Hierarchical N-Body problem on graphics processor unit

Galactic simulation is an important cosmological computation, and represents a classical N-body problem suitable for implementation on vector processors. Barnes-Hut algorithm is a hierarchical N-Body method used to simulate such galactic evolution systems. Stream processing architectures expose data locality and concurrency available in multimedia applications. On the other hand, there are numerous compute-intensive scientific or engineering applications that can potentially benefit from such computational and communication models. These applications are traditionally implemented on vector processors. Stream architecture based graphics processor units (GPUs) present a novel computational alternative for efficiently implementing such high-performance applications. Rendering on a stream architecture sustains high performance, while user-programmable modules allow implementing complex algorithms efficiently. GPUs have evolved over the years, from being fixed-function pipelines to user programmable processors. In this thesis, we focus on the implementation of Barnes-Hut algorithm on typical current-generation programmable GPUs. We exploit computation and communication requirements present in Barnes-Hut algorithm to expose their suitability for user-programmable GPUs. Our implementation of the Barnes-Hut algorithm is formulated as a fragment shader targeting the selected GPU. We discuss implementation details, design issues, results, and challenges encountered in programming the fragment shader

Cytotoxicity, Morphology and Chemical Composition of Two Luting Cements: An in Vitro Study

Objective: To assess the cytotoxicity, surface morphology, elemental compositions and chemical characterization of two commonly used luting cement. Material and Methods: The two luting types of cement used were Elite Cement® and Hy-Bond Resiglass®. Freshly mixed (n=6) and set form (n=6) of each cement was placed in medium to obtain extracts. The extract from each sample was exposed to L929 mouse fibroblasts (1x104cells/well). Alamar Blue Assay assessed cell viability. Surface morphology and elemental composition were evaluated using scanning electron microscopy and energy dispersive spectroscopy. The chemical characterization was performed by Fourier Transform Infrared Spectroscopy. One-way ANOVA and post-hoc Tukey analysis were conducted to assess results. Results: Hy-Bond Resiglass® was the more cytotoxic of the two types of cement in both freshly mixed (68.10 +5.16; p<0.05) and set state (87.58 +4.86; p<0.05), compared to Elite Cement® both freshly mixed (77.01 +5.45; p<0.05) and set state (89.39 +5.66; p<0.05). Scanning electron microscopy revealed a more irregular and porous structure in Hy-Bond Resiglass® compared to Elite Cement®. Similarly, intense peaks of aluminium, tungsten and fluorine were observed in energy dispersive spectroscopy in Hy-Bond Resiglass. Conclusion: All these three elements (aluminium, tungsten and fluorine) have cytotoxic potential. The Fourier transform infrared spectroscopy revealed the presence of hydroxyethyl methacrylate in Hy-Bond Resiglass®, which has a cytotoxic potential

Comment : Utopianism and Communitarianism

千葉大学公共研究センター21世紀プログラム「持続可能な福祉社会に向けた公共研究拠点

Production of Plant Secondary Metabolites: Examples, Tips and Suggestions for Biotechnologists

Plants are sessile organisms and, in order to defend themselves against exogenous (a)biotic constraints, they synthesize an array of secondary metabolites which have important physiological and ecological effects. Plant secondary metabolites can be classified into four major classes: terpenoids, phenolic compounds, alkaloids and sulphur-containing compounds. These phytochemicals can be antimicrobial, act as attractants/repellents, or as deterrents against herbivores. The synthesis of such a rich variety of phytochemicals is also observed in undifferentiated plant cells under laboratory conditions and can be further induced with elicitors or by feeding precursors. In this review, we discuss the recent literature on the production of representatives of three plant secondary metabolite classes: artemisinin (a sesquiterpene), lignans (phenolic compounds) and caffeine (an alkaloid). Their respective production in well-known plants, i.e., Artemisia, Coffea arabica L., as well as neglected species, like the fibre-producing plant Urtica dioica L., will be surveyed. The production of artemisinin and caffeine in heterologous hosts will also be discussed. Additionally, metabolic engineering strategies to increase the bioactivity and stability of plant secondary metabolites will be surveyed, by focusing on glycosyltransferases (GTs). We end our review by proposing strategies to enhance the production of plant secondary metabolites in cell cultures by inducing cell wall modifications with chemicals/drugs, or with altered concentrations of the micronutrient boron and the quasi-essential element silicon

Surveillance and treatment of primary hepatocellular carcinoma (aka. STOP HCC): protocol for a prospective cohort study of high-risk patients for HCC using GALAD-score.

Vietnam and Saudi Arabia have high disease burden of primary hepatocellular carcinoma (HCC). Early detection in asymptomatic patients at risk for HCC is a strategy to improve survival outcomes in HCC management. GALAD score, a serum-based panel, has demonstrated promising clinical utility in HCC management. However, in order to ascertain its potential role in the surveillance of the early detection of HCC, GALAD needs to be validated prospectively for clinical surveillance of HCC (i.e., phase IV biomarker validation study). Thus, we propose to conduct a phase IV biomarker validation study to prospectively survey a cohort of patients with advanced fibrosis or compensated cirrhosis, irrespective of etiologies, using semi-annual abdominal ultrasound and GALAD score for five years. We plan to recruit a cohort of 1,600 patients, male or female, with advanced fibrosis or cirrhosis (i.e., F3 or F4) and MELD ≤ 15, in Vietnam and Saudi Arabia (n = 800 each). Individuals with a liver mass ≥ 1 cm in diameter, elevated alpha-fetoprotein (AFP) (≥ 9 ng/mL), and/or elevated GALAD score (≥ -0.63) will be scanned with dynamic contrast-enhanced magnetic resonance imaging (MRI), and a diagnosis of HCC will be made by Liver Imaging Reporting and Data System (LiRADS) assessment (LiRADS-5). Additionally, those who do not exhibit abnormal imaging findings, elevated AFP titer, and/or elevated GALAD score will obtain a dynamic contrast-enhanced MRI annually for five years to assess for HCC. Only MRI nearest to the time of GALAD score measurement, ultrasound and/or AFP evaluation will be included in the diagnostic validation analysis. MRI will be replaced with an abdominal computed tomography scan when MRI results are poor due to patient conditions such as movement etc. Gadolinium-ethoxybenzyl-diethylenetriamine pentaacetic acid-enhanced MRI will not be carried out in study sites in both countries. Bootstrap resampling technique will be used to account for repeated measures to estimate standard errors and confidence intervals. Additionally, we will use the Cox proportional hazards regression model with covariates tailored to the hypothesis under investigation for time-to-HCC data as predicted by time-varying biomarker data. The present work will evaluate the performance of GALAD score in early detection of liver cancer. Furthermore, by leveraging the prospective cohort, we will establish a biorepository of longitudinally collected biospecimens from patients with advanced fibrosis or cirrhosis to be used as a reference set for future research in early detection of HCC in the two countries. Name of the registry: ClinicalTrials.gov Registration date: 22 April 2022 Trial registration number: NCT05342350 URL of trial registry record

Role of Pro-Inflammatory Cytokines and Biochemical Markers in the Pathogenesis of Type 1 Diabetes: Correlation with Age and Glycemic Condition in Diabetic Human Subjects

<div><p>Background</p><p>Type 1 diabetes mellitus is a chronic inflammatory disease involving insulin producing β-cells destroyed by the conjoined action of auto reactive T-cells, inflammatory cytokines and monocytic cells. The aim of this study was to elucidate the status of pro-inflammatory cytokines and biochemical markers and possible correlation of these factors towards outcome of the disease.</p><p>Methods</p><p>The study was carried out on 29 T1D subjects and 20 healthy subjects. Plasma levels of oxidative stress markers, enzymatic and non-enzymatic antioxidants were estimated employing biochemical assays. The levels of pro-inflammatory cytokines such as by IL-1β & IL-17 in the serum were determined by ELISA, while the expression of TNF-α, IL-23 & IFN-γ was ascertained by qRT-PCR.</p><p>Results</p><p>The onset of T1D disease was accompanied with elevation in levels of Plasma malondialdehyde, protein carbonyl content and nitric oxide while plasma vitamin C, reduced glutathione and erythrocyte sulfhydryl groups were found to be significantly decreased in T1D patients as compared to healthy control subjects. Activity of antioxidant enzymes, superoxide dismutase, catalase, glutathione reductase and glutathione-s-transferase showed a significant suppression in the erythrocytes of T1D patients as compared to healthy subjects. Nevertheless, the levels of pro-inflammatory cytokines IL-1β and IL-17A were significantly augmented (***p≤.001) on one hand, while expression of T cell based cytokines IFN-γ, TNF-α and IL-23 was also up-regulated (*p≤.05) as compared to healthy human subjects.</p><p>Conclusion</p><p>The level of pro-inflammatory cytokines and specific biochemical markers in the serum of the patient can be exploited as potential markers for type 1 diabetes pathogenesis. The study suggests that level of inflammatory markers is up-regulated in T1D patients in an age dependent manner.</p></div

Changes in the level of pro-inflammatory cytokines in the T1D patients with age.

<p>Serum levels of pro-inflammatory cytokines (A) IL-1β (B) IL-17A and expression fold in the whole blood of pro-inflammatory cytokines (C) IFN-γ and (D) TNF-α in healthy control subjects and T1D patients of age groups ≤15 years and >15 years. Data represent mean ± Standard Deviations from three separate experiments. Statistical significance was determined by unpaired student’s t-test and represented as *p≤0.05, **p<0.01 and ***p<0.001. p≤0.05 was considered statistically significant.</p

Biochemical parameters of healthy control subjects and T1D patients with fasting blood sugar (BS) ≤160 mg/dl and >160mg/dl.

<p>Biochemical parameters of healthy control subjects and T1D patients with fasting blood sugar (BS) ≤160 mg/dl and >160mg/dl.</p