Miracle-dz/UniFAR-FTUs huggingface dataset:
Herpes Simplex Virus 2 Virion Host Shutoff Endoribonuclease Activity Is Required To Disrupt Stress Granule Formation

ABSTRACT We previously established that cells infected with herpes simplex virus 2 (HSV-2) are disrupted in their ability to form stress granules (SGs) in response to oxidative stress and that this disruption is mediated by virion host shutoff protein (vhs), a virion-associated endoribonuclease. Here, we test the requirement for vhs endoribonuclease activity in disruption of SG formation. We analyzed the ability of HSV-2 vhs carrying the point mutation D215N, which ablates its endoribonuclease activity, to disrupt SG formation in both transfected and infected cells. We present evidence that ablation of vhs endoribonuclease activity results in defects in vhs-mediated disruption of SG formation. Furthermore, we demonstrate that preformed SGs can be disassembled by HSV-2 infection in a manner that requires vhs endoribonuclease activity and that, befitting this ability to promote SG disassembly, vhs is able to localize to SGs. Together these data indicate that endoribonuclease activity must be maintained in order for vhs to disrupt SG formation. We propose a model whereby vhs-mediated destruction of SG mRNA promotes SG disassembly and may also prevent SG assembly. IMPORTANCE Stress granules (SGs) are transient cytoplasmic structures that form when a cell is exposed to stress. SGs are emerging as potential barriers to viral infection, necessitating a more thorough understanding of their basic biology. We identified virion host shutoff protein (vhs) as a herpes simplex virus 2 (HSV-2) protein capable of disrupting SG formation. As mRNA is a central component of SGs and the best-characterized activity of vhs is as an endoribonuclease specific for mRNA in vivo, we investigated the requirement for vhs endoribonuclease activity in disruption of SG formation. Our studies demonstrate that endoribonuclease activity is required for vhs to disrupt SG formation and, more specifically, that SG disassembly can be driven by vhs endoribonuclease activity. Notably, during the course of these studies we discovered that there is an ordered departure of SG components during their disassembly and, furthermore, that vhs itself has the capacity to localize to SGs.
Integral equation methods for extreme-parameter materials and novel boundary conditions

Aalto University, P.O. Box 11000, FI-00076 Aalto www.aalto. fi Author Johannes Markkanen Name of the doctoral dissertation Integral equation methods for extreme-parameter materials and novel boundary conditions Publisher School of Electrical Engineering Unit Department of Radio Science and Engineering Series Aalto University publication series DOCTORAL DISSERTATIONS 109/2013 Field of research Electromagnetics Manuscript submitted 4 March 2013 Date of the defence 8 August 2013 Permission to publish granted (date) 16 May 2013 Language English Monograph Article dissertation (summary + original articles) Abstract This thesis aims to develop accurate and efficient numerical methods for modeling electromagnetic properties of materials with extreme parameters and nonconventional boundary conditions. Materials with the permittivity and permeability dyadics being strongly inhomogeneous or anisotropic or having parameters near zero or infinity are considered as extreme materials. Nonconventional boundary conditions investigated in this thesis are called DB and D'B' boundary conditions, which require the vanishing of the normal components of the fluxes (DB) or their normal derivatives (D'B'). This thesis aims to develop accurate and efficient numerical methods for modeling electromagnetic properties of materials with extreme parameters and nonconventional boundary conditions. Materials with the permittivity and permeability dyadics being strongly inhomogeneous or anisotropic or having parameters near zero or infinity are considered as extreme materials. Nonconventional boundary conditions investigated in this thesis are called DB and D'B' boundary conditions, which require the vanishing of the normal components of the fluxes (DB) or their normal derivatives (D'B'). This thesis consists of three main topics. In the first part, a surface integral equation-based solution for electromagnetic wave scattering by objects with the DB boundary condition is developed. The integral equations are solved by the method of moments. The DB boundary condition is enforced by restricting the freedom of the unknown surface current densities. The developed method is then used for analyzing electromagnetic scattering by the ideal DB objects. The second part examines properties of different volume integral equation formulations and their discretizations. The accuracy and stability of these formulations are analyzed when the material parameters are complicated or pushed to the extreme limits. It is shown that the formulation with the equivalent volume currents as unknowns is more stable than the conventional ones when the material parameters are extremely anisotropic. The third part focuses on material approximations of the DB and D'B' boundary conditions in terms of an interface against some extreme-parameter material. Scattering properties of these approximations are investigated by using the volume integral equation method developed in the second part.
Large-Scale Performance Analysis of Sweep3D with the Scalasca Toolset

Cray XT and IBM Blue Gene systems present current alternative approaches to constructing leadership computer systems relying on applications being able to exploit very large configurations of processor cores, and associated analysis tools must also scale commensurately to isolate and quantify performance issues that manifest at the largest scales. In studying the scalability of the Scalasca performance analysis toolset to several hundred thousand MPI processes on XT5 and BG/P systems, we investigated a progressive execution performance deterioration of the well-known ASCI Sweep3D compact application. Scalasca runtime summarization analysis quantified MPI communication time that correlated with computational imbalance, and automated trace analysis confirmed growing amounts of MPI waiting times. Further instrumentation, measurement and analyses pinpointed a conditional section of highly imbalanced computation which amplified waiting times inherent in the associated wavefront communication that seriously degraded overall execution efficiency at very large scales. By employing effective data collation, management and graphical presentation, in a portable and straightforward to use toolset, Scalasca was thereby able to demonstrate performance measurements and analyses with 294,912 processes.
C ∗ -Algebras Associated with Quadratic Dynamical System

In this paper we consider enveloping C *-algebras of *-algebras given by generators and defining relations of the following form A = CX, X * | XX * = f (X * X), where f is a Hermitian mapping. Some properties of these algebras associated with simple dynamical systems (f, R) are studied. As an example quadratic dynamical systems are considered.
Diffraction Line Profile Analysis of 3D Wedge Samples of Ti-6Al-4V Fabricated Using Four Different Additive Manufacturing Processes

Wedge-shaped samples were manufactured by four different Additive Manufacturing (AM) processes, namely selective laser melting (SLM), electron beam melting (EBM), direct metal deposition (DMD), and wire and arc additive manufacturing (WAAM), using Ti-6Al-4V as the feed material. A high-resolution powder diffractometer was used to measure the diffraction patterns of the samples whilst rotated about two axes to collect detected neutrons from all possible lattice planes. The diffraction pattern of a LaB6 standard powder sample was also measured to characterize the instrumental broadening and peak shapes necessary for the Diffraction Line Profile Analysis. The line profile analysis was conducted using the extended Convolution Multiple Whole Profile (eCMWP) procedure. Once analyzed, it was found that there was significant variation in the dislocation densities between the SLMed and the EBMed samples, although having a similar manufacturing technique. While the samples fabricated via WAAM and the DMD processes showed almost similar dislocation densities, they were, however, different in comparison to the other two AM processes, as expected. The hexagonal (HCP) crystal structure of the predominant α-Ti phase allowed a breakdown of the percentage of the Burgers’ vectors possible for this crystal structure. All four techniques exhibited different combinations of the three possible Burgers’ vectors, and these differences were attributed to the variation in the cooling rates experienced by the parts fabricated using these AM processes.
A note on the estimation of Nakagami-m fading parameter

A number of previous publications address the issue of estimating the m-parameter in Nakagami fading. The purpose of this article is not to derive a new estimator; but rather, to bring to the attention of the community the fact that this issue has been solved in the literature for more than four decades. Numerical results are presented to demonstrate that none of the other proposed estimators exceeds the performance of the classical one by Greenwood and Durand (1960).
Effects of Ganopoly® (A Ganoderma lucidum Polysaccharide Extract) on the Immune Functions in Advanced‐Stage Cancer Patients

Preclinical studies have established that the Ganoderma lucidum polysaccharide (GLPS) fractions have potent anti‐tumor activity, which has been associated with the immuno‐stimulating effects of GLPS. However, it is unclear whether GLPS has immuno‐modulating effects in humans in vivo. This study aimed to investigate the effects of Ganopoly®, the polysaccharides fractions extracted from G. lucidum, on the immune function of advanced‐stage cancer patients. Thirty‐four advance‐stage cancer patients were entered onto this study, and treated with 1800 mg Ganopoly®, three times daily orally before meals for 12 weeks. Immune parameters (cytokines, T cell subsets, mitotic response to phytohemagglutinin (PHA) and natural killer (NK) activity) were compared between baseline and after 12‐week treatment. Thirty patients are assessable for their immune functions. Treatment of Ganopoly® for 12 weeks resulted in a significant (P < 0.05) increase in the mean plasma concentrations of interleukin (IL‐2), IL‐6, and interferon (IFN)‐γ, whereas the levels of IL‐1 and tumor necrosis factor (TNF‐α) were significantly (P < 0.05) decreased. A marked variability among patients with advanced‐stage cancer was observed in the numbers of each lymphocyte subset at baseline. The mean absolute number of CD56+ cells was significantly (P < 0.05) increased after 12‐week treatment of Ganopoly®, whereas the numbers of CD3+, CD4+, and CD8+ were just marginally increased compared to baseline levels, with the CD4:CD8 T cell ratios unchanged. PHA responses after 12‐week treatment with Ganopoly® were enhanced in most patients, when compared to pretreatment baselines (P < 0.05). In addition, Ganopoly® treatment resulted in a significant increase (P < 0.05) in the mean NK activity compared to baselines (34.5 ± 11.8% vs 26.6 ± 8.3%). The present study indicates that Ganopoly® enhanced the immune responses in patients with advanced‐stage cancer. Clinical evaluations of response and toxicity are ongoing.
The Personal Human Oral Microbiome Obscures the Effects of Treatment on Periodontal Disease

Periodontitis is a progressive disease of the periodontium with a complex, polymicrobial etiology. Recent Next-Generation Sequencing (NGS) studies of the microbial diversity associated with periodontitis have revealed strong, community-level differences in bacterial assemblages associated with healthy or diseased periodontal sites. In this study, we used NGS approaches to characterize changes in periodontal pocket bacterial diversity after standard periodontal treatment. Despite consistent changes in the abundance of certain taxa in individuals whose condition improved with treatment, post-treatment samples retained the highest similarity to pre-treatment samples from the same individual. Deeper phylogenetic analysis of periodontal pathogen-containing genera Prevotella and Fusobacterium found both unexpected diversity and differential treatment response among species. Our results highlight how understanding interpersonal variability among microbiomes is necessary for determining how polymicrobial diseases respond to treatment and disturbance.
Gross growth efficiencies of protozoan and metazoan zooplankton and their dependence on food concentration, predator‐prey weight ratio, and taxonomic group

A comprehensive dataset on the gross growth efficiency (GGE) of planktonic protozoans and metazoans was gathered from the literature in order to (1) identify typical ranges of values, (2) to reexamine the taxon specificity of GGE, and (3) to evaluate the impact of food concentration, predator‐prey weight ratio, and temperature on GGE. All taxa (i.e. nano/microflagellates, dinoflagellates, ciliates, rotifers, cladocerans, and copepods) were found to have mean and median GGE of ∼20–30%. Contrary to the common practice of using different values of GGE for ciliates and crustaceans, I found that the GGE hardly differed between taxa. Variability within all taxa was high and could only partially be attributed to the independent variables mentioned above. The dependency of GGE on food concentrations was the most reliable relationship identified by multiple regression. Establishing further generalizations regarding the dependency of GGE on other factors was hampered by methodological differences among studies and taxa and the lack of information on other potentially important factors such as the elemental composition of prey items. Future studies of GGE should recognize the importance of these factors.
Effects of Diazepam and Flumazenil on Sedation and Hypoxic Ventilatory Response

We evaluated the effects of a benzodiazepine antagonist, flumazenil (Ro 15–1788), 1 mg intravenous, on the hypoxic ventilatory response in 10 healthy patients who had received diazepam 0.97 ± 0.34 mglminute (mean ± so) for sedation during minor operative procedures. When assessed using a sedation analog scale, flumazenil significantly decreased diazepam-induced sedation. In only two of the five patients with evidence of diazepam-induced depression of the ventilatory response to hypoxia was there significant reversal of this depression after flumazenil administration. Finally, patients in whom the duration of sedation with diazepam was shorter (78 ± 14 minutes) had a significantly greater decrease in the slope of their hypoxic ventilatory response curve (1.3 ± 0.8 L-min−1-%sat−1 [-43% from baseline]) than did patients with longer sedation times (145 ± 37 minutes duration; 2.0 ± 0.8 L-min−1-%sat−1 [-5% from baseline]). These data suggest that flumazenil, 1 mg intravenous, is only partially effective in reversing diazepam-induced depression of hypoxic ventilatory drive and that tolerance may develop to the respiratory depressant effects of diazepam.
Tuberculosis Management Practices of Private Practitioners in Pune Municipal Corporation, India

Background Private Practitioners (PP) are the primary source of health care for patients in India. Limited representative information is available on TB management practices of Indian PP or on the efficacy of India’s Revised National Tuberculosis Control Programme (RNTCP) to improve the quality of TB management through training of PP. Methods We conducted a cross-sectional survey of a systematic random sample of PP in one urban area in Western India (Pune, Maharashtra). We presented sample clinical vignettes and determined the proportions of PPs who reported practices consistent with International Standards of TB Care (ISTC). We examined the association between RNTCP training and adherence to ISTC by calculating odds ratios and 95% confidence intervals. Results Of 3,391 PP practicing allopathic medicine, 249 were interviewed. Of these, 55% had been exposed to RNTCP. For new pulmonary TB patients, 63% (158/249) of provider responses were consistent with ISTC diagnostic practices, and 34% (84/249) of responses were consistent with ISTC treatment practices. However, 48% (120/249) PP also reported use of serological tests for TB diagnosis. In the new TB case vignette, 38% (94/249) PP reported use of at least one second line anti-TB drug in the treatment regimen. RNTCP training was not associated with diagnostic or treatment practices. Conclusion In Pune, India, despite a decade of training activities by the RNTCP, high proportions of providers resorted to TB serology for diagnosis and second-line anti-TB drug use in new TB patients. Efforts to achieve universal access to quality TB management must account for the low quality of care by PP and the lack of demonstrated effect of current training efforts.
Quorum-sensing-regulated virulence factors in Pseudomonas aeruginosa are toxic to Lucilia sericata maggots

Maggot debridement therapy (MDT) is widely used for debridement of chronic infected wounds; however, for wounds harbouring specific bacteria limited effect or failure of the treatment has been described. Here we studied the survival of Lucilia sericata maggots encountering Pseudomonas aeruginosa PAO1 in a simple assay with emphasis on the quorum-sensing (QS)-regulated virulence. The maggots were challenged with GFP-tagged P. aeruginosa wild-type (WT) PAO1 and a GFP-tagged P. aeruginosa ΔlasR rhlR (ΔRR) QS-deficient mutant in different concentrations. Maggots were killed in the presence of WT PAO1 whereas the challenge with the QS mutant showed a survival reduction of ∼25 % compared to negative controls. Furthermore, bacterial intake by the maggots was lower in the presence of WT PAO1 compared to the PAO1 ΔRR mutant. Maggot excretions/secretions (ES) were assayed for the presence of QS inhibitors; only high doses of ES showed inhibition of QS in P. aeruginosa. Thus P. aeruginosa was shown to be toxic to L. sericata maggots. This, coupled to the preferential feeding by the maggots and reduced ingestion of P. aeruginosa, could explain MDT failure in wounds colonized by P. aeruginosa. Wounds heavily colonized with P. aeruginosa should be a counterindication for MDT unless used in combination with a pre-treatment with other topical therapeutics targeting P. aeruginosa.
HRP injection in lobule VI‐VII of the cerebellar cortex reveals a bilateral inferior olive projection in granuloprival rats

In immature rats, Purkinje cells receive synapses from multiple climbing fibers. During development, this multi‐innervation regresses and only one climbing fiber innervates each Purkinje cell in the adult. The multi‐innervation of immature rats is maintained in the adult if the precursors of the cerebellar granule cells are destroyed by early postnatal X‐irradiation. The present study was undertaken to determine the origin of climbing fibers projecting to lobule VI‐VII of the cerebellum in X‐irradiated granuloprival rats. Olivary neurons were labelled by retrograde transport of wheat germ agglutinin conjugated to horseradish peroxidase, which was injected by iontophoresis in the right vermis of lobule VI‐VII. Three‐dimensional reconstructions of the inferior olive were made for granuloprival and control rats. No significant variation in the shape and dimension of the olive was observed between the two groups. Labeled cells were found in the middle part of the median accessory olive (MAO). In control rats, stained cells were found only in the contralateral MAO, whereas in the granuloprival rats they were located in both the contralateral and the ipsilateral MAO. Homologous zones were marked in control and granuloprival rats in the middle part of MAO. In granuloprival rats, there was a symmetry in the distribution of the stained cells in the ipsi‐ and contralateral MAO along the three axes. Therefore, polyinnervation involves homologous regions of both inferior olivary nuclei. J. Comp. Neurol. 449:65–75, 2002. © 2002 Wiley‐Liss, Inc.
Three-dimensional analysis on resistance tomography sensors and its application in inspection of milk flow

3D simulation of ERT sensor is established with multi-physical coupling software COMSOL and MATLAB7.0, analyze the limitation of ERT system 3D sensor field and deeply study the influence on the established fields by sizes of electrodes and frequency characteristics. Thus, design two kinds of sensors of pointed electrode array and rectangular-shaped electrode array and also carry out comparison test on frequency characteristics during the detection of milk flows. The result shows that increasing width and height of electrodes is favorable for improving uniformity of sensitivity field in a radial and axial distributions. It also shows that increasing area of electrodes can reduce “Contact resistance” and have more stable frequency characteristic, which is good for increasing SNR of ERT system, thereby, providing evidence and convenience for optimization design of sensors and reconstruction of images.
Study on Behaviour of Steel Fiber with Biaxial Geogrid Confined Concrete

Concrete is a heterogeneous mixture. The behaviour of concrete in addition of any relevant materials needs proper investigations. The steel fibres in concrete enhance the shear capacity of concrete members and Biaxial Geo-grids in Concrete enhance the tensile capacity of concrete members. The concrete is very poor in tension as well as in shear but strong in compression. The main aim of the study is to investigate the tensile and flexural behaviour of Biaxial Geo-grid with and without steel fibres and compared with regular conventional specimens. In this study Compression test on cubes, Split tensile test on cylinders and Flexure test on prisms with one point loading were performed with the 0.5%, 1% , 1.5% volume fraction of hooked fibres with Biaxial Geo-grids into consideration. The experimental tests with the Biaxial Geo-grid and 1.5% volume fraction of hooked steel fibres showed significant improvement in all strengthening aspects. Further this study helps to know the possibility of Biaxial Geo-grid and steel fibres as substitute for tensile and shear reinforcement.
Windbreak effects within infinite wind farms

Building upon a recent study that showed windbreaks to be effective in increasing the power output of a wind turbine, the potential of windbreaks in a large wind farm is explored using simplified formulations. A top-down boundary layer approach is combined with methods of estimating both the roughness effects of windbreaks and the induced inviscid speed-up for nearby turbines to investigate power production impact for several layouts of infinite wind farms. Results suggest that the negative impact of windbreak wakes for an infinite wind farm will outweigh the local inviscid speed-up for realistic inter-turbine spacings, with the break-even point expected at a spacing of ∼25 rotor diameters. However, the possibility that windbreaks may be applicable in finite and other wind farm configurations remains open. Inspection of the windbreak porosity reveals an impact on the magnitude of power perturbation, but not whether the change is positive or negative. Predictions from the boundary-layer approach are validated with power measurements from large-eddy simulations.