken coccidiosis is mostly caused by simultaneous infection of several Eimeria species, and host immunity against Eimeria is species-specific. It is urgent to identify common immunodominant antigen of Eimeria for developing multivalent anticoccidial vaccines. In this study, sporozoite proteins of Eimeria tenella, Eimeria acervulina and Eimeria maxima were analyzed by two-dimensional electrophoresis (2DE). Western bot analysis was performed on the yielded 2DE gel using antisera of E. tenella E. acervulina and E. maxima respectively. Next, the detected immunodominant spots were identified by comparing the data from MALDI-TOF-MS/MS with available databases. Finally, Eimeria common antigens were identified by comparing amino acid sequence between the three Eimeria species. The results showed that analysis by 2DE of sporozoite proteins detected 629, 626 and 632 protein spots from E. tenella, E. acervulina and E. maxima respectively. Western bot analysis revealed 50 (E. tenella), 64 (E. acervulina) and 57 (E. maxima) immunodominant spots from the sporozoite 2DE gels of the three Eimeria species. The immunodominant spots were identified as 33, 27 and 25 immunodominant antigens of E. tenella, E. acervulina and E. maxima respectively. Fifty-four immunodominant proteins were identified as 18 ortholog proteins among the three Eimeria species. Finally, 5 of the 18 ortholog proteins were identified as common immunodominant antigens including elongation factor 2 (EF-2), 14-3-3 protein, ubiquitin-conjugating enzyme domain-containing protein (UCE) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH). In conclusion, our results not only provide Eimeria sporozoite immunodominant antigen map and additional immunodominant antigens, but also common immunodominant antigens for developing multivalent anticoccidial vaccines.
Patterns of Specificity of the Pathogen Escovopsis across the Fungus-Growing Ant Symbiosis

Parasites evolve within complex abiotic and biotic environments. Because of this, it is often challenging to ascertain how evolutionary and ecological processes together affect parasite specialization. Here, we use the fungus-growing ant system, which consists of ancient, likely coevolved, complex communities, to explore the ecological and evolutionary forces shaping host-parasite specificity. We use a comparative phylogenetic framework to determine whether patterns of specificity between the fungal parasite Escovopsis and its host fungi at fine phylogenetic scales reflect patterns of specificity at broader phylogenetic levels. In other words, we ask whether parasite specificity across broad host phylogenetic relationships is maintained by specificity toward more closely related hosts. We couple this exploration with manipulations of the community context within which host-parasite interactions are taking place to evaluate how community complexity alters parasite specificity. Regardless of host community complexity, parasites displayed a consistent pattern of specialization on native hosts, that is, those that they are found attacking in nature, with the potential for occasional switching to hosts distantly related to their native hosts. These results suggest that, even within a complex community context, pairwise host and parasite adaptation and coadaptation can be the primary drivers of the evolution and maintenance of parasite specificity.
Collaborative Filtering with Graph-Based Implicit Feedback

Introducing consumed items as users' implicit feedback in matrix factorization (MF) method, SVD++ is one of the most effective collaborative filtering methods for personalized recommender systems. However, powerful SVD++ has two limitations: (i) only the user-side implicit feedback is utilized instead of item-side implicit feedback which can also enrich item representations; (ii) in SVD++, the interacted items are equally weighted when combining the implicit feedback, which cannot reflect user's true preferences accurately. To tackle the above limitations, this paper proposes Graph-based collaborative filtering (GCF) model, Weighted Graph-based collaborative filtering (W-GCF) model and Attentive Graph-based collaborative filtering (A-GCF) model, which (i). generalize the implicit feedback to item side based on the user-item bipartite graph; (ii). flexibly learn the weights of individuals in the implicit feedback to improve the model's capacity. Comprehensive experiments show that the proposed models outperform state-of-the-art models. For sparse implicit feedback scenarios, additional improvement is further achieved by leveraging the two-step implicit feedback information.
Within- and Among-Population Variation in Chytridiomycosis-Induced Mortality in the Toad Alytes obstetricans

Background Chytridiomycosis is a fungal disease linked to local and global extinctions of amphibians. Susceptibility to chytridiomycosis varies greatly between amphibian species, but little is known about between- and within-population variability. However, this kind of variability is the basis for the evolution of tolerance and resistance evolution to disease. Methodology/Principal Findings In a common garden experiment, we measured mortality after metamorphosis of Alytes obstetricans naturally infected with Batrachochytrium dendrobatidis. Mortality rates differed significantly among populations and ranged from 27 to 90%. Within populations, mortality strongly depended on mass at and time through metamorphosis. Conclusions/Significance Although we cannot rule out that the differences observed resulted from differences in skin microbiota, different pathogen strains or environmental effects experienced by the host or the pathogen prior to the start of the experiment, we argue that genetic differences between populations are a likely source of at least part of this variation. To our knowledge, this is the first study showing differences in survival between and within populations under constant laboratory conditions. Assuming that some of this intraspecific variation has a genetic basis, this may suggest that there is the potential for the evolution of resistance or tolerance, which might allow population persistence.
Effects of Androgen on Androgen Receptor Expression in Rat Testicular and Epididymal Cells: A Quantitative Immunohistochemical Study1

Abstract Androgen is essential for maintenance of spermatogenesis in the testis and for maturation of spermatozoa in the epididymis. The effects of androgen are mediated through its receptor (AR), the levels of which are, in turn, regulated by androgen. Previous studies have shown that AR concentrations in Leydig and Sertoli cells are differentially regulated during development. The aim of the present study was to determine if cell-type-specific regulation of AR by androgen occurs in testicular and epididymal cells during adulthood. Adult male rats were treated with the LHRH-antagonist Azaline B (100 g/day) by osmotic pump for 1, 2, 3, 4, or 8 wk to suppress endogenous androgen, with identical numbers of intact control animals at each time period. An androgen replacement group was simultaneously treated with the antagonist and a synthetic androgen, 7α-methyl-19-nortestosterone (MENT), during the final 4 wk of the experiment. Levels of nuclear AR protein in specific cell types were quantified by immunohistochemistry in conjunction with computer-assisted image analysis. Levels of AR in testicular cells declined sharply after treatment with the LHRH antagonist. In Sertoli cells, nuclear AR levels decreased to 8% of control (P < 0.01) after 4 wk treatment; and to 12% and 17% of control (P < 0.01) in Leydig and myoid cells, respectively. Androgen replacement resulted in complete recovery of nuclear AR levels in Sertoli cells (93%, P > 0.05) but in only partial recovery in myoid (69%, P < 0.01) and Leydig cells (56%, P < 0.01). In the epididymis, tubular epithelial cells and stromal cells differed in their responses to the LHRH antagonist. After 1 wk, nuclear AR levels in caput stromal cells decreased dramatically to 34% of control (P < 0.01) and in cauda stromal cells to 43% (P < 0.01). In contrast, the decline of AR levels in epididymal epithelial cells was not as dramatic as that in stromal cells. After 1 wk, the decline in the caput and cauda was to 87% and 76% of control, respectively. After 8 wk, nuclear AR levels in stromal cells further declined to 1.1% in caput and 1.4% in cauda, whereas in the epithelial cells, a smaller decline in nuclear AR was noted (to 30% in the caput and 45% in the cauda). After androgen replacement with MENT, nuclear AR levels recovered to more than 90% of control in both epididymal cell types. These results indicate that AR levels in the nuclei of adult Sertoli cells depend mainly on the level of androgen, whereas in the adult Leydig and myoid cells, the androgen dependency is more limited. The results also indicate that in the epididymis, stromal cells are more sensitive than epithelial cells to the regulation of AR levels by androgen.
Soil Surface Water Content Estimation by Full-Waveform GPR Signal Inversion in the Presence of Thin Layers

We analyzed the effect of shallow thin layers on the estimation of soil surface water content using full-waveform inversion of off-ground ground penetrating radar (GPR) data. Strong dielectric contrasts are expected to occur under fast wetting or drying weather conditions, thereby leading to constructive and destructive interferences with respect to surface reflection. First, synthetic GPR data were generated and subsequently inverted considering different thin-layer model configurations. The resulting inversion errors when neglecting the thin layer were quantified, and then, the possibility to reconstruct these layers was investigated. Second, laboratory experiments reproducing some of the numerical experiment configurations were conducted to assess the stability of the inverse solution with respect to actual measurement and modeling errors. Results showed that neglecting shallow thin layers may lead to significant errors on the estimation of soil surface water content(¿¿>0.03 m3/m3), depending on the contrast. Accounting for these layers in the inversion process strongly improved the results, although some optimization issues were encountered. In the laboratory, the proposed full-waveform method permitted to reconstruct thin layers with a high resolution up to 2 cm and to retrieve the soil surface water content with an rmse less than 0.02 m3/m3, owing to the full-waveform inverse modeling. These results suggest that the proposed GPR approach is promising for field-scale mapping of soil surface water content of nondispersive soils with low electrical conductivity and for instances when soil layering is encountered.
The Spatial–Temporal Perspective: The Study of the Propagation of Modern Social Worms

Due to the critical security threats imposed by social worms, such as Twitter and Facebook, modeling and simulation study of the propagation dynamics of social worms is essential to predict their potential for damage and to understand the propagation characteristics. Modern social worms exhibit one new feature, reinfection-notification. It indicates that malicious messages are sent by neighbors whenever any susceptible or infected recipients open the malicious attachments, and a user will get reminders when new messages come to a social account. Meanwhile, there are two critical problems: dynamic host usage and temporal message processing. First, from a spatial perspective, previous models have not taken into account that public hosts in different locations are shared by several users arising from human mobility, namely, dynamic host usage. Second, from a temporal perspective, the problem of temporal message processing results from the improper assumption that during this period of message checking, unread messages all are read by default, or under the condition that some parts of messages have been read, but the rest of unread messages are no longer processed afterward. To address these problems, we present a novel social worm simulation model in this paper, which adopts “social network-based sharing” and “sorting and attenuation” methods. We perform comprehensive theoretical analyses and experimental evaluation to validate our simulation model. The results show that our model is more suitable for modeling the complicated propagation behaviors of modern social worms in hierarchical networks.
A Markov model of safety message broadcasting for vehicular networks

Some safety applications in vehicular ad-hoc networks (VANETs) require the dissemination of safety information to all nearby vehicles in a broadcast fashion. Each vehicle should periodically broadcast its state information up to a safety range around itself to avoid likely collisions. This causes a congested channel in dense areas especially in multi-lane roads and leads to significant performance reduction. In this paper, using a Markov model, we analytically derive the percentage of channel utilization as well as the packet transmission rate based on the contention window size, carrier sense range, density of vehicles and packet generation rate. Unlike the previous models, the devised Markov model enables us to derive the probability of packet obsolescence before broadcasting from the probability mass function of service delay. Also, we can evaluate the performance of tracking applications for large and small contention window sizes. The extensive simulations carried out confirm the accuracy of our model.