FastEpistasis: a high performance computing solution for quantitative trait epistasis.

Motivation: Genome-wide association studies have become widely used tools to study effects of genetic variants on complex diseases. While it is of great interest to extend existing analysis methods by considering interaction effects between pairs of loci, the large number of possible tests presents a significant computational challenge. The number of computations is further multiplied in the study of gene expression quantitative trait mapping, in which tests are performed for thousands of gene phenotypes simultaneously. Results: We present FastEpistasis, an efficient parallel solution extending the PLINK epistasis module, designed to test for epistasis effects when analyzing continuous phenotypes. Our results show that the algorithm scales with the number of processors and offers a reduction in computation time when several phenotypes are analyzed simultaneously. FastEpistasis is capable of testing the association of a continuous trait with all single nucleotide polymorphism ( SNP) pairs from 500 000 SNPs, totaling 125 billion tests, in a population of 5000 individuals in 29, 4 or 0.5 days using 8, 64 or 512 processors.

Hand-disinfectant alcoholic vapors in incubators

Objective: To analyze the atmosphere inside incubators regarding alcoholic solvent such as isopropanol or ethanol which are commonly used in hand disinfecting solutions. Design: Observational. Setting: The third level neonatal unit of the Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland. Patients: Nine neonates with median (range) gestational age of 29 4/7 (25 5/7-39 0/7) weeks and birth weight of 960 (550-3050) grams. All neonates were inside incubators. Interventions: Alcoholic vapors inside incubators were directly and cumulatively measured by photoionisation and gas chromatography respectively after absorption on a charcoal sampling tube. Results: Eleven studies (mean study time: 230 ± 19 minutes) were performed. Highly variable isopropanol/ethanol concentrations profiles were found inside incubators. Peak value for isopropanol was 1982 part per million and for ethanol was 906 part per million. Conclusions: Incubators' inner atmosphere can be highly polluted by alcohol vapors. To reduce them staff should respect long evaporation time between hands disinfection and manipulations inside incubators. The use of an ethanol-based disinfecting solution, because of its short evaporation time, could be favored. As alcohol vapor toxicity for neonate remains largely unknown, further studies could be welcome.

Effects of adrenergic blockade on hepatic glucose production during ethanol administration.

Acute ethanol administration stimulates sympathetic nervous system activity. The present study was designed to determine whether this sympathetic activation affects glycogenolysis and total hepatic glucose production (HGP) during ethanol-induced inhibition of gluconeogenesis. Nineteen volunteers participated in four protocols. Two protocols aimed to study--using combined infusion of [6,6-2H2]glucose and [U-13C]glucose, VCO2 and 13CO2 measurements--the effects of ethanol infusion alone (n = 10) or with propranolol (n = 6) or phentolamine infusion (n = 4) on HGP, glucose disposal (Rd), glucose oxidation [13C]Glcox and non-oxidative glucose disposal (NOGD = Rd - [13C]Glcox). The fourth protocol assessed the effects of saline infusion alone on HGP. Using ethanol, HGP decreased by 23%, Rd by 20% and glycaemia by 9% (all P < 0.001); heart rate increased by 10%, whereas blood pressure remained unchanged. The effects were not observed with saline, except a slight (10%) decrease in HGP (P < 0.01 vs. ethanol). Ethanol did not affect [13C]Glcox but decreased NOGD by 73% (P < 0.001). Propranolol or phentolamine did not alter any of the effects of ethanol on glucose metabolism, but decreased mean arterial pressure. Propranolol prevented the ethanol-induced increase in heart rate. In conclusion, ethanol decreased blood glucose by decreasing HGP, presumably by inhibiting gluconeogenesis. Sympathetic activation prevented the decrease in blood pressure produced by ethanol but did not stimulate glycogenolysis.

Critical values of nitrogen indices in tomato plants grown in soil and nutrient solution determined by different statistical procedures

The objective of this study was to establish critical values of the N indices, namely soil-plant analysis development (SPAD), petiole sap N-NO3 and organic N in the tomato leaf adjacent to the first cluster (LAC), under soil and nutrient solution conditions, determined by different statistical approaches. Two experiments were conducted in randomized complete block design with four repli-cations. Tomato plants were grown in soil, in 3 L pot, with five N rates (0, 100, 200, 400 and 800 mg kg-1) and in solution at N rates of 0, 4, 8, 12 and 16 mmol L-1. Experiments in nutrient solution and soil were finished at thirty seven and forty two days after transplanting, respectively. At those times, SPAD index and petiole sap N-NO3 were evaluated in the LAC. Then, plants were harvested, separated in leaves and stem, dried at 70ºC, ground and weighted. The organic N was determined in LAC dry matter. Three statistical procedures were used to calculate critical N values. There were accentuated discrepancies for critical values of N indices obtained with plants grown in soil and nutrient solution as well as for different statistical procedures. Critical values of nitrogen indices at all situations are presented.

In vitro and in vivo evaluation of sunitinib eluting beads

Background: Chemoembolization is used to treat liver malignancies. However recurrence occurs frequently, possibly because of neoangiogenesis triggered by ischemia caused by the embolic agent. In this context, the combination of an embolic agent with an anti-angiogenic drug seems appealing. This study characterizes the in vitro loading and release profile of sunitinib eluting beads of different sizes and their pharmacokinetic profile in a rabbit model. Methods: 70-150 μm and 100-300 μm drug eluting beads (DC Bead, Biocompatibles UK) were loaded by incubation in a sunitinib hydrochloride solution. Drug was quantified by spectrophotometry at 430 nm. Drug release was measured over one-week periods and normalized using an internal standard in 30% ethanol in NaCl 0.9%. New-Zealand white rabbits were used. Eight animals received 0.2 ml of 100-300 μm DC Bead loaded with 6 mg of sunitinib in the hepatic artery (group 1) and 4 animals received 6 mg of sunitinib p.o. (group 2). Half of the animals were sacrificed after 6 hours and half after24 hours. Liver enzymes were measured at 0, 6 and 24 hours in both groups. Plasmatic sunitinib concentration was determined by tandem mass spectroscopy (LC MS/MS) at 0, 1, 2, 3, 4, 5, 6 and 24 hours. At sacrifice, the livers were harvested and sunitinib concentration in liver tissue was assessed by LC MS/MS. Results: High drug loading was obtained for both microsphere bead sizes. Particle shrinking was observed with adsorption of sunitinib. Almost complete release of sunitinib was detected under physiological conditions, with very similar release for 70-150 μm and 100-300 μm (t50%=1.2 h) DC Bead. Conclusions: Sunitinib eluting beads are well tolerated by rabbits when administered in the hepatic artery. No unexpected toxicity was observed. Very high drug concentration can be obtained at the site of embolization with minimal systemic passage.

Detecting the oxidative reactivity of nanoparticles: a new protocol for reducing artifacts

Understanding the oxidative reactivity of nanoparticles (NPs; <100 nm) could substantially contribute to explaining their toxicity. We attempted to refine the use of 2′7-dichlorodihydrofluorescein (DCFH) to characterize NP generation of reactive oxygen species (ROS). Several fluorescent probes have been applied to testing oxidative reactivity, but despite DCFH being one of the most popular for the detection of ROS, when it has been applied to NPs there have been an unexplainably wide variability in results. Without a uniform methodology, validating even robust results is impossible. This study, therefore, identified sources of conflicting results and investigated ways of reducing occurrence of artificial results. Existing techniques were tested and combined (using their most desirable features) to form a more reliable method for the measurement of NP reactivity in aqueous dispersions. We also investigated suitable sample ranges necessary to determine generation of ROS. Specifically, ultrafiltration and time-resolved scan absorbance spectra were used to study possible optical interference when using high sample concentrations. Robust results were achieved at a 5 µM DCFH working solution with 0.5 unit/mL horseradish peroxidase (HRP) dissolved in ethanol. Sonication in DCFH-HRP working solution provided more stable data with a relatively clean background. Optimal particle concentration depends on the type of NP and in general was in the µg/mL range. Major reasons for previously reported conflicting results due to interference were different experimental approaches and NP sample concentrations. The protocol presented here could form the basis of a standardized method for applying DCFH to detect generation of ROS by NPs.

Larvicidal potential of Sapindus saponaria to control the cattle tick Boophilus microplus

The objective of this study was to evaluate the larvicidal potential of a crude ethanol extract (CEE) of soapberry Sapindus saponaria stem peel on the cattle tick Boophilus microplus. Tick larvae obtained by incubating engorged females, collected from naturally infested cattle, were placed in envelopes of filter paper impregnated with different concentrations of CEE in the test group, and distilled water in the control group. Four repetitions were made with each solution (n>120). Mortality was observed after 48 hours. Lethal concentration values of 1,258 ppm (LC50) and 6,360 ppm (LC99) were obtained.

Pattern-based sensing of nucleotides in aqueous solution with a multicomponent indicator displacement assay

A multicomponent indicator displacement assay ( MIDA) based on an organometallic receptor and three dyes can be used for the identification and quantification of nucleotides in aqueous solution at neutral pH.

The release of antidiuretic hormone is appropriate in response to hypovolemia and/or sodium administration in children with severe head injury: a trial of lactated Ringer's solution versus hypertonic saline.

We conducted an open, randomized, and prospective study to determine the effect of hypertonic saline on the secretion of antidiuretic hormone (ADH) and aldosterone in children with severe head injury (Glasgow coma scale <8). Thirty-one consecutive patients at a level III pediatric intensive care unit at a children's hospital received either lactated Ringer's solution (Ringer's group, n = 16) or hypertonic saline (Hypertonic Saline group, n = 15) over a 3-day period. Serum ADH levels were significantly larger in the Hypertonic Saline group as compared with the Ringer's group (P = 0.001; analysis of variance) and were correlated to sodium intake (Ringer's group: r = 0.39, R(2) = 0.15, P = 0.02; Hypertonic Saline group: r = 0.42, R(2) = 0.18, P = 0.02) and volume of fluids given IV (Ringer's group: r = 0.38, R(2) = 0.15, P = 0.02; Hypertonic Saline group: r = 0.32, R(2) = 0.1, P = not significant). Correlation of ADH to plasma osmolality was significant if plasma osmolality was >280 mOsm/kg (r = 0.5, R(2) = 0.25, P = 0.06), indicating an osmotic threshold for ADH release. Serum aldosterone levels were larger on the first day than during Days 2 and 3 in both groups and inversely correlated to serum sodium levels only in the Ringer's group (r = -0.55, R(2) = 0.3, P < 0.001). This group received a significantly larger fluid volume on Day 1 (P = 0.05, Mann-Whitney U-test) than did patients in the Hypertonic Saline group, indicating hypovolemia during the first day. Head-injured children have appropriate levels of ADH. They may be hypovolemic during the first day of treatment, especially if they receive lactated Ringer's solution. IMPLICATIONS: In head-injured patients, we recommend fluid restriction to avoid inappropriate secretion of antidiuretic hormone. In a prospective, randomized, and controlled study in 31 children, we were able to show that the antidiuretic hormone levels are appropriate in response to hypovolemia, sodium load, or both.

Exotic terrains in the Alps - A solution for a single Jurassic ocean

The Brianconnais area is explained as a large scale exotic terrain separating from Europe during the opening of the Valais ocean. It's displacement history during the Alpine evolution allows to replace older concepts of multiple oceans separating narrow strips of continental crust.

Farm scale alcohol production : the Iowa State University ethanol distillery, 1981.

This publication was prepared to describe how the Iowa State University distillery has been operating, including information on distillery size, equipment, tanks, condenser, heat exchanger, pumps and the process. Photos and diagrams are also included.

Mortality of Plutella xylostella larvae treated with Aspidosperma pyrifolium ethanol extracts

The objective of this work was to assess the effects of Aspidosperma pyrifolium ethanol extracts on cabbage moth (Plutella xylostella) larvae. The ethanol extracts of the stem bark, fruits and roots of A. pyrifolium were obtained by classical phytochemical methods, and the resulting subfractions were tested on P. xylostella, using 4 and 5 mg L-1. The crude ethanol extract of the stem bark was more lethal. The alkaloid-rich aqueous subfraction derived from the stem bark extract caused 100% larval mortality at 4 mg L-1. Insecticidal activity was associated with the presence of the monoterpenoid indole alkaloids aspidofractinine, 15-demethoxypyrifoline, and N-formylaspidofractinine. These alkaloids presented excellent insecticidal properties against P. xylostella.

Patterns of protein and carbohydrate accumulation during somatic embryogenesis of Acca sellowiana

The aim of this work was to quantify the protein, starch and total sugars levels during histodifferentiation and development of somatic embryos of Acca sellowiana Berg. For histological observations, the samples were dehydrated in a battery of ethanol, embedded in historesin and stained with toluidine blue (morphology), coomassie blue (protein bodies) and periodic acid-Schiff (starch). Proteins were extracted using a buffer solution, precipitated using ethanol and quantified using the Bradford reagent. Total sugars were extracted using a methanol-chloroform-water (12:5:3) solution and quantified by a reaction with anthrone at 0.2%. Starch was extracted using a 30% perchloric acid solution and quantified by a reaction with anthrone at 0.2%. During the somatic embryogenesis' in vitro morphogenesis and differentiation processes, the total protein levels decreased and the soluble sugars levels increased during the first 30 days in culture and remained stable until the 120th day. On the other hand, total protein levels increased according to the progression in the developmental stages of the somatic embryos. The levels of total sugars and starch increased in the heart and cotyledonary stages, and decreased in the torpedo and pre-cotyledonary stages. These compounds play a central role in the development of somatic embryos of Acca sellowiana.