Big Data and Analysis of Data Transfers for International Research Networks Using NetSage

Modern science is increasingly data-driven and collaborative in nature. Many scientific disciplines, including genomics, high-energy physics, astronomy, and atmospheric science, produce petabytes of data that must be shared with collaborators all over the world. The National Science Foundation-supported International Research Network Connection (IRNC) links have been essential to enabling this collaboration, but as data sharing has increased, so has the amount of information being collected to understand network performance. New capabilities to measure and analyze the performance of international wide-area networks are essential to ensure end-users are able to take full advantage of such infrastructure for their big data applications. NetSage is a project to develop a unified, open, privacy-aware network measurement, and visualization service to address the needs of monitoring today's high-speed international research networks. NetSage collects data on both backbone links and exchange points, which can be as much as 1Tb per month. This puts a significant strain on hardware, not only in terms storage needs to hold multi-year historical data, but also in terms of processor and memory needs to analyze the data to understand network behaviors. This paper addresses the basic NetSage architecture, its current data collection and archiving approach, and details the constraints of dealing with this big data problem of handling vast amounts of monitoring data, while providing useful, extensible visualization to end users

A sustainable method of effluent disposal: case study of Antalya sea outfall, Turkey

Antalya city, located along the Turkish Mediterranean coast, lacked a proper sanitation system till 1996. An integrated water & wastewater project has been implemented to protect groundwater resources used for drinking and seawater quality. The project involved collection, treatment and final disposal of effluents by a deep sea outfall system. A current research project has been realized to evaluate performance of Antalya Sea Outfall. Seasonal in-situ measurements and bacteriological monitoring studies have been realized. The discharged wastewater plume is observed to be submerged in summer and to reach sea surface in winter condition. The results of the monitoring program exhibit considerable spatial and temporal variations. The resultant total and fecal coliform numbers comply well with the Turkish Standards for the use of coastal and sea water for recreation

Identification of 2-Aminothiazole-4-Carboxylate Derivatives Active against Mycobacterium tuberculosis H37Rv and the β-Ketoacyl-ACP Synthase mtFabH

Background Tuberculosis (TB) is a disease which kills two million people every year and infects approximately over one-third of the world's population. The difficulty in managing tuberculosis is the prolonged treatment duration, the emergence of drug resistance and co-infection with HIV/AIDS. Tuberculosis control requires new drugs that act at novel drug targets to help combat resistant forms of Mycobacterium tuberculosis and reduce treatment duration. Methodology/Principal Findings Our approach was to modify the naturally occurring and synthetically challenging antibiotic thiolactomycin (TLM) to the more tractable 2-aminothiazole-4-carboxylate scaffold to generate compounds that mimic TLM's novel mode of action. We report here the identification of a series of compounds possessing excellent activity against M. tuberculosis H37Rv and, dissociatively, against the β-ketoacyl synthase enzyme mtFabH which is targeted by TLM. Specifically, methyl 2-amino-5-benzylthiazole-4-carboxylate was found to inhibit M. tuberculosis H37Rv with an MIC of 0.06 µg/ml (240 nM), but showed no activity against mtFabH, whereas methyl 2-(2-bromoacetamido)-5-(3-chlorophenyl)t​hiazole-4-carboxylateinhibited mtFabH with an IC50 of 0.95±0.05 µg/ml (2.43±0.13 µM) but was not active against the whole cell organism. Conclusions/Significance These findings clearly identify the 2-aminothiazole-4-carboxylate scaffold as a promising new template towards the discovery of a new class of anti-tubercular agents

Surface potential change in bioactive polymer during the process of biomimetic apatite formation in a simulated body fluid

A bioactive polyethylene substrate can be produced by incorporation of sulfonic functional groups (-SO3H) on its surface and by soaking in a calcium hydroxide saturated solution. Variation of the surface potential of the polyethylene modified with -SO3H groups with soaking in a simulated body fluid (SBF) was investigated using a laser electrophoresis zeta-potential analyzer. To complement the study using laser electrophoresis, the surface was examined by X-ray photoelectron spectroscopy (XPS), thin film X-ray diffraction (TF-XRD), field-emission scanning electron microscopy (FE-SEM) and energy-dispersive electron X-ray spectroscopy (EDS). Comparing the zeta potential of sulfonated and Ca(OH)2-treated polyethylene with its surface structure at each interval of these soaking times in SBF, it is apparent that the polymer has a negative surface potential when it forms -SO3H groups on its surface. The surface potential of the polymer increases when it forms amorphous calcium sulfate. The potential decreases when it forms amorphous calcium phosphate, revealing a constant negative value after forming apatite. The XPS and zeta potential analysis demonstrated that the surface potential of the polyethylene was highly negatively charged after soaking in SBF for 0.5 h, increased for higher soaking times (up to 48 h), and then decreased. The negative charge of the polymer at a soaking time of 0.5 h is attributed to the presence of -SO3H groups on the surface. The initial increase in the surface potential was attributed to the incorporation of positively charged calcium ions to form calcium sulfate, and then the subsequent decrease was assigned to the incorporation of negatively charged phosphate ions to form amorphous calcium phosphate, which eventually transformed into apatite. These results indicate that the formation of apatite on bioactive polyethylene in SBF is due to electrostatic interaction of the polymer surface and ions in the fluid

Formation of bone-like apatite on polymeric surfaces modified with -SO3H groups

Sulfonic groups (-SO3H) were covalently attached on different polymeric surfaces enabling them to induce apatite nucleation, for developing bioactive apatite-polymer composites with a bonelike 3-dimensional structure. High molecular weight polyethylene (HMWPE) and ethylene-co-vinyl alcohol co-polymer (EVOH) were used. The polymers were soaked in two types of sulphate-containing solutions with different concentrations, sulphuric acid (H2SO4) and chlorosulfonic acid (ClSO3H). To incorporate calcium ions into to the sulfonated polymers, the samples were soaked in a saturated Ca(OH)2 solution for 24 hours. After soaking of the samples in a simulated body fluid (SBF), formation of an apatite layer on both surfaces was observed. The results obtained prove the validity of the proposed concept and show that the -SO3H groups are effective on inducing apatite nucleation on the surface of these polymers.(undefined

Exact Solution Methods for the kk-item Quadratic Knapsack Problem

The purpose of this paper is to solve the 0-1 $k$-item quadratic knapsack problem $(kQKP)$, a problem of maximizing a quadratic function subject to two linear constraints. We propose an exact method based on semidefinite optimization. The semidefinite relaxation used in our approach includes simple rank one constraints, which can be handled efficiently by interior point methods. Furthermore, we strengthen the relaxation by polyhedral constraints and obtain approximate solutions to this semidefinite problem by applying a bundle method. We review other exact solution methods and compare all these approaches by experimenting with instances of various sizes and densities.Comment: 12 page

Litters Health Status and Growth Parameters in the Sows Feeding Diets Supplemented with Probiotic Actisaf Sc 47® within Pregnancy Or Lactation

The aim of this study was to investigate the effect of supplementing standard diets for pregnant and lactating sows with live yeast culture (Saccharomyces cerevisiae) on their health status, as well as the health status and growth parameters of their litters during lactation. A total of 120 sows were divided into three groups: the first group was fed diets supplemented with probiotics during pregnancy (G+P, n=40), the second group was fed these diets during lactation (L+P, n=40), and the third group was the control group which was not fed diets supplemented with probiotics (C, n = 40). During the lactation period, a significantly (p<0.01) smaller proportion of probiotic treated sows (G+P=7.5%, L+P=12.5%) manifested clinical signs of the uterus and/or the udder disease in comparison with the control sows (22.5%). The incidence of infectious diarrhea in the nursing piglets was significantly (p<0.05) lower in the treated sows (12.5%) compared to the control sows (27.5 %). The average number of weaned piglets per litter (p/l) and average litter weight at weaning (lw) (G+P=11.6 p/l and 103.6 kg lw, L+P=11.1 p/l and 102.8 kg lw, C=10 p/l and 79 kg lw) were significantly higher (p<0.01 or p<0.05) in sows treated with probiotic compared to the control sows. These results clearly show that the use of probiotic significantly improves the health status of sows and nursing piglets, as well as the piglets growth parameters

Optimization by thermal cycling

Thermal cycling is an heuristic optimization algorithm which consists of cyclically heating and quenching by Metropolis and local search procedures, respectively, where the amplitude slowly decreases. In recent years, it has been successfully applied to two combinatorial optimization tasks, the traveling salesman problem and the search for low-energy states of the Coulomb glass. In these cases, the algorithm is far more efficient than usual simulated annealing. In its original form the algorithm was designed only for the case of discrete variables. Its basic ideas are applicable also to a problem with continuous variables, the search for low-energy states of Lennard-Jones clusters.Comment: Submitted to Proceedings of the Workshop "Complexity, Metastability and Nonextensivity", held in Erice 20-26 July 2004. Latex, 7 pages, 3 figure

Genetic disruption of sod1 gene causes glucose intolerance and impairs b-cell function

Oxidative stress has been associated with insulin resistance and type 2 diabetes. However, it is not clear whether oxidative damage is a cause or a consequence of the metabolic abnormalities present in diabetic subjects. The goal of this study was to determine whether inducing oxidative damage through genetic ablation of superoxide dismutase 1 (SOD1) leads to abnormalities in glucose homeostasis. We studied SOD1-null mice and wild-type (WT) littermates. Glucose tolerance was evaluated with intraperitoneal glucose tolerance tests. Peripheral and hepatic insulin sensitivity was quantitated with the euglycemic-hyperinsulinemic clamp. b-Cell function was determined with the hyperglycemic clamp and morphometric analysis of pancreatic islets. Genetic ablation of SOD1 caused glucose intolerance, which was associated with reduced in vivo b-cell insulin secretion and decreased b-cell volume. Peripheral and hepatic insulin sensitivity were not significantly altered in SOD1-null mice. High-fat diet caused glucose intolerance in WT mice but did not further worsen the glucose intolerance observed in standard chow-fed SOD1-null mice. Our findings suggest that oxidative stress per se does not play a major role in the pathogenesis of insulin resistance and demonstrate that oxidative stress caused by SOD1 ablation leads to glucose intolerance secondary to b-cell dysfunction. © 2013 by the American Diabetes Association

Restoring Vision through “Project Prakash”: The Opportunities for Merging Science and Service

“So how does this help society?” is a question we are often asked as scientists. The lack of immediate and tangible results cannot be held against a scientific project but statements of future promise in broad and inchoate terms can sometimes pass the benefit-buck indefinitely. There is no incentive against over-stating the benefits, especially when they are hypothetical and lie in the distant future. Few scientists will say their science is not designed to serve society. Yet the proliferation of “potential benefits” in grant proposals and the Discussion sections of research papers, in the absence of tangible translations, can make the service element of science seem like a cliched ritual. Its repetition hollows out its meaning, breeding cynicism about the idea that basic science can be of service