Streaming Analytics and Workflow Automation for DFS

Researchers reuse data from past studies to avoid costly re-collection of experimental data. However, large-scale data reuse is challenging due to lack of consensus on metadata representations among research groups and disciplines. Dataset File System (DFS) is a semi-structured data description format that promotes such consensus by standardizing the semantics of data description, storage, and retrieval. In this paper, we present analytic-streams – a specification for streaming data analytics with DFS, and streaming-hub – a visual programming toolkit built on DFS to simplify data analysis work-flows. Analytic-streams facilitate higher-order data analysis with less computational overhead, while streaming-hub enables storage, retrieval, manipulation, and visualization of data and analytics. We discuss how they simplify data pre-processing, aggregation, and visualization, and their implications on data analysis workflows

Antimicrobial Properties of Ethanolic and Methanolic Extracts of Finger millet (Eleusine coracana (L.) Gaertn.) Varieties Cultivated in Sri Lanka

The emerging significance of natural antimicrobial agents creates an imperative need to identify novel plant sources with antimicrobial activities. The objective of the present study was to evaluate antibacterial, antifungal and β-lactamase enzyme inhibitory activities of ethanolic and methanolic extracts of Ravi, Rawana and Oshadha finger millet varieties. Flours of whole grains of the finger millet varieties were extracted with absolute ethanol and methanol separately. Antibacterial activities against six antibiotic-sensitive and four antibiotic-resistant pathogenic bacterial strains were evaluated using the resazurin reduction assay. Antifungal activities against six antimicrobial-sensitive pathogenic fungal strains were evaluated using the agar tube dilution method. β-Lactamase enzyme inhibitory activity was evaluated using a standard method. Both ethanolic and methanolic extracts of the three finger millet varieties showed dose-dependent inhibitory activities against the tested antibiotic-sensitive and antibiotic-resistant bacterial strains while exhibiting high inhibitions against Gram-positive antibiotic-sensitive bacterial strains when compared to Gram-negative antibiotic-sensitive bacterial strains. The findings revealed the antibacterial potential of both ethanolic and methanolic extracts of the three finger millet varieties against antibiotic-sensitive Staphylococcus aureus (ATCC® 6538™) and Bacillus subtilis (ATCC® 23857™) strains and the minimum inhibitory concentrations of the extracts against S. aureus and B. subtilis were found to be 2.1 and 1.8 mg/ml, respectively. However, none of the extracts can be considered as significantly active against the tested antibiotic-sensitive and antibiotic-resistant bacterial strains when compared to the standard drugs. In addition, none of the extracts can be considered as active against the tested fungal strains at the tested concentrations. Nevertheless, all extracts showed more activities against the tested bacterial strains when compared to the tested fungal strains. Since all extracts showed less than 40% β-lactamase inhibitory activities even at 2 mg/ml concentration, they do not qualify as promising sources of β-lactamase inhibitors at the tested concentration.KEYWORDS: Antibacterial activity, Antifungal activity, Finger millet, β-Lactamase enzyme inhibitory activit

Yield, Feeding Value and Ensiling Characteristics of Clone-13 (\u3ci\u3ePennisetum purpureum\u3c/i\u3e)

A study was carried out to find out the effect of frequency of defoliation on yield and feeding value of clone-13 (Pennisetum purpureum) in Sri Lanka. Three frequency of harvesting, namely 45, 60 and 75 days were used and, fresh yield per plot was measured. Sub samples were taken for dry matter determination and proximate analysis. According to results, frequency of harvesting of 60 days can be recommended for clone-13 under no fertilizer regime. In addition, effect of growth stage on ensiling characteristics of clone-13 was also studied. Clone-13 was harvested at 45, 60, 75 or 90 days and, ensiled alone or with 5% coconut (Cocos nucifera L.) scrapings or 5% rice (Oriza sativa) bran in laboratory silos. Therefore, altogether 12 treatments were used in the study with 5 replicates. Silos were opened after 6 weeks and, physical and ensiling characteristics were studied. Physical characteristics of silage were satisfactory and had a yellowish brown colour, pleasant aroma and a moist texture. Highest volatile fatty acids and crude protein contents were observed with 45 days old grass silage whereas lowest in 90 days old grass silage. Addition of rice bran and coconut scrapings improved the fermentation characteristics of silage compared to no additives

Plasma lipid species at type 1 diabetes onset predict residual beta-cell function after 6 months

INTRODUCTION: The identification of metabolomic dysregulation appears promising for the prediction of type 1 diabetes and may also reveal metabolic pathways leading to beta-cell destruction. Recent studies indicate that regulation of multiple phospholipids precede the presence of autoantigens in the development of type 1 diabetes. OBJECTIVES: We hypothesize that lipid biomarkers in plasma from children with recent onset type 1 diabetes will reflect their remaining beta-cell function and predict future changes in beta-cell function. METHODS: We performed targeted lipidomic profiling by electrospray ionization tandem mass spectrometry to acquire comparative measures of 354 lipid species covering 25 lipid classes and subclasses in plasma samples from 123 patients < 17 years of age followed prospectively at 1, 3, 6 and 12 months after diagnosis. Lipidomic profiles were analysed using liner regression to investigate the relationship between plasma lipids and meal stimulated C-peptide levels at each time point. P-values were corrected for multiple comparisons by the method of Benjamini and Hochberg. RESULTS: Linear regression analysis showed that the relative levels of cholesteryl ester, diacylglycerol and triacylglycerol at 1 month were associated to the change in c-peptide levels from 1 to 6 months (corrected p-values of 4.06E-03, 1.72E-02 and 1.72E02, respectively). Medium chain saturated and monounsaturated fatty acids were the major constituents of the di- and triacylglycerol species suggesting a link with increased lipogenesis. CONCLUSION: These observations support the hypothesis of lipid disturbances as explanatory factors for residual beta-cell function in children with new onset type 1 diabetes

Star Formation in the Era of the Three Great Observatories

This paper summarizes contributions and suggestions as presented at the Chandra Workshop Star Formation in the Era of Three Great Observatories conducted in July 2005. One of the declared goals of the workshop was to raise recognition within the star formation research community about the sensible future utilization of the space observatories Spitzer, Hubble, and Chandra in their remaining years of operation to tackle imminent questions of our understanding of stellar formation and the early evolution of stars. A white paper was generated to support the continuous and simultaneous usage of observatory time for star formation research. The contents of this paper have been presented and discussed at several other meetings during the course of 2005 and January 2006.Comment: Conference Summary "White Paper", Accepted by PASP, 9 pages including 3 figure

Identification, Review, and Systematic Cross-Validation of microRNA Prognostic Signatures in Metastatic Melanoma

In metastatic melanoma, it is vital to identify and validate biomarkers of prognosis. Previous studies have systematically evaluated protein biomarkers or mRNA-based expression signatures. No such analyses have been applied to microRNA (miRNA)-based prognostic signatures. As a first step, we identified two prognostic miRNA signatures from publicly available data sets (Gene Expression Omnibus/The Cancer Genome Atlas) of global miRNA expression profiling information. A 12-miRNA signature predicted longer survival after surgery for resection of American Joint Committee on Cancer stage III disease (>4 years, no sign of relapse) and outperformed American Joint Committee on Cancer standard-of-care prognostic markers in leave-one-out cross-validation analysis (error rates 34% and 38%, respectively). A similar 15-miRNA biomarker derived from The Cancer Genome Atlas miRNA-seq data performed slightly worse (39%) than these current biomarkers. Both signatures were then assessed for replication in two independent data sets and subjected to systematic cross-validation together with the three other miRNA-based prognostic signatures proposed in the literature to date. Five miRNAs (miR-142-5p, miR-150-5p, miR-342-3p, miR-155-5p, and miR-146b-5p) were reproducibly associated with patient outcome and have the greatest potential for application in the clinic. Our extensive validation approach highlighted among multiple independent cohorts the translational potential and limitations of miRNA signatures, and pointed to future directions in the analysis of this emerging class of markers

Silicon Supplementation by Rice Hull Leachate on the Growth, Yield, Fruit Parameters and Anthracnose Disease Resistance of Capsicum ‘MuriaF1’

Silicon has prooven beneficial in growth, yield and disease resistance of plants. Currently, the differentchemical sources; sodium silicate, potassium silicate and calcium silicate have been used to supply Si forplants. However, rice hull is one of the natural sources of Si which has not properly utilized. It has beenreported that 5 g of rice hull leach 40 ppm of soluble Si in a week of soaking period. Thus, this research wasconducted to investigate the effect of rice hull leachate as a Si source, on growth, yield and fruit parametersand also disease resistance of hydroponically grown Capsicum annum L. ‘Muria F1’. Leaching studies wereconducted to determine the optimum level of Si leached by rice hull, by soaking them in different time periods(days). This leachate was incorporated to the plants grown in hydroponic media supplemented with twodifferent nutrient solutions i.e Nutrient formula (NF) and Albert solution.The growth, yield and fruit qualityparameters were measured and the resistance against anthracnose disease was assessed by artificialinoculation of fruits with Colletotrichum gloeosporioides and measuring the lesion area. Capsicum plantsgrown in rice hull leachate with either nutrient solution showed significant increase in, shoot length (>12%),number of leaves (>27%), leaf area (>42%) fruit length (>12%), fruit fresh weight (>37%) and yield(>44%) and also a significant reduction of anthracnose disease (>43%) compared to control. The resultsrevealed that rice hull leachate could be used as a low cost silicon source in hydroponic media to enhanceperformance of Capsicum cv. Muria F1.Keywords: Rice hull, Capsicum annum L., silicon, Colletotrichum gloeosporioides, hydroponic

Dietary fibers, starch fractions and nutritional composition of finger millet varieties cultivated in Sri Lanka

Soluble, insoluble and total dietary fiber contents, rapidly and slowly digestible starch contents, arabinoxylans, β-glucans, fructans, resistant starch, amylose and total sugar contents, minerals and trace elements compositions and proximate compositions of three finger millet varieties, namely Ravi, Rawana and Oshadha, were evaluated using standard protocols. There were no significant differences (P≥ 0.05) among the rapidly digestible starch, arabinoxylans, β-glucans, fructans, amylose, total sugar, protein, crude fat and crude fiber contents of Ravi, Rawana and Oshadha varieties. Total dietary fiber contents varied between 13.01% (Ravi) and 13.79% (Oshadha). Slowly digestible starch contents ranged from 43.38% (Ravi) to 49.15% (Oshadha) and resistant starch contents ranged from 3.75% (Ravi) to 4.58% (Oshadha). Ash content of Ravi (3.22%) was significantly higher (P < 0.05) than ash contents of other two varieties. Average sodium, magnesium, potassium, calcium, iron, zinc and phosphorous contents of three finger millet varieties were 12.04, 141.78, 407.15, 345.62, 3.49, 1.89 and 331.07 mg/100 g, respectively. Findings of the present study indicated that studied finger millet varieties were good sources of dietary fibers (including resistant starch) as well as minerals and trace elements (especially potassium, calcium, phosphorous and iron) when compared to commonly consumed cereals such as rice and wheat

Relationships between plasma lipids species, gender, risk factors and Alzheimer’s disease

Background: Lipid metabolism is altered in Alzheimer’s disease (AD); however, the relationship between AD risk factors (age, APOE ɛ4, and gender) and lipid metabolism is not well defined. Objective: We investigated whether altered lipid metabolism associated with increased age, gender, and APOE status may contribute to the development of AD by examining these risk factors in healthy controls and also clinically diagnosed AD individuals. Methods: We performed plasma lipidomic profiling (582 lipid species) of the Australian Imaging, Biomarkers and Lifestyle flagship study of aging cohort (AIBL) using liquid chromatography-mass spectrometry. Linear regression and interaction analysis were used to explore the relationship between risk factors and plasma lipid species. Results: We observed strong associations between plasma lipid species with gender and increasing age in cognitively normal individuals. However, APOE ɛ4 was relatively weakly associated with plasma lipid species. Interaction analysis identified differential associations of sphingolipids and polyunsaturated fatty acid esterified lipid species with AD based on age and gender, respectively. These data indicate that the risk associated with age, gender, and APOE ɛ4 may, in part, be mediated by changes in lipid metabolism. Conclusion: This study extends our existing knowledge of the relationship between the lipidome and AD and highlights the complexity of the relationships between lipid metabolism and AD at different ages and between men and women. This has important implications for how we assess AD risk and also for potential therapeutic strategies involving modulation of lipid metabolic pathways

Мониторинг воспроизводства и влияния фекального прогестерона на репродуктивную цикличность циклов самбарского оленя Шри-Ланки (Rusa unicolor unicolor)

Sambar deer hinds, estrus, progesterone, estrous cycle, Sri LankaThis study examines the length of the estrous cycle in 16 Sambar deer hinds in National zoological gardens in Dehiwala and Kegalle, Sri Lanka (NZGDK) assessed with the use of changes in progesterone concentrations, along with the changes in the profile of this hormone and by the visual estrus manifestations. The objectives of the present study were to characterize ovarian activity throughout the estrous cycle and the non-pregnant luteal phase of captive sambar deer in Sri Lanka. These objectives were achieved with the use of radioimmunoassay (RIA) to measure fecal concentrations of progesterone and visual estrus manifestation. Fecal samples were collected from non-pregnant sambar deer hinds (aged 2–4 years)over the period of six months on daily basis, both during breeding and non-breeding seasons. Estrous cycles were recorded in non-pregnant females, based on fecal progesterone concentrations. The average estrous cycle length was 26.1±2.08 days (mean ± SEM) and 2.10 ± 0.51 days in the inter-luteal phase.The average fecal progesterone concentrations attained the peak mid-luteal values of 2.74 ng mL–1. There appeared to be variation in fecal progesterone amplitude between animals and between dates, but the low frequency of sampling prohibited confirmation of trends. Behavioral estrus was detected only when the average progesterone concentrations were less than 0.07 ng mL–1. However, not all periods of depressed progesterone secretion were associated with the observed estrus. Behavioral estrus was detected in hinds when progesterone concentrations were less than 0.07 ng mL–1; a subsequent rise in progesterone indicated ovulation taking place at this time