Miracle-dz/UniFAR-FTUs huggingface dataset:
Hemagglutinin and neuraminidase genes of influenza B viruses circulating in Riyadh, Saudi Arabia during 2010–2011: Evolution and sequence analysis

Influenza viruses are known as continuing threats to human public health every year worldwide. Evolutionary dynamics of influenza B viruses in humans are in a unique progression having two lineages; B/Yam and B/Vic‐like viruses, which are circulating simultaneously worldwide. There is a considerable lack of data on influenza B viruses circulating in Saudi Arabia. During the winter‐spring season of 2010–2011, 80 nasopharyngeal aspirates were collected from hospitalized patients with flu‐like symptoms in Riyadh. Screening of samples by one‐step RT‐PCR identified three (3.8%) influenza B viruses. Sequencing of hemagglutinin (HA) and neuraminidase (NA) genes was performed to analyze influenza B viruses circulating in Riyadh as compared to the globally circulating strains. Several common and six unique amino acid substitutions were observed for both HA and NA genes of influenza B Saudi strains. Three unique substitutions (T182A, D196N, and K254R) were identified in HA gene of the B/Yam‐like Riyadh strains. In NA gene, a unique common substitution (D53G) was found in all Riyadh strains, while two unique substitutions (L38P, G233R) were recognized only in B/Vic‐like Riyadh strains. Riyadh strains were also found to contain N‐glycosylation site in HA gene of both B/Vic and B/Yam lineages at positions 197–199 (NET) and 196–198 (NNK/DNK), respectively. The significance of these mutations on the antigenicity of both lineages is discussed herein. The unique changes observed in HA and NA genes of influenza B Riyadh strains support strongly the need for continuous surveillance and monitoring of new evolving strains that might pose threat to the Saudi community. J. Med. Virol. 86:1003–1016, 2014. © 2013 Wiley Periodicals, Inc.
Control of system calls from outside of virtual machines

A virtual machine monitor (VMM) can isolate virtual machines (VMs) for trusted programs from VMs for untrusted ones. The security of VMs for untrusted programs can be enhanced by monitoring and controlling the behavior of the VMs with security systems running in a VM for trusted programs. However, programs running outside of a monitored VM usually obtain only low-level events and states such as interrupts and register values. Therefore, it is not straight-forward for the programs to understand the high-level behavior of an operating system in a monitored VM and to control resources managed by the operating system. In this paper, we propose a security system that controls the execution of processes from the outside of VMs. It consists of a modified VMM and a program running in a trusted VM. The system intercepts system calls invoked in a monitored VM and controls the execution according to a security policy. To fill the semantic gap between low-level events and high-level behavior, the system uses knowledge of the structure of a given operating system kernel. The user creates the knowledge with a tool when building an operating system. We implemented the system using Xen, and measured the overhead through experiments using microbenchmarks and a benchmark for the Apache web server.
Effects of the 633-nm laser on the behavior and morphology of primary fibroblast culture

We previously described the influence of low-level laser therapy (LLLT) on the primary fibroblast ATCC CRL1471 CCD-19SK passage 7 in culture, metabolic changes and statistical significance absorption of 3[H]Hydroxyproline after 2 irradiations (12 hour intervals) with Ar:DYE Laser, 633 nm wavelength, output power 38 mw, spot size 3.5 cm, power density 4 mw/cm2, energy density plus or minus 2 J/cm2. The aim of this work is to investigate, by using the same procedure, the behavior of the confluence monolayer fibroblasts culture when a central scratch of 0.4 - 1 mm and 2 irradiations is performed, by means of the study of the colony formation, haptotaxis (direction) and chemotaxis- chemokinesis (movement). The results indicate that all these phenomena appear sooner in the LLLT cultures than in non-treated cultures. Thus we can confirm that LLLT induces fibroblast biological effects.
The Effects of Cryogenic Treatment on the Thermal Conductivity of GRCop-84

The mechanical properties of many materials have been enhanced via cryogenic treatment, which is a cold temperature process performed after traditional heat treatment. In this research the effect of cryogenic treatment on GRCop-84 was examined. Cryogenically and non-cryogenically treated samples were tested identically to determine whether cryogenic treatment has a significant affect on the thermal conductivity of GRCop-84. Optical and electron microscopy were used to characterize the material properties. Cryogenic treatment includes a temper that appears to be responsible for the enhancements observed in GRCop-84.
Transition metal catalysis in macromolecular design

Metal-mediated polymerization is fast becoming an essential tool for the fine control of macromolecular architecture. Advanced Catalysis demonstrates how the field of transition metal-catalyzed polymer syntheses has moved beyond the simple use of single-site catalysts to new applications and "advanced" techniques of architectural control. This book defines and presents "next generation" techniques and trends for polymer architecture control for an immediate grasp on the future of this exciting field.
A Reappraisal of Women's Health Initiative Estrogen-Alone Trial: Long-Term Outcomes in Women 50–59 Years of Age

The Women's Health Initiative (WHI) Estrogen-Alone Trial randomized postmenopausal women, 50 to 79 years of age, with prior hysterectomy, to conjugated equine estrogens (CEE) or placebo with a 5.9-year median duration of CEE use. In 2013, the WHI published outcomes for additional extended follow-up. Reported here for the first time is an analysis of the number needed to treat with CEE rather than placebo for younger women (50–59 years) to prevent an adverse long-term outcome. For every 76 women randomized to CEE at 50–59 years, one less myocardial infarction occurred during the 13-year cumulative long-term follow-up. For every 37 women randomized to CEE at 50–59 years, one less woman experienced a global index endpoint (including coronary heart disease, invasive breast cancer, stroke, pulmonary embolism, colorectal cancer, hip fracture, and death) during the 13-year follow-up. Younger women (50–59 years), compared to older women, had more favorable cumulative long-term outcomes for MI and global index. Though a subgroup analysis is not an adequate basis for making primary prevention guideline recommendations, the WHI Estrogen-Alone Trial outcomes strongly suggest that a similar course of estrogen initiated at 50–59 years in postmenopausal women with prior hysterectomy results in significant long-term health benefit.
Human glutathione S-transferase polymorphisms associated with prostate cancer in the Brazilian population.

OBJECTIVE To evaluate the influence of polymorphisms in GSTA1, GSTM1, GSTT1, and GSTP1 in the risk of developing Prostate Cancer (PCa) in a population of Rio de Janeiro and compare the distribution of allele and genotype frequencies of the polymorphisms analyzed in the present study population with other regions in the country and different ethnic groups. MATERIALS AND METHODS We analyzed a sample of the Brazilian population, comprising 196 patients with PCa treated by the urology services of the Brazilian National Cancer Institute (INCA) and Mario Kroeff Hospital (HMK), and 208 male blood donors from the Clementino Fraga Filho Hospital, Federal University of Rio de Janeiro (UFRJ). The polymorphisms were determined in DNA, extracted from peripheral blood leucocytes using the Polymerase Chain Reaction and Restriction Fragment Length Polymorphism (PCR-RFLP). RESULTS Our results showed that the distribution of polymorphisms can vary significantly according to the Brazilian region and ethnic groups. The distribution of allele and genotype frequencies of the polymorphism GSTA1 was statistically different between cases and controls. Genotypes (A / B + B / B) were associated with protection (OR = 0.61, 95% CI = 0.40-0.92) for PCa in comparison to genotype A / A. CONCLUSION The distribution of genotype frequencies of the polymorphism GSTA1 was statistically different between the case and control groups (p = 0.023), and the presence of genotypes A / B and B / B suggests a protective role against the risk of PCa compared to genotype A / A. This is the first study that reports the genotypic frequency of this polymorphism and its association with PCa in a Brazilian population sample.
Skolem-type Difference Sets for Cycle Systems

Cyclic m-cycle systems of order v are constructed for all m 3, and all v 1(mod 2m). This result has been settled previously by several authors. In this paper, we provide a dierent solution, as a consequence of a more general result, which handles all cases using similar methods and which also allows us to prove necessary and sucient conditions for the existence of a cyclic m-cycle system of Kv F for all m 3, and all v 2(mod 2m).
High‐Q Microwave Dielectrics in the (Mg1−xCox)2TiO4 Ceramics

The microwave dielectric properties and the microstructures of (Mg1−xCox)2TiO4 ceramics prepared by the conventional solid-state route were investigated. Lattice parameters were also measured for specimens with different x. The formation of solid solution (Mg1−xCox)2TiO4 (x=0.02–0.1) was confirmed by the X-ray diffraction patterns, energy dispersive X-ray analysis, and the lattice parameters measured. By increasing x from 0 to 0.05, the Q×f of the specimen can be tremendously boosted from 150 000 GHz to a maximum of 286 000 GHz. A fine combination of microwave dielectric properties (ɛr∼15.7, Q×f∼286 000 GHz at 10.4 GHz, τf∼−52.5 ppm/°C) was achieved for (Mg0.95Co0.05)2TiO4 ceramics sintered at 1390°C for 4 h. Ilmenite-structured (Mg0.95Co0.05)TiO3 was detected as a second phase. The presence of the second phase would cause no significant variation in the dielectric properties of the specimen because it possesses compatible properties compared with that of the main phase. In addition, only a small deviation in the dielectric properties was monitored for specimens with x=0.04–0.05 at 1360°–1420°C. It not only provides a wide process window but also ensures an extremely reliable material proposed as a very promising dielectric for low-loss microwave and millimeter wave applications.
Attitude toward mouthguard utilization among North Indian school children

Objectives: The present study was designed to evaluate the attitude toward mouthguard utilization among 8—11-year-old athletically active schoolchildren in Ludhiana, Punjab, India. Materials and Methods: A cross-sectional survey was conducted among 2,000 schoolchildren aged 8—11 years of both the sexes, attending private schools in Ludhiana, Punjab, India. Children were questioned about their perceptions regarding the protective role of mouthguards and the reasons behind not using mouthguards. The data were summarized and analyzed using the statistical software Statistical Package for the Social Sciences (SPSS) version 18.0. Results: The prevalence of mouthguard use was found to be only 4.25%. However, 78% of the children believed that mouthguards could protect them from injuries. On the other hand, a majority of the children using mouthguards (74.11%) said they would be willing to play without a mouthguard. Of the 85 children using mouthguards, 76 reported problems. Children using dentist-made mouthguards reported it to be expensive while the children wearing boil and bite mouthguards reported several other problems such as difficulty in speaking and interference with breathing. Conclusion: It was deduced that the usage of mouthguards in this age group was inadequate and dentists need to be targeted for recommendation of properly fitting custom-made mouthguards to the parents of susceptible children so that a positive behavior toward mouthguards is reinforced.
An error driven approach to query segmentation

Query segmentation is the task of splitting a query into a sequence of non-overlapping segments that completely cover all tokens in the query. The majority of query segmentation methods are unsupervised. In this paper, we propose an error-driven approach to query segmentation (EDQS) with the help of search logs, which enables unsupervised training with guidance from the system-specific errors. In EDQS, we first detect the system's errors by examining the consistency among the segmentations of similar queries. Then, a model is trained by the detected errors to select the correct segmentation of a new query from the top-n outputs of the system. Our evaluation results show that EDQS can significantly boost the performance of state-of-the-art query segmentation methods on a publicly available data set.
Room-temperature fabrication of highly oriented ZnO nanoneedle arrays by anodization of zinc foil

Highly oriented ZnO nanoneedle arrays were electrochemically prepared by anodization of zinc foil in a freshly prepared zincate saturated aqueous solution at room temperature. Typically, the needles have a length of 550–650 nm with a tip diameter of 10–15 nm and a root diameter of 50–60 nm, and grow along their [001] direction. The crystal structure of the ZnO nanoneedles was confirmed by scanning and transmission electron micrographs, x-ray diffraction patterns and photoluminescence spectra.
Higher-order binding-time analysis

The partial evaluation process requires a binding-time analysis. Binding-time analysis seeks to determine which parts of a program's result is determined when some part of the input is known. Domain projections provide a very general way to encode a description of which parts of a data structure are static (known), and which are dynamic (not static). For first-order functional languages Launchbury [Lau91a] has developed an abstract interpretation technique for binding-time analysis in which the basic abstract value is a projection. Unfortunately this technique does not generalise easily to higher-order languages. This paper develops such a generalisation: a projection-based abstract interpretation suitable for higher-order binding-time analysis. Launchbury [Lau91b] has shown that binding-time analysis and strictness analysis are equivalent problems at first order, and for projection-based analyses have exactly the same safety condition. We argue that the same is true at higher order, and hence our development also leads to a higher-order projection-based strictness analysis. The principal limitation of our technique is the restriction to monomorphic typing.
Simulation Study of Cutting Forces, Stresses and Temperature during Nanometric Cutting of Single Crystal Silicon

Wear of diamond tool has always been a limiting factor in ductile regime machining of large size silicon components. In order to understand the tool wear phenomena, it is non-trivial to know the process outputs especially cutting forces, stresses and temperature during nanometric turning. In this paper, a realistic potential energy function has been deployed through molecular dynamic (MD) simulation, to simulate the process outputs of single diamond turning operation against single crystal silicon. The simulation result suggests that wear mechanism of diamond tool is fundamentally governed by these process parameters and thus critical.
High-level delay estimation for technology-independent logic equations

A simple model is presented for estimating the delay of a multi-level combinational logic description prior to a technology-dependent mapping phase. The model proposes that delay through a node varies logarithmically with both the complexity and the fanout of the node's logic equation. This is a consequence of the observation that in high performance circuits, both the fan-in and fan-out of cells are bounded by small numbers. Model parameters are derived for three different CMOS ASIC (application specific integrated circuit) libraries, and the authors show how the predicted delays compare with the actual delays for three different industrial designs in each library. This model can serve as a proxy for delay during technology-independent logic optimization, much as literal counts serve as proxies for area. <<ETX>>
Development of plasmonic substrates for biosensing

The transmission of normally incident light through arrays of subwavelength holes (nanoholes) in gold thin films is enhanced at the wavelengths that satisfy the surface plasmon resonance (SPR) condition. Our group has been active on the implementation of schemes for the application of this phenomenon for chemical sensing. For instance, we have shown that the interaction between adsorbates with nanoholes modified the SP resonance conditions, leading to a shift in the wavelength of maximum transmission. The output sensitivity of this substrate was found to be 400 nm RIU-1 (refractive index units), which is comparable to other grating-based surface plasmon resonance devices. The array of nanoholes was also integrated into a microfluidic system and the characteristics of the solution flow and detection systems were evaluated. In this work, we will concentrate on improving the efficiency of the nanohole arrays for applications in chemical in chemical sensing. Attempts to improve the sensitivity of the device will be discussed. In-hole sensing is suggested as an alternative to decrease the number of probe molecules, and enhance sensitivity. A biaxial sensing scheme will also be introduced. The biaxial scheme allows for polarization-modulation detection that can account for background fluctuations. A flow-through approach should lead to an optimized transport situation of the analytes to the immobilized species at the surface, which should significantly improve the time and sensitivity of the analysis. Finally, we will discuss the implementation of multiplexing detection using these arrays. Multiplexing detection in zero-order transmission is simpler to implement than the common multiplexing imaging from angle-resolved SPR.
Construction of an attenuated Salmonella enterica serovar Paratyphi A vaccine strain harboring defined mutations in htrA and yncD

The global epidemic features of enteric fever have changed greatly in recent years. The incidence of enteric fever caused by Salmonella enterica serovar Paratyphi A has progressively increased. In some areas of Asia, infections with S. Paratyphi A have exceeded those with S. Typhi, resulting in S. Paratyphi A becoming the main causative agent of enteric fever. However, two currently licensed typhoid vaccines do not confer adequate cross‐protection against S. Paratyphi A infection. Therefore, development of specific vaccines against enteric fever caused by S. Paratyphi A is urgently needed. In the present study, an attenuated strain was constructed by double deletion of the htrA and yncD genes in a wild‐type strain of S. Paratyphi A and its safety and immunogenicity assessed. In a mouse model, the 50% lethal dose of the double deletion mutant and the wild‐type strain were 3.0 × 108 CFU and 1.9 × 103 CFU, respectively, suggesting that the double deletion resulted in remarkably decreased bacterial virulence. Bacterial colonization of the double deletion mutant in the livers and spleens of infected mice was strikingly less than that of the wild‐type strain. A single nasal administration of the attenuated vaccine candidate elicited high concentrations of anti‐LPS and anti‐flagellin IgG in a mouse model and protected immunized mice against lethal challenge with the wild‐type strain. Thus, our findings suggest that the attenuated vaccine strain is a promising candidate worthy of further evaluation both as a human enteric fever vaccine and as a vaccine delivery vector for heterologous antigens.
A loose and sketchy approach in a mediated reality environment

In this paper, we present sketchy-ar-us, a modified, real-time version of the Loose and Sketchy algorithm used to render graphics in an AR environment. The primary challenge was to modify the original algorithm to produce a NPR effect at interactive frame rate. Our algorithm renders moderately complex scenes at multiple frames per second. Equipped with a handheld visor, visitors can see the real environment overlaid with virtual objects with both the real and virtual content rendered in a non-photorealistic style.
Grain size control in AA5083: thermomechanical processing and particle stimulated nucelation

Abstract : Superplastic forming is an emerging industrial technology that allows the production of complex shapes in metallic materials including aluminum. A critical characteristic of materials that are capable of sustaining superplastic forming is a fine grain size. In this study a commercial aluminum-magnesium-manganese alloy received in the as-cast condition was subjected to various thermomechanical processes intended to refine the grain size. Particle stimulated nucleation (PSN) theory was employed to develop the thermomechanical processes. These processes all involved initial homogenization and hot working. Subsequent annealing treatments were intended to control the size and size distribution of second phase particles, such as Al6Mn. Strain energy was introduced through cold rolling followed by recrystallization anneals. Samples were analyzed using orientation-imaging microscopy to examine the effect of processing variables on the recrystallized grain size.
Optimal Estimation of Multivariate ARMA Models

Autoregressive moving average (ARMA) models are a fundamental tool in timeseries analysis that offer intuitive modeling capability and efficient predictors. Unfortunately, the lack of globally optimal parameter estimation strategies for these models remains a problem:application studies often adopt the simpler autoregressive model that can be easily estimated by maximizing (a posteriori) likelihood. We develop a (regularized, imputed) maximum likelihood criterion that admits efficient global estimation via structured matrix norm optimization methods. An empirical evaluation demonstrates the benefits of globally optimal parameter estimation over local and moment matching approaches.
Performance Improvement of MFCs by Treatment of Carbon Cloth Anode with Ultrasonic or Spent Anolyte

In order to improve the power generation of microbial fuel cells (MFCs), carbon cloth anode was treated with ultrasonic or spent anolyte in this work. The maximum power density of a single-chamber air-cathode MFC was improved from 611.5 mW/m2 to 754.3 mW/m2 and 811.7 mW/m2, and the reactor start-up time was shortened by 7.3% and 22.7% respectively after treatments of the anode with ultrasonic and spent anolyte. Polarization tests reveal that the treated anodes have a smaller electrode polarization at high current densities than the control. MFCs with the treated anodes exhibited lower internal resistances than the untreated anode, which may arise from the enhanced substrate oxidation activity and extra-cellular electron transfer efficiency on these anodes. Results from this study indicated that treatment of anode with ultrasonic or spent anolyte was a simple and effective approach for improving the performance of MFCs.
Optoacoustic Tomography Using Accelerated Sparse Recovery and Coherence Factor Weighting

Sparse recovery algorithms have shown great potential to accurately reconstruct images using limited-view optoacoustic (photoacoustic) tomography data sets, but these are computationally expensive. In this paper, we propose an improvement of the fast converging Split Augmented Lagrangian Shrinkage Algorithm method based on least square QR inversion for improving the reconstruction speed. We further show image fidelity improvement when using a coherence factor to weight the reconstruction result. Phantom and in vivo measurements show that the accelerated Split Augmented Lagrangian Shrinkage Algorithm method with coherence factor weighting offers images with reduced artifacts and provides faster convergence compared with existing sparse recovery algorithms.