Parallel Laboratory Research Articles

A parallel laboratory for simulation and visualization of seismic wavefields

The use of parallel computers makes simulation of elastic waves feasible throughout large structures by means of recent advances in domain decomposition methods. We introduce a competitive parallel algorithm for the propagation of elastic waves in complex heterogeneous media using finite-element discretization. This parallel method, called the multiblock method, performs more efficiently than classical domain decomposition techniques based on substructuration, such as the Schur complement technique. It reduces considerably the amount of communication amongst processors because the interface problem between subdomains is solved by taking advantage of Huygens' principle for wave propagation. We provide some numerical examples and detailed studies on the efficiency and performance of the algorithm, proving that it is competitive and less costly, from the computational viewpoint, than algorithms based on the Schur technique.

CONTROL OF REINFORCEMENT CORROSION BY SURFACE TREATMENT OF CONCRETE.

It is known from laboratory studies that reinforcement corrosion in carbonated concrete can be controlled simply by ensuring that the concrete remains relatively dry. An apparently obvious and cost effective way of excluding external moisture from building components which are not exposed to effects of capillary suction from groundwater, etc. is by applying a waterproof coating to the surface of the concrete. A research programme was undertaken for six years, with the primary aim of assessing whether coatings with appropriate characteristics could maintain suitably dry conditions within concrete in real carbonated structures. A secondary aim was to determine whether a similar predicted extension of the service life could be achieved if corrosion of the reinforcement were induced by internal chlorides. It was recognized from the outset that trials on real structures should be planned so that critical questions that determine the feasibility of the protection technique might be answered. This paper gives an account of the procedures adopted to select appropriate reinforced concrete buildings and characterize repetitive components to allow adequate comparison between the treated materials and controls. It also deals with the selection of candidate surface treatments by specialist manufacturers, the application of these materials according to recommended procedures, the implementation of relevant in-situ monitoring techniques and the extraction of small specimens from the structures for parallel laboratory trials. Results showed that an appropriate elastomeric coating with good crack-bridging properties, fairly low adhesion and good resistance to weathering can maintain a coherent crack-free covering that excludes external moisture and controls the corrosion rate of the reinforcement in carbonated concrete at acceptable levels over a period of at least five years. When corrosion was caused by internal chlorides, however, the concrete could not be maintained in a sufficiently dry condition to provide adequate long term protection to the steel.

Control of reinforcement corrosion by surface treatment of concrete

It is known from laboratory studies that reinforcement corrosion in carbonated concrete can be controlled simply by ensuring that the concrete remains relatively dry. An apparently obvious and cost effective way of excluding external moisture from building components which are not exposed to effects of capillary suction from groundwater, etc. is by applying a waterproof coating to the surface of the concrete. A research programme was undertaken for six years, with the primary aim of assessing whether coatings with appropriate characteristics could maintain suitably dry conditions within concrete in real carbonated structures. A secondary aim was to determine whether a similar predicted extension of the service life could be achieved if corrosion of the reinforcement were induced by internal chlorides. It was recognized from the outset that trials on real structures should be planned so that critical questions that determine the feasibility of the protection technique might be answered. This paper gives an account of the procedures adopted to select appropriate reinforced concrete buildings and characterize repetitive components to allow adequate comparison between the treated materials and controls. It also deals with the selection of candidate surface treatments by specialist manufacturers, the application of these materials according to recommended procedures, the implementation of relevant in-situ monitoring techniques and the extraction of small specimens from the structures for parallel laboratory trials. Results showed that an appropriate elastomeric coating with good crack-bridging properties, fairly low adhesion and good resistance to weathering can maintain a coherent crack-free covering that excludes external moisture and controls the corrosion rate of the reinforcement in carbonated concrete at acceptable levels over a period of at least five years. When corrosion was caused by internal chlorides, however, the concrete could not be maintained in a sufficiently dry condition to provide adequate long term protection to the steel.

Strategies for Assessing the Implications of Malformed Frogs for Environmental Health

The recent increase in the incidence of deformities among natural frog populations has raised concern about the state of the environment and the possible impact of unidentified causative agents on the health of wildlife and human populations. An open workshop on Strategies for Assessing the Implications of Malformed Frogs for Environmental Health was convened on 4-5 December 1997 at the National Institute of Environmental Health Sciences in Research Triangle Park, North Carolina. The purpose of the workshop was to share information among a multidisciplinary group with scientific interest and responsibility for human and environmental health at the federal and state level. Discussions highlighted possible causes and recent findings directly related to frog deformities and provided insight into problems and strategies applicable to continuing investigation in several areas. Possible causes of the deformities were evaluated in terms of diagnostics performed on field amphibians, biologic mechanisms that can lead to the types of malformations observed, and parallel laboratory and field studies. Hydrogeochemistry must be more integrated into environmental toxicology because of the pivotal role of the aquatic environment and the importance of fates and transport relative to any potential exposure. There is no indication of whether there may be a human health factor associated with the deformities. However, the possibility that causal agents may be waterborne indicates a need to identify the relevant factors and establish the relationship between environmental and human health in terms of hazard assessment.

Strategies for assessing the implications of malformed frogs for environmental health.

The recent increase in the incidence of deformities among natural frog populations has raised concern about the state of the environment and the possible impact of unidentified causative agents on the health of wildlife and human populations. An open workshop on Strategies for Assessing the Implications of Malformed Frogs for Environmental Health was convened on 4-5 December 1997 at the National Institute of Environmental Health Sciences in Research Triangle Park, North Carolina. The purpose of the workshop was to share information among a multidisciplinary group with scientific interest and responsibility for human and environmental health at the federal and state level. Discussions highlighted possible causes and recent findings directly related to frog deformities and provided insight into problems and strategies applicable to continuing investigation in several areas. Possible causes of the deformities were evaluated in terms of diagnostics performed on field amphibians, biologic mechanisms that can lead to the types of malformations observed, and parallel laboratory and field studies. Hydrogeochemistry must be more integrated into environmental toxicology because of the pivotal role of the aquatic environment and the importance of fates and transport relative to any potential exposure. There is no indication of whether there may be a human health factor associated with the deformities. However, the possibility that causal agents may be waterborne indicates a need to identify the relevant factors and establish the relationship between environmental and human health in terms of hazard assessment.

A comparison of mesophilic composting and unamended land treatment for the bioremediation of aged tar residues in soil

AbstractA field study was conducted to compare the effectiveness of land treatment and mesophilic composting in removing aged polycyclic aromatic hydrocarbons (PAH) from soil. The soil composting treatment, which had 20 percent (w/w) fresh organic matter incorporated into the soil, reached mesophilic temperatures of 45 to 50°C at week 3–4 and was effective in reducing PAH from 2240 mg/kg to 120 mg/kg after 224 days of treatment. Conventional land treatment with and without added cow manure (5 percent w/w) was less effective in removing the PAH from the soil than was the mesophilic soil composting treatment. In a parallel laboratory trial, PAH concentrations were reduced below 500 mg/kg (the target cleanup concentration for the site) when the contaminated soil was amended with 20 to 30 percent (w/w) fresh organic matter after 186 days of treatment. PAH degradation was lower in the laboratory trial compared with the field trial and no self‐heating of soil was demonstrated in the laboratory. Based on the relatively high total heterotrophic and naphthalene‐degrading microbial populations in the nonsterile treatments, it was apparent that the absence of microorganisms was unlikely to have limited the biodegradation of PAH in the current study. Fresh organic matter amendments of green tree waste and cow manure, regular mixing of the compost, and maintenance of moisture by regular watering were critical factors in achieving the target PAH concentrations.

IN SITU BIOASSAY CHAMBER FOR ASSESSMENT OF SEDIMENT TOXICITY AND BIOACCUMULATION USING BENTHIC INVERTEBRATES

In this study, we describe the construction of a simple, inexpensive bioassay chamber for testing sediment toxicity (survival and growth) and bioaccumulation under field conditions using the midge Chironomus tentans and the oligochaete Lumbriculus variegatus, The test chamber is comprised of a Lexan® or Plexiglass core tube containing several screened ports to facilitate water exchange. A rubber stopper, equipped with a small plastic holding vessel to hold organisms, is secured on top of the test chamber before deploying the tube. Once the test chamber is pushed into the sediment to a depth of approximately 20 cm, the bioassay is initiated by releasing the test organisms from the holding chamber into the test chamber. We evaluated the performance of this in situ bioassay system by conducting 10-d exposures at two contaminated and two reference sites, and in a transplanted control sediment. Performance in the field test was compared to parallel 10-d laboratory tests. Survival of C. tentans was 68 and 72% at the two reference sites. Corresponding survival in these sediments in laboratory tests was 96 and 75%. Survival in the transplanted control sediment was 97%. Although significant differences between sediments in the absolute values of survival and growth were observed in both field and laboratory exposures to contaminated sediments, the relative pattern of response for these endpoints was comparable between the laboratory and the field. Variability (coefficient of variation) associated with both survival and growth was generally greater in field exposures (20-86%) than in laboratory exposures (5-72%). A portion of this variability seemed to reflect the occurrence of predatory species, because we observed a significant relationship between the number of predatory species and survival of C. tentans. In tests with L. variegatus, survival of worms was 85% in the reference sediment and 40 to 76% in two contaminated sediments. At all sites, a sufficient tissue mass of worms was collected after 10 d to facilitate assessment of bioaccumulation. The results of this study demonstrate that the proposed in situ bioassay can be used successfully to assess toxicity and bioaccumulation in contaminated sediments.

Anaerobic treatment of liquid fraction of hen manure in UASB reactors

The anaerobic treatment of liquid fraction of hen manure was studied in two parallel laboratory 2·6 l UASB reactors at 35°C. The granular sludge from a laboratory UASB reactor treating synthetic wastewater was used as a seed sludge. The liquid fraction of hen manure was obtained directly from an industrial farm located in Moscow region after separation of diluted manure in situ into solid and liquid fractions. Before feeding, the waste water was preacidified under microaerobic conditions at laboratory ambient temperature (18–20°C) for 1–2 days. The influent COD was 10·5–20 g/l of which volatile fatty acids (VFA) were 3·9–6·7 g COD/l, pH was between 6·2–7·1. The initial organic loading rate (OLR) was 1 g COD/l day −1, then it was stepwise increased to the values of 11–12 g COD/l day −1. Under these OLR and hydraulic retention time of 1–2 days, both reactors demonstrated optimal stability with treatment efficiencies on total COD reduction of 70–75%. The biogas production rate at the OLR of 11–12 g COD/l day −1 was 3·5–3·6 l/l day −1 (methane content — 79–81%) and effluent pH of about 8.

Comparison of the microbial barrier properties of a needleless and a conventional needle-based intravenous access system

Background: Sporadic reports of increased infection rates involving needleless access systems, especially in home-care settings, have raised questions concerning the safety of all needleless systems. Addressing this concern, Baxter Healthcare Corporation and the Centers for Disease Control and Prevention performed parallel laboratory studies comparing the microbial barrier properties of the Interlink (trademark of Baxter Healthcare Corporation, Deerfield, Ill) needleless system with a conventional intravenous access system. Methods: Studies of needleless and conventional systems evaluated fluid path contamination introduced through injection site septa, which were intentionally inoculated with high levels of bacteria and subsequently punctured with and without alcohol swabbing disinfection before access. Results: With disinfection, the combined effects of the disinfection technique and the barrier properties of the septa prevented the transfer of organisms into the fluid path in 94% to 96% of needleless test articles and 96% to 100% of conventional test articles. Without disinfection, the barrier properties of the septa alone prevented the transfer of organisms into the fluid path in 20% to 69% of needleless test articles and 10% to 28% of conventional test articles. Conclusions: The data demonstrate the needleless system performs as well as the conventional intravenous access system with respect to the risk of microbial contamination and reinforce the need for appropriate septum disinfection before accessing either system (AJIC Am J Infect Control 1998;26:437-41).

Microbial Destruction of Feldspars

It now seems clear that feldspar weathering dynamics in natural systems is not well modelled by the typical inorganic and abiotic laboratory experiment. In particular, the role of micro-organisms in feldspar weathering has only recently been directly examined or documented. Mounting evidence, however suggests that bacteria attached to feldspar surfaces can greatly accelerate the rate of feldspar dissolution, but two important questions remain why, and how. Here we report the results of field experiments combined with parallel laboratory experiments that help constrain the question of how, and suggests a hypothesis for why; microorganisms may destroy feldspars to gain access to trace or limiting nutrients, primarily by the production of organic ligands.

Self management of oral anticoagulant therapy after heart valve replacement.

Patients with mechanical heart valves require lifelong oral anticoagulant treatment which entails frequent blood sampling and dosage adjustment. The purpose of this study was to investigate the feasibility of letting heart valve operated patients manage blood specimen analysis and dosage adjustment themselves. A total of 21 patients were enrolled in the study and followed for at least 9 months postoperatively. Immediately after the heart valve operation they were trained in operating a CoaguChek international normal ratio (INR) monitor to analyze capillary whole blood samples. Subsequently training in dosage adjustment was accomplished and all patients were considered fully capable of self management after 30 weeks. In the training period, parallel laboratory INR measurements were made at 3-4 week intervals for reference. A control group of 20 patients was matched, respectively, to the study group. The INR target range was 2.0-3.0. Out of the 21 study patients 19 continued self management beyond 9 months. The median INR value obtained with the monitor was within therapeutic target range for all study patients and only 15 out of 20 control patients were within this range. The mean systematic deviation between laboratory and CoaguChek INR was 7.8% but each patient had a constant characteristic deviation from -11 to +21%. The study patients were within therapeutic target range 77% of the time compared with 53% for the control patients. Self management of oral anticoagulation is feasible for selected patients and constitutes a significant service improvement compared with conventional management. The CoaguChek monitor seems sufficiently accurate and reliable for self testing and the treatment quality is comparable or even better than conventional management. Assessment of the rate of bleeding and thrombo-embolic events shall be settled in studies comprising larger number of patients.

Natural thermal stress and heat‐shock protein expression in Drosophila larvae and pupae

1. Whether Drosophila larvae and pupae naturally experience temperatures that can cause heat damage or death is poorly understood, but bears directly on numerous investigations of the thermal biology and heat‐shock response in Drosophila. Accordingly, the temperatures of necrotic fruit, which Drosophila larvae and pupae inhabit, the temperatures of larvae and pupae outside the laboratory, and the levels of the heat‐shock protein hsp 70 expressed by larvae in nature were examined. 2. When necrotic fruit was sunlit, internal temperatures rose to levels that can harm indwelling insects. Fruit size and evaporative water loss affected these temperatures. Temperatures of larvae and pupae in the field commonly exceeded 35 °C, with living larvae recorded at >44°C and pupae at >41°C. Natural mortality was evident, presumably because of heat. 3. In the laboratory, these temperatures kill larvae rapidly, with LT50s (time taken for half the sample to be killed) of 30 min at 39 °C, 15 min at 40 °C and 8·5 min at 41 °C. Gradual transfer from 25°C to these temperatures resulted in no lesser mortality than did direct transfer. 4. Hsp 70 levels in lysates of whole larvae were measured by ELISA (enzyme‐link immunosorbent assay) with an hsp 70‐specific antibody. For larvae within necrotic apples experimentally transferred from shade to sun and within necrotic fruit in situ, hsp 70 levels equalled or exceeded levels detected in parallel laboratory studies of whole larvae or cells in culture. 5. These data provide an ecological context for studies of thermal stress and the heat‐shock response in Drosophila that has heretofore been lacking.

Solepur: A Soil Treatment Process for Pig Slurry with Subsequent Denitrification of Drainage Water

The soil purification capacity for treating pig slurry was evaluated over five years using a hydrologically isolated field treatment plant, the so-called “Solepur” process. This involves three operations: (1) overdosing the managed field with surplus slurry, (2) collecting and treating the nitrate rich leachate, (3) irrigating the final treated water over other fields. The facility consists of (1) a managed field (3280 mr2) which allows the total recovery of all the leachate water which percolates through growing ryegrass, Lolium perenne, to which the pig slurry is applied, (2) a storage-pump-reactor system for denitrification and (3) a non-managed field for completing treatment. The purpose of this study was to evaluate over a five year monitoring period, the feasibility and performances of such a process, and to determine the optimum operating conditions. From 1991 to 1995, 4931 mr3/ha of raw pig slurry was applied to the managed field, which represents a nominal load of 986 mr3 ha - 1 yr - 1. This process decreased the COD of pig slurry by 99·9% and removed 99·9% of phosphorus and approximately 90% of nitrogen. The Solepur’s final product is a limpid leachate containing a very low concentration of organic matter, but with relatively high nitrate levels resulting from oxidation of slurry nitrogen in soil. The extent of nitrification efficiency was satisfactorily demonstrated both through soil inorganic-N profiles and through continuous analysis of the leachate water leaving the overdosed field which shows nitrate concentration up to 1500 mg/l. Subsequently, the nitrogen removal from the nitrate rich leachate was achieved through batch denitrification sequences: raw pig slurry (which supplies carbon to support biological denitrification) is added to a volume of 150 to 250 mr3 of drainage water (representing a nitrogen load of 10 to 40 kg N) in the ratio 1:20 to 1:100 v/v. Parallel laboratory tests showed the influence of C/NO - 3-N ratio on the efficiency of nitrate nitrogen removal and demonstrated the feasibility of semi-continuous denitrification. It was confirmed that a C/NO - 3-N ratio of three is necessary to achieve a complete denitrification sequence. The results conclusively show that the Solepur process is a promising waste treatment system.

Experiences with on-line measurements at a wastewater treatment plant for extended nitrogen removal

On-line sensors have been used at the Klagshamn treatment plant to measure the concentration of suspended solids in the raw wastewater, in the primary effluent and in the secondary effluent. By means of the sensors the short-term performance of the primary and the secondary treatment have been evaluated. The sensors are important when the total discharges of pollutants from the plant are to be considered during storm water events. Parallel on-line measurements and laboratory analyses of grab samples have shown that the used sensor type, based on NIR technique, reflects the concentrations rather well. The on-line measurement in the raw wastewater is rather unreliable due to clogging which means that using this application for control can be questioned.

Parallel threads

One objective in establishing our NSF ILI funded parallel computation laboratory was to use closed, formal laboratory assignments to introduce parallelism throughout the core computer science curriculum. We discuss laboratory assignments developed for the Computer Organization (CS 3) and Algorithms (CS 4) courses. The CS 3 lab introduces parallelism based upon processor replication and two-performance indices for evaluating performance of parallel algorithms, speedup and efficiency. One factor that effects performance on MIMD message passage architectures, the ratio of computation to communication, is also introduced. The CS 4 lab guides students in developing a parallel version of Dijkstra's single source shortest path algorithm. A case study using parallel addition assists students in identifying potential parallelism by examining the data dependency of computations. Students working in teams of two develop a pseudo-code version of the single source shortest path algorithm for an abstract parallel machine. They also analyze the speedup and efficiency of an implementation of the algorithm for one, four and eight processors.

Non-lethal defoliation to impair the foliar uptake of fallout radionuclides by forest trees

The foliar uptake of fallout radionuclides is the most important way of contamination of plant species. The Chernobyl accident showed that the management of contaminated forest is not an easy task. Studies on countermeasures after a nuclear accident performed within the European RESSAC programme (Rehabilitation of Soils and Surfaces after an Accident) were undertaken to impair the internal contamination of woody parts of forest trees as well as perennial cultures like vine or orchards. The first non-lethal defoliation experiments were to examine the selection of appropriate defoliants. The five compounds experimented are non-toxic to man and wildlife. Some which give good results are normally used to chemically dress vine without adverse effect on plant health and are expected to be non-lethal defoliants. Parallel laboratory experiments on the translocation kinetics of soluble labelled caesium and strontium deposited on the leaves proved that only 2% of the deposited activity is translocated into the stem of poplar and oak after 200 h. These kinetics compared to those of defoliants may suggest that this countermeasure would be efficient in impairing the contamination of woody parts of forest trees.

Non-lethal defoliation to impair the foliar uptake of fallout radionuclides by forest trees

The foliar uptake of fallout radionuclides is the most important way of contamination of plant species. The Chernobyl accident showed that the management of contaminated forest is not an easy task. Studies on countermeasures after a nuclear accident performed within the European RESSAC programme (Rehabilitation of Soils and Surfaces after an Accident) were undertaken to impair the internal contamination of woody parts of forest trees as well as perennial cultures like vine or orchards. The first non-lethal defoliation experiments were to examine the selection of appropriate defoliants. The five compounds experimented are non-toxic to man and wildlife. Some which give good results are normally used to chemically dress vine without adverse effect on plant health and are expected to be non-lethal defoliants. Parallel laboratory experiments on the translocation kinetics of soluble labelled caesium and strontium deposited on the leaves proved that only 2% of the deposited activity is translocated into the stem of poplar and oak after 200 h. These kinetics compared to those of defoliants may suggest that this countermeasure would be efficient in impairing the contamination of woody parts of forest trees.

Blood esterase inhibition in birds as an index of organophosphorus contamination: field and laboratory studies

: With the aim of developing a nondestructive biomarker (serum 'B' esterases) for monitoring bird populations exposed to azamethiphos S((6-chloro-2-oxooxazolo(4,5-b)pyridin-3(2H)-yl)methyl) 0,0-dimethyl phosphorothioate (9Cl), parallel laboratory and field studies were performed. In japanese quail (Coturnix coturnix japonica) treated with azamethiphos at 10 mg kg(-1), serum butyrylcholinesterase (BChE) and carboxylesterase (CE) activities were inhibited by 88% and 35%, respectively, after 24 h. A gradual recovery was observed after 48 and 72 h. With a higher dose (50 mg kg(-1)), the birds died, or were killed 3 h after dosing. Serum BChE and brain acetylcholinesterase (AChE), in birds that were sampled at 3 h, were inhibited by 98% and 92%, respectively. Hepatic microsomal and serum CEs were also inhibited. There was a statistically significant correlation (r=0.9808, p<0.001) between the activities of serum BChE and brain AChE. Swallows (Hirundo rustica) nesting in a stable treated with azamethiphos showed a drastic reduction in BChE (56%) and CE (36%) 24 h after treatment of the stable.

Prediction of nitrogen availability and rice yield in lowland soils: Nitrogen mineralization parameters

Field experiments were conducted under flooded soil conditions using Maahas clay amended with urea and rice straw-sesbania mixtures during the wet and dry seasons. Parallel laboratory incubation tests were done. The objectives were 1) to determine N mineralization patterns and establish the relationship between mineralization parameters and either N availability or grain yield, and 2) to correlate the results of organic N mineralization studies in the laboratory with data from field experiments. The N mineralization patterns of flooded soils in the laboratory followed a logistic function. In laboratory studies, mineralization potential was positively correlated with extractable soil NH4+-N at the end of the incubation period (cumulative available N). Likewise, mineralization potential calculated from laboratory studies was positively correlated with N uptake and grain yield from field studies. Extractable (NH4++NO3−)-N in the field correlated positively with extractable NH4+-N in the laboratory. The extractable NH4+-N from laboratory incubations at 14 days after transplanting, panicle initiation, and maturity was also highly and positively correlated with grain yield from field experiments.

Environmental cues of estrus in the North American red squirrel (Tamiasciurus hudsonicus Bangs)

During three breeding seasons, variation in the timing of estrus was monitored in wild red squirrels (Tamiasciurus hudsonicus) in a jack pine forest in central Alberta. The proximate environmental factors that affect the timing of the onset of the breeding season in female squirrels, and variation in dates of estrus, were studied in parallel laboratory and field manipulations. Wild squirrels given ad libitum sunflower seed experienced a positive energy balance (weight gains) earlier in the season than did females on a normal diet. Seed addition advanced dates of estrus by an average of 3 weeks. Three potential cuing mechanisms for the seasonal onset of estrus were proposed and tested: onset of estrus is cued by (i) a simple response to net energy gain, (ii) an interaction between an endogenous circannual rhythm and net energy gain, or (iii) an interaction between annual changes in photoperiod and net energy gain in the absence of a circannual rhythm. Our results refute the first and third mechanisms, and support the idea that red squirrels have a circannual reproductive cycle entrained by photoperiod. Net energy gain interacts with this annual cycle to fine tune the time of ovulation. In laboratory experiments, female squirrels exposed to increasing day length experienced estrus within the normal season. Squirrels kept in constant short-day conditions (&lt; 12 h), had delayed estrus cycles. Short-day conditions did not prevent the annual cycle of reproduction, indicating that an endogenous rhythm exists and is entrained by increasing day length. Comparisons with hibernating squirrels are discussed.