Rice ragged stunt oryzavirus genome segment S4 could encode an RNA dependent RNA polymerase and a second protein of unknown function

The complete nucleotide sequence of genome segment S4 of rice ragged stunt oryzavirus (RRSV, Thai-isolate) was determined. The 3823 bp sequence contains two large open reading frames (ORFs). ORF1, spanning nucleotides 12 to 3776, is capable of encoding a protein of M(r) 141,380 (P4a). The P4a amino acid sequence predicted from the nucleotide sequence contains sequence motifs conserved in RNA-dependent RNA polymerases (RDRPs). When compared for evolutionary relationships with RDRPs of other reoviruses using the amino acid sequences around the conserved GDD motif, P4a was shown to be more related to Nilaparvata lugens reovirus and reovirus serotype 3 than to rice dwarf phytoreovirus, bovine rotavirus or bluetongue virus. The ORF2, spanning nucleotides 491 to 1468, is out of frame with ORF1 and is capable of encoding a protein of 36, 920 (P4b). Coupled in vitro transcription-translation from cloned ORF2 in wheat germ extract confirmed the existence of ORF2 but in vivo production and possible function of P4b is yet to be determined.

Combining recommender and reputation systems to produce better online advice

Although recommender systems and reputation systems have quite different theoretical and technical bases, both types of systems have the purpose of providing advice for decision making in e-commerce and online service environments. The similarity in purpose makes it natural to integrate both types of systems in order to produce better online advice, but their difference in theory and implementation makes the integration challenging. In this paper, we propose to use mappings to subjective opinions from values produced by recommender systems as well as from scores produced by reputation systems, and to combine the resulting opinions within the framework of subjective logic.

A simple method for EPID-based in vivo dosimetry for radiotherapy treatments of head-and-neck cancers

This study used a homogeneous water-equivalent model of an electronic portal imaging device (EPID), contoured as a structure in a radiotherapy treatment plan, to produce reference dose images for comparison with in vivo EPID dosimetry images. Head and neck treatments were chosen as the focus of this study, due to the heterogeneous anatomies involved and the consequent difficulty of rapidly obtaining reliable reference dose images by other means. A phantom approximating the size and heterogeneity of a typical neck, with a maximum radiological thickness of 8.5 cm, was constructed for use in this study. This phantom was CT scanned and a simple treatment including five square test fields and one off-axis IMRT field was planned. In order to allow the treatment planning system to calculate dose in a model EPID positioned a distance downstream from the phantom to achieve a source-to-detector distance (SDD) of 150 cm, the CT images were padded with air and the phantom’s “body” contour was extended to encompass the EPID contour. Comparison of dose images obtained from treatment planning calculations and experimental irradiations showed good agreement, with more than 90% of points in all fields passing a gamma evaluation, at γ (3%, 3mm )Similar agreement was achieved when the phantom was over-written with air in the treatment plan and removed from the experimental beam, suggesting that water EPID model at 150 cm SDD is capable of providing accurate reference images for comparison with clinical IMRT treatment images, for patient anatomies with radiological thicknesses ranging from 0 up to approximately 9 cm. This methodology therefore has the potential to be used for in vivo dosimetry during treatments to tissues in the neck as well as the oral and nasal cavities, in the head-and-neck region.

Study on dynamic system optimum assignment to establish marginal time equilibrium

Several analytical methods for Dynamic System Optimum (DSO) assignment have been proposed but they are basically classified into two kinds. This chapter attempts to establish DSO by equilbrating the path dynamic marginal time (DMT). The authors analyze the path DMT for a single path with tandem bottlenecks and showed that the path DMT is not the simple summation of DMT associated with each bottleneck along the path. Next, the authors examined the DMT of several paths passing through a common bottleneck. It is shown that the externality at the bottleneck is shared by the paths in proportion to their demand from the current time until the queue vanishes. This share of the externality is caused by the departure rate shift under first in first out (FIFO) and the externality propagates to the downstream bottlenecks. However, the externalities propagates to the downstream are calculated out if downstream bottlenecks exist. Therefore, the authors concluded that the path DMT can be evaluated without considering the propagation of the externalities, but just as in the evaluation of the path DMT for a single path passing through a series of bottlenecks between the origin and destination. Based on the DMT analysis, the authors finally proposed a heuristic solution algorithm and verified it by comparing the numerical solution with the analytical one.

Molecular network analysis using reverse phase protein microarrays for patient tailored therapy.

The practice of medicine has always aimed at individualized treatment of disease. The relationship between patient and physician has always been a personal one, and the physician's choice of treatment has been intended to be the best fit for the patient's needs. The necessary pooling/grouping of disease families and their assignment to a number of drugs or treatment methods has, consequently, led to an increase in the number of effective therapies. However, given the heterogeneity of most human diseases, and cancer specifically, it is currently impossible for the treating clinician to effectively predict a patient's response and outcome based on current technologies, much less the idiosyncratic resistances and adverse effects associated with the limited therapeutic options.

Sonochemical nanoplungers : crystalline gold nanowires by cavitational extrusion through nanoporous alumina

Rapid, simple, catalyst-free, room-temperature sonochemical fabrication of long (up to 30 mm), ultra-thin (about 20 nm), crystalline gold nanowires on nanoporous anodic alumina membranes is reported. It is demonstrated that the nanowires nucleate and grow inside the nanosized pores and then form a dense network on the bottom side of the membrane. A growth mechanism is proposed based on the formation of through channels in the Al2O3 membrane by sonochemical etching, followed by nanowire nucleation in the channels and their further extrusion out of the pores by acoustic cavitation. This process can be used for the fabrication of metal nanowires with highly controllable diameter and density, suitable for numerous applications such as nanoelectronic, nanofluidic, and optoelectronic components and devices.

Interface of graphane with copper : a van der Waals density-functional study

Various forms of hydrogenated graphene have been produced to date by several groups, while the synthesis of pure graphane has not been achieved yet. The study of the interface between graphane, in all its possible hydrogenation configurations, and catalyst metal surfaces can be pivotal to assess the feasibility of direct CVD growth methods for this material. We investigated the adhesion of graphane to a Cu(111) surface by adopting the vdW-DF2-C09 exchange-correlation functional, which is able to describe dispersion forces. The results are further compared with the PBE and the LDA exchange-correlation functionals. We calculated the most stable geometrical configurations of the slab/graphane interface and evaluated how graphane's geometrical parameters are modified. We show that dispersion forces play an important role in the slab/graphane adhesion. Band structure calculations demonstrated that in the presence of the interaction with copper, the band gap of graphane is not only preserved, but also enlarged, and this increase can be attributed to the electronic charge accumulated at the interface. We calculated a substantial energy barrier at the interface, suggesting that CVD graphane films might act as reliable and stable insulating thin coatings, or also be used to form compound layers in conjunction with metals and semiconductors.

Cyclododecane as support material for clean and facile transfer of large-area few-layer graphene

The transfer of chemical vapor deposited graphene is a crucial process, which can affect the quality of the transferred films and compromise their application in devices. Finding a robust and intrinsically clean material capable of easing the transfer of graphene without interfering with its properties remains a challenge. We here propose the use of an organic compound, cyclododecane, as a transfer material. This material can be easily spin coated on graphene and assist the transfer, leaving no residues and requiring no further removal processes. The effectiveness of this transfer method for few-layer graphene on a large area was evaluated and confirmed by microscopy, Raman spectroscopy, x-ray photoemission spectroscopy, and four-point probe measurements. Schottky-barrier solar cells with few-layer graphene were fabricated on silicon wafers by using the cyclododecane transfer method and outperformed reference cells made by standard methods.

Rapid and highly efficient growth of graphene on copper by chemical vapor deposition of ethanol

The growth of graphene by chemical vapor deposition on metal foils is a promising technique to deliver large-area films with high electron mobility. Nowadays, the chemical vapor deposition of hydrocarbons on copper is the most investigated synthesis method, although many other carbon precursors and metal substrates are used too. Among these, ethanol is a safe and inexpensive precursor that seems to offer favorable synthesis kinetics. We explored the growth of graphene on copper from ethanol, focusing on processes of short duration (up to one min). We investigated the produced films by electron microscopy, Raman and X-ray photoemission spectroscopy. A graphene film with high crystalline quality was found to cover the entire copper catalyst substrate in just 20 s, making ethanol appear as a more efficient carbon feedstock than methane and other commonly used precursors.

Physiological and biomechanical responses to walking underwater on a non-motorised treadmill: Effects of different exercise intensities and depths in middle-aged healthy women

Non-motorised underwater treadmills are commonly used in fitness activities. However, no studies have examined physiological and biomechanical responses of walking on non-motorised treadmills at different intensities and depths. Fifteen middle-aged healthy women underwent two underwater walking tests at two different depths, immersed either up to the xiphoid process (deep water) or the iliac crest (shallow water), at 100, 110, 120, 130 step-per-minute (spm). Oxygen consumption (VO2), heart rate (HR), blood lactate concentration, perceived exertion and step length were determined. Compared to deep water, walking in shallow water exhibited, at all intensities, significantly higher VO2 (+13.5%, on average) and HR (+8.1%, on average) responses. Water depth did not influence lactate concentration, whereas perceived exertion was higher in shallow compared to deep water, solely at 120 (+40%) and 130 (+39.4%) spm. Average step length was reduced as the intensity increased (from 100 to 130 spm), irrespective of water depth. Expressed as a percentage of maximum, average VO2 and HR were: 64–76% of peak VO2 and 71–90% of maximum HR, respectively at both water depths. Accordingly, this form of exercise can be included in the “vigorous” range of exercise intensity, at any of the step frequencies used in this study.

Fast growth of polycrystalline graphene by chemical vapor deposition of ethanol on copper

High conductive graphene films can be grown on metal foils by chemical vapor deposition (CVD). We here analyzed the use of ethanol, an economic precursor, which results also safer than commonly-used methane. A comprehensive range of process parameters were explored in order to obtain graphene films with optimal characteristics in view of their use in optoelectronics and photovoltaics. Commercially-available and electro-polished copper foils were used as substrates. By finely tuning the CVD conditions, we obtained few-layer (2-4) graphene films with good conductivity (-500 Ohm/sq) and optical transmittance around 92-94% at 550 nm on unpolished copper foils. The growth on electro-polished copper provides instead predominantly mono-layer films with lower conductivity (>1000 Ohm/sq) and with a transmittance of 97.4% at 550 nm. As for the device properties, graphene with optimal properties as transparent conductive film were produced by CVD on standard copper with specific process conditions.

Brief report: Intestinal dysbiosis in ankylosing spondylitis

Objective Ankylosing spondylitis (AS) is a common, highly heritable immune-mediated arthropathy that occurs in genetically susceptible individuals exposed to an unknown but likely ubiquitous environmental trigger. There is a close relationship between the gut and spondyloarthritis, as exemplified in patients with reactive arthritis, in whom a typically self-limiting arthropathy follows either a gastrointestinal or urogenital infection. Microbial involvement in AS has been suggested; however, no definitive link has been established. The aim of this study was to determine whether the gut in patients with AS carries a distinct microbial signature compared with that in the gut of healthy control subjects. Methods Microbial profiles for terminal ileum biopsy specimens obtained from patients with recent-onset tumor necrosis factor antagonist-naive AS and from healthy control subjects were generated using culture-independent 16S ribosomal RNA gene sequencing and analysis techniques. Results Our results showed that the terminal ileum microbial communities in patients with AS differ significantly (P < 0.001) from those in healthy control subjects, driven by a higher abundance of 5 families of bacteria (Lachnospiraceae [P = 0.001], Ruminococcaceae [P = 0.012], Rikenellaceae [P = 0.004], Porphyromonadaceae [P = 0.001], and Bacteroidaceae [P = 0.001]) and a decrease in the abundance of 2 families of bacteria (Veillonellaceae [P = 0.01] and Prevotellaceae [P = 0.004]). Conclusion We show evidence for a discrete microbial signature in the terminal ileum of patients with AS compared with healthy control subjects. The microbial composition was demonstrated to correlate with disease status, and greater differences were observed between disease groups than within disease groups. These results are consistent with the hypothesis that genes associated with AS act, at least in part, through effects on the gut microbiome.

The hardness of revising defeasible preferences

Non-monotonic reasoning typically deals with three kinds of knowledge. Facts are meant to describe immutable statements of the environment. Rules define relationships among elements. Lastly, an ordering among the rules, in the form of a superiority relation, establishes the relative strength of rules. To revise a non-monotonic theory, we can change either one of these three elements. We prove that the problem of revising a non-monotonic theory by only changing the superiority relation is a NP-complete problem.

Magnetic and morphological properties of ferrofluid-impregnated hydroxyapatite/collagen scaffolds

In this article we present the morphological and magnetic characterization of ferrofluid-impregnated biomimetic scaffolds made of hydroxyapatite and collagen used for bone reconstruction. We describe an innovative and simple impregnation process by which the ferrofluid is firmly adsorbed onto the hydroxyapatite/collagen scaffolds. The process confers sufficient magnetization to attract potential magnetic carriers, which may be used to transport bioactive agents that favour bone regeneration. The crystalline structure of the magnetite contained in the ferrofluid is preserved and its quantity, estimated from the weight gain due to the impregnation process, is consistent with that obtained from energy dispersive X-ray spectroscopy. The magnetization, measured with a superconducting quantum interference device, is uniform throughout the scaffolds, demonstrating the efficiency of the impregnation process. The field emission gun scanning electron microscopy characterization demonstrates that the process does not alter the morphology of the hydroxyapatite/collagen scaffolds, which is essential for the preservation of their bioactivity and consequently for their effectiveness in promoting bone formation.

Advanced CUBIC protocols for whole-brain and whole-body clearing and imaging

Here we describe a protocol for advanced CUBIC (Clear, Unobstructed Brain/Body Imaging Cocktails and Computational analysis). The CUBIC protocol enables simple and efficient organ clearing, rapid imaging by light-sheet microscopy and quantitative imaging analysis of multiple samples. The organ or body is cleared by immersion for 1–14 d, with the exact time required dependent on the sample type and the experimental purposes. A single imaging set can be completed in 30–60 min. Image processing and analysis can take <1 d, but it is dependent on the number of samples in the data set. The CUBIC clearing protocol can process multiple samples simultaneously. We previously used CUBIC to image whole-brain neural activities at single-cell resolution using Arc-dVenus transgenic (Tg) mice. CUBIC informatics calculated the Venus signal subtraction, comparing different brains at a whole-organ scale. These protocols provide a platform for organism-level systems biology by comprehensively detecting cells in a whole organ or body.