Treatment of Slaughter House Wastewater in a Sequencing Batch Reactor: Performance Evaluation and Biodegradation Kinetics

PubMed Central

Kundu, Pradyut; Debsarkar, Anupam; Mukherjee, Somnath

2013-01-01

Slaughterhouse wastewater contains diluted blood, protein, fat, and suspended solids, as a result the organic and nutrient concentration in this wastewater is vary high and the residues are partially solubilized, leading to a highly contaminating effect in riverbeds and other water bodies if the same is let off untreated. The performance of a laboratory-scale Sequencing Batch Reactor (SBR) has been investigated in aerobic-anoxic sequential mode for simultaneous removal of organic carbon and nitrogen from slaughterhouse wastewater. The reactor was operated under three different variations of aerobic-anoxic sequence, namely, (4+4), (5+3), and (3+5) hr. of total react period with two different sets of influent soluble COD (SCOD) and ammonia nitrogen (NH4 +-N) level 1000 ± 50 mg/L, and 90 ± 10 mg/L, 1000 ± 50 mg/L and 180 ± 10 mg/L, respectively. It was observed that from 86 to 95% of SCOD removal is accomplished at the end of 8.0 hr of total react period. In case of (4+4) aerobic-anoxic operating cycle, a reasonable degree of nitrification 90.12 and 74.75% corresponding to initial NH4 +-N value of 96.58 and 176.85 mg/L, respectively, were achieved. The biokinetic coefficients (k, K s, Y, k d) were also determined for performance evaluation of SBR for scaling full-scale reactor in future operation. PMID:24027751

Bacteria of the Candidate Phylum TM7 are Prevalent in Acidophilic Nitrifying Sequencing-Batch Reactors

PubMed Central

Hanada, Akiko; Kurogi, Takashi; Giang, Nguyen Minh; Yamada, Takeshi; Kamimoto, Yuki; Kiso, Yoshiaki; Hiraishi, Akira

2014-01-01

Laboratory-scale acidophilic nitrifying sequencing-batch reactors (ANSBRs) were constructed by seeding with sewage-activated sludge and cultivating with ammonium-containing acidic mineral medium (pH 4.0) with or without a trace amount of yeast extract. In every batch cycle, the pH varied between 2.7 and 4.0, and ammonium was completely converted to nitrate. Attempts to detect nitrifying functional genes in the fully acclimated ANSBRs by PCR with previously designed primers mostly gave negative results. 16S rRNA gene-targeted PCR and a subsequent denaturating gradient gel electrophoresis analysis revealed that a marked change occurred in the bacterial community during the overall period of operation, in which members of the candidate phylum TM7 and the class Gammaproteobacteria became predominant at the fully acclimated stage. This result was fully supported by a 16S rRNA gene clone library analysis, as the major phylogenetic groups of clones detected (>5% of the total) were TM7 (33%), Gammaproteobacteria (37%), Actinobacteria (10%), and Alphaproteobacteria (8%). Fluorescence in situ hybridization with specific probes also demonstrated the prevalence of TM7 bacteria and Gammaproteobacteria. These results suggest that previously unknown nitrifying microorganisms may play a major role in ANSBRs; however, the ecophysiological significance of the TM7 bacteria predominating in this process remains unclear. PMID:25241805

Effects of chlortetracycline amended feed on anaerobic sequencing batch reactor performance of swine manure digestion.

PubMed

Dreher, Teal M; Mott, Henry V; Lupo, Christopher D; Oswald, Aaron S; Clay, Sharon A; Stone, James J

2012-12-01

The effects of antimicrobial chlortetracycline (CTC) on the anaerobic digestion (AD) of swine manure slurry using anaerobic sequencing batch reactors (ASBRs) was investigated. Reactors were loaded with manure collected from pigs receiving CTC and no-antimicrobial amended diets at 2.5 g/L/d. The slurry was intermittently fed to four 9.5L lab-scale anaerobic sequencing batch reactors, two with no-antimicrobial manure, and two with CTC-amended manure, and four 28 day ASBR cycles were completed. The CTC concentration within the manure was 2 8 mg/L immediately after collection and 1.02 mg/L after dilution and 250 days of storage. CTC did not inhibit ASBR biogas production extent, however the volumetric composition of methane was significantly less (approximately 13% and 15% for cycles 1 and 2, respectively) than the no-antimicrobial through 56 d. CTC decreased soluble chemical oxygen demand and acetic acid utilization through 56 d, after which acclimation to CTC was apparent for the duration of the experiment. Copyright © 2012 Elsevier Ltd. All rights reserved.

Fe(II) oxidation during acid mine drainage neutralization in a pilot-scale Sequencing Batch Reactor.

PubMed

Zvimba, J N; Mathye, M; Vadapalli, V R K; Swanepoel, H; Bologo, L

2013-01-01

This study investigated Fe(II) oxidation during acid mine drainage (AMD) neutralization using CaCO3 in a pilot-scale Sequencing Batch Reactor (SBR) of hydraulic retention time (HRT) of 90 min and sludge retention time (SRT) of 360 min in the presence of air. The removal kinetics of Fe(II), of initial concentration 1,033 ± 0 mg/L, from AMD through oxidation to Fe(III) was observed to depend on both pH and suspended solids, resulting in Fe(II) levels of 679 ± 32, 242 ± 64, 46 ± 16 and 28 ± 0 mg/L recorded after cycles 1, 2, 3 and 4 respectively, with complete Fe(II) oxidation only achieved after complete neutralization of AMD. Generally, it takes 30 min to completely oxidize Fe(II) during cycle 4, suggesting that further optimization of SBR operation based on both pH and suspended solids manipulation can result in significant reduction of the number of cycles required to achieve acceptable Fe(II) oxidation for removal as ferric hydroxide. Overall, complete removal of Fe(II) during AMD neutralization is attractive as it promotes recovery of better quality waste gypsum, key to downstream gypsum beneficiation for recovery of valuables, thereby enabling some treatment-cost recovery and prevention of environmental pollution from dumping of sludge into landfills.

Indomethacin nanocrystals prepared by different laboratory scale methods: effect on crystalline form and dissolution behavior

NASA Astrophysics Data System (ADS)

Martena, Valentina; Censi, Roberta; Hoti, Ela; Malaj, Ledjan; Di Martino, Piera

2012-12-01

The objective of this study is to select very simple and well-known laboratory scale methods able to reduce particle size of indomethacin until the nanometric scale. The effect on the crystalline form and the dissolution behavior of the different samples was deliberately evaluated in absence of any surfactants as stabilizers. Nanocrystals of indomethacin (native crystals are in the γ form) (IDM) were obtained by three laboratory scale methods: A (Batch A: crystallization by solvent evaporation in a nano-spray dryer), B (Batch B-15 and B-30: wet milling and lyophilization), and C (Batch C-20-N and C-40-N: Cryo-milling in the presence of liquid nitrogen). Nanocrystals obtained by the method A (Batch A) crystallized into a mixture of α and γ polymorphic forms. IDM obtained by the two other methods remained in the γ form and a different attitude to the crystallinity decrease were observed, with a more considerable decrease in crystalline degree for IDM milled for 40 min in the presence of liquid nitrogen. The intrinsic dissolution rate (IDR) revealed a higher dissolution rate for Batches A and C-40-N, due to the higher IDR of α form than γ form for the Batch A, and the lower crystallinity degree for both the Batches A and C-40-N. These factors, as well as the decrease in particle size, influenced the IDM dissolution rate from the particle samples. Modifications in the solid physical state that may occur using different particle size reduction treatments have to be taken into consideration during the scale up and industrial development of new solid dosage forms.

Denitrifying capability and community dynamics of glycogen accumulating organisms during sludge granulation in an anaerobic-aerobic sequencing batch reactor

PubMed Central

Bin, Zhang; Bin, Xue; Zhigang, Qiu; Zhiqiang, Chen; Junwen, Li; Taishi, Gong; Wenci, Zou; Jingfeng, Wang

2015-01-01

Denitrifying capability of glycogen accumulating organisms (GAOs) has received great attention in environmental science and microbial ecology. Combining this ability with granule processes would be an interesting attempt. Here, a laboratory-scale sequencing batch reactor (SBR) was operated to enrich GAOs and enable sludge granulation. The results showed that the GAO granules were cultivated successfully and the granules had denitrifying capability. The batch experiments demonstrated that all NO3−-N could be removed or reduced, some amount of NO2−-N were accumulated in the reactor, and N2 was the main gaseous product. SEM analysis suggested that the granules were tightly packed with a large amount of tetrad-forming organisms (TFOs); filamentous bacteria served as the supporting structures for the granules. The microbial community structure of GAO granules was differed substantially from the inoculant conventional activated sludge. Most of the bacteria in the seed sludge grouped with members of Proteobacterium. FISH analysis confirmed that GAOs were the predominant members in the granules and were distributed evenly throughout the granular space. In contrast, PAOs were severely inhibited. Overall, cultivation of the GAO granules and utilizing their denitrifying capability can provide us with a new approach of nitrogen removal and saving more energy. PMID:26257096

Denitrifying capability and community dynamics of glycogen accumulating organisms during sludge granulation in an anaerobic-aerobic sequencing batch reactor.

PubMed

Bin, Zhang; Bin, Xue; Zhigang, Qiu; Zhiqiang, Chen; Junwen, Li; Taishi, Gong; Wenci, Zou; Jingfeng, Wang

2015-08-10

Denitrifying capability of glycogen accumulating organisms (GAOs) has received great attention in environmental science and microbial ecology. Combining this ability with granule processes would be an interesting attempt. Here, a laboratory-scale sequencing batch reactor (SBR) was operated to enrich GAOs and enable sludge granulation. The results showed that the GAO granules were cultivated successfully and the granules had denitrifying capability. The batch experiments demonstrated that all NO3(-)-N could be removed or reduced, some amount of NO2(-)-N were accumulated in the reactor, and N2 was the main gaseous product. SEM analysis suggested that the granules were tightly packed with a large amount of tetrad-forming organisms (TFOs); filamentous bacteria served as the supporting structures for the granules. The microbial community structure of GAO granules was differed substantially from the inoculant conventional activated sludge. Most of the bacteria in the seed sludge grouped with members of Proteobacterium. FISH analysis confirmed that GAOs were the predominant members in the granules and were distributed evenly throughout the granular space. In contrast, PAOs were severely inhibited. Overall, cultivation of the GAO granules and utilizing their denitrifying capability can provide us with a new approach of nitrogen removal and saving more energy.

Denitrifying capability and community dynamics of glycogen accumulating organisms during sludge granulation in an anaerobic-aerobic sequencing batch reactor

NASA Astrophysics Data System (ADS)

Bin, Zhang; Bin, Xue; Zhigang, Qiu; Zhiqiang, Chen; Junwen, Li; Taishi, Gong; Wenci, Zou; Jingfeng, Wang

2015-08-01

Denitrifying capability of glycogen accumulating organisms (GAOs) has received great attention in environmental science and microbial ecology. Combining this ability with granule processes would be an interesting attempt. Here, a laboratory-scale sequencing batch reactor (SBR) was operated to enrich GAOs and enable sludge granulation. The results showed that the GAO granules were cultivated successfully and the granules had denitrifying capability. The batch experiments demonstrated that all NO3--N could be removed or reduced, some amount of NO2--N were accumulated in the reactor, and N2 was the main gaseous product. SEM analysis suggested that the granules were tightly packed with a large amount of tetrad-forming organisms (TFOs); filamentous bacteria served as the supporting structures for the granules. The microbial community structure of GAO granules was differed substantially from the inoculant conventional activated sludge. Most of the bacteria in the seed sludge grouped with members of Proteobacterium. FISH analysis confirmed that GAOs were the predominant members in the granules and were distributed evenly throughout the granular space. In contrast, PAOs were severely inhibited. Overall, cultivation of the GAO granules and utilizing their denitrifying capability can provide us with a new approach of nitrogen removal and saving more energy.

A comparison of anaerobic 2, 4-dichlorophenoxy acetic acid degradation in single-fed and sequencing batch reactor systems

NASA Astrophysics Data System (ADS)

Elefsiniotis, P.; Wareham, D. G.; Fongsatitukul, P.

2017-08-01

This paper compares the practical limits of 2, 4-dichlorophenoxy acetic acid (2,4-D) degradation that can be obtained in two laboratory-scale anaerobic digestion systems; namely, a sequencing batch reactor (SBR) and a single-fed batch reactor (SFBR) system. The comparison involved synthesizing a decade of research conducted by the lead author and drawing summative conclusions about the ability of each system to accommodate industrial-strength concentrations of 2,4-D. In the main, 2 L liquid volume anaerobic SBRs were used with glucose as a supplemental carbon source for both acid-phase and two-phase conditions. Volatile fatty acids however were used as a supplemental carbon source for the methanogenic SBRs. The anaerobic SBRs were operated at an hydraulic retention time of 48 hours, while being subjected to increasing concentrations of 2,4-D. The SBRs were able to degrade between 130 and 180 mg/L of 2,4-D depending upon whether they were operated in the acid-phase or two-phase regime. The methanogenic-only phase did not achieve 2,4-D degradation however this was primarily attributed to difficulties with obtaining a sufficiently long SRT. For the two-phase SFBR system, 3.5 L liquid-volume digesters were used and no difficulty was experienced with degrading 100 % of the 2,4-D concentration applied (300 mg/L).

First-order kinetics of landfill leachate treatment in a pilot-scale anaerobic sequence batch biofilm reactor.

PubMed

Contrera, Ronan Cleber; da Cruz Silva, Katia Cristina; Morita, Dione Mari; Domingues Rodrigues, José Alberto; Zaiat, Marcelo; Schalch, Valdir

2014-12-01

This paper reports the kinetics evaluation of landfill leachate anaerobic treatment in a pilot-scale Anaerobic Sequence Batch Biofilm Reactor (AnSBBR). The experiment was carried out at room temperature (23.8 ± 2.1 °C) in the landfill area in São Carlos-SP, Brazil. Biomass from the bottom of a local landfill leachate stabilization pond was used as inoculum. After acclimated and utilizing leachate directly from the landfill, the AnSBBR presented efficiency over 70%, in terms of COD removal, with influent COD ranging from 4825 mg L(-1) to 12,330 mg L(-1). To evaluate the kinetics of landfill leachate treatment, temporal profiles of CODFilt. concentration were performed and a first-order kinetics model was adjusted for substrate consumption, obtaining an average k1 = 4.40 × 10(-5) L mgTVS(-1) d(-1), corrected to 25 °C. Considering the temperature variations, a temperature-activity coefficient θ = 1.07 was obtained. Statistical "Randomness" and "F" tests were used to successfully validate the model considered. Thus, the results demonstrate that the first-order kinetic model is adequate to model the anaerobic treatment of the landfill leachate in the AnSBBR. Copyright © 2014 Elsevier Ltd. All rights reserved.

Feeding schemes and C/N ratio of a laboratory-scale step-fed sequencing batch reactor for liquid swine manure treatment.

PubMed

Wu, Sarah Xiao; Zhu, Jun; Chen, Lide

2017-07-03

This study was undertaken to investigate the effect of two split feeding schemes (600 mL/200 mL and 400 mL/400 mL, designated as FS1 and FS2, respectively) on the performance of a step-fed sequencing batch reactor (SBR) in treating liquid swine manure for nutrient removal. The SBR was run on an 8-h cycle with a repeated pattern of anaerobic/anoxic/aerobic phases in each cycle and the two feedings always occurred at the beginning of each anaerobic phase. A low-level aeration was used (1.0 L/m 3 .sec) for the anoxic/aerobic phase to facilitate nitrification and phosphorus uptake while reducing the energy consumption. The results showed that FS1 reduced NH 4 + -N by 98.7% and FS2 by 98.3%. FS1 had 12.3 mg/L NO 3 -N left in the effluent, while FS2 had 4.51 mg/L. For soluble phosphorus removal, FS1 achieved 95.2%, while FS2 reached only 68.5%. Both feeding schemes achieved ≥ 95% removal of COD. A good power regression was observed between total nitrogen (sum of all three nitrogen species) and the carbon to nitrogen (C/N) ratio, with the correlation coefficients of 0.9729 and 0.9542 for FS1 and FS2, respectively, based on which it was concluded that higher C/N ratios were required to achieve higher nitrogen removal efficiencies.

Use of an anaerobic sequencing batch reactor for parameter estimation in modelling of anaerobic digestion.

PubMed

Batstone, D J; Torrijos, M; Ruiz, C; Schmidt, J E

2004-01-01

The model structure in anaerobic digestion has been clarified following publication of the IWA Anaerobic Digestion Model No. 1 (ADM1). However, parameter values are not well known, and uncertainty and variability in the parameter values given is almost unknown. Additionally, platforms for identification of parameters, namely continuous-flow laboratory digesters, and batch tests suffer from disadvantages such as long run times, and difficulty in defining initial conditions, respectively. Anaerobic sequencing batch reactors (ASBRs) are sequenced into fill-react-settle-decant phases, and offer promising possibilities for estimation of parameters, as they are by nature, dynamic in behaviour, and allow repeatable behaviour to establish initial conditions, and evaluate parameters. In this study, we estimated parameters describing winery wastewater (most COD as ethanol) degradation using data from sequencing operation, and validated these parameters using unsequenced pulses of ethanol and acetate. The model used was the ADM1, with an extension for ethanol degradation. Parameter confidence spaces were found by non-linear, correlated analysis of the two main Monod parameters; maximum uptake rate (k(m)), and half saturation concentration (K(S)). These parameters could be estimated together using only the measured acetate concentration (20 points per cycle). From interpolating the single cycle acetate data to multiple cycles, we estimate that a practical "optimal" identifiability could be achieved after two cycles for the acetate parameters, and three cycles for the ethanol parameters. The parameters found performed well in the short term, and represented the pulses of acetate and ethanol (within 4 days of the winery-fed cycles) very well. The main discrepancy was poor prediction of pH dynamics, which could be due to an unidentified buffer with an overall influence the same as a weak base (possibly CaCO3). Based on this work, ASBR systems are effective for parameter

Meeting Report: Batch-to-Batch Variability in Estrogenic Activity in Commercial Animal Diets—Importance and Approaches for Laboratory Animal Research

PubMed Central

Heindel, Jerrold J.; vom Saal, Frederick S.

2008-01-01

We report information from two workshops sponsored by the National Institutes of Health that were held to a) assess whether dietary estrogens could significantly impact end points in experimental animals, and b) involve program participants and feed manufacturers to address the problems associated with measuring and eliminating batch-to-batch variability in rodent diets that may lead to conflicting findings in animal experiments within and between laboratories. Data were presented at the workshops showing that there is significant batch-to-batch variability in estrogenic content of commercial animal diets, and that this variability results in differences in experimental outcomes. A combination of methods were proposed to determine levels of total estrogenic activity and levels of specific estrogenic constituents in soy-containing, casein-containing, and other soy-free rodent diets. Workshop participants recommended that researchers pay greater attention to the type of diet being used in animal studies and choose a diet whose estrogenic activity (or lack thereof) is appropriate for the experimental model and end points of interest. Information about levels of specific phytoestrogens, as well as estrogenic activity caused by other contaminants and measured by bioassay, should be disclosed in scientific publications. This will require laboratory animal diet manufacturers to provide investigators with information regarding the phytoestrogen content and other estrogenic compounds in commercial diets used in animal research. PMID:18335108

Meeting report: batch-to-batch variability in estrogenic activity in commercial animal diets--importance and approaches for laboratory animal research.

PubMed

Heindel, Jerrold J; vom Saal, Frederick S

2008-03-01

We report information from two workshops sponsored by the National Institutes of Health that were held to a) assess whether dietary estrogens could significantly impact end points in experimental animals, and b) involve program participants and feed manufacturers to address the problems associated with measuring and eliminating batch-to-batch variability in rodent diets that may lead to conflicting findings in animal experiments within and between laboratories. Data were presented at the workshops showing that there is significant batch-to-batch variability in estrogenic content of commercial animal diets, and that this variability results in differences in experimental outcomes. A combination of methods were proposed to determine levels of total estrogenic activity and levels of specific estrogenic constituents in soy-containing, casein-containing, and other soy-free rodent diets. Workshop participants recommended that researchers pay greater attention to the type of diet being used in animal studies and choose a diet whose estrogenic activity (or lack thereof) is appropriate for the experimental model and end points of interest. Information about levels of specific phytoestrogens, as well as estrogenic activity caused by other contaminants and measured by bioassay, should be disclosed in scientific publications. This will require laboratory animal diet manufacturers to provide investigators with information regarding the phytoestrogen content and other estrogenic compounds in commercial diets used in animal research.

The influence of pH adjustment on kinetics parameters in tapioca wastewater treatment using aerobic sequencing batch reactor system

NASA Astrophysics Data System (ADS)

Mulyani, Happy; Budianto, Gregorius Prima Indra; Margono, Kaavessina, Mujtahid

2018-02-01

The present investigation deals with the aerobic sequencing batch reactor system of tapioca wastewater treatment with varying pH influent conditions. This project was carried out to evaluate the effect of pH on kinetics parameters of system. It was done by operating aerobic sequencing batch reactor system during 8 hours in many tapioca wastewater conditions (pH 4.91, pH 7, pH 8). The Chemical Oxygen Demand (COD) and Mixed Liquor Volatile Suspended Solids (MLVSS) of the aerobic sequencing batch reactor system effluent at steady state condition were determined at interval time of two hours to generate data for substrate inhibition kinetics parameters. Values of the kinetics constants were determined using Monod and Andrews models. There was no inhibition constant (Ki) detected in all process variation of aerobic sequencing batch reactor system for tapioca wastewater treatment in this study. Furthermore, pH 8 was selected as the preferred aerobic sequencing batch reactor system condition in those ranging pH investigated due to its achievement of values of kinetics parameters such µmax = 0.010457/hour and Ks = 255.0664 mg/L COD.

40 CFR 205.57-7 - Acceptance and rejection of batch sequence.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 24 2010-07-01 2010-07-01 false Acceptance and rejection of batch sequence. 205.57-7 Section 205.57-7 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) NOISE ABATEMENT PROGRAMS TRANSPORTATION EQUIPMENT NOISE EMISSION CONTROLS Medium and Heavy Trucks § 205...

Comparison of some characteristics of aerobic granules and sludge flocs from sequencing batch reactors.

PubMed

Li, J; Garny, K; Neu, T; He, M; Lindenblatt, C; Horn, H

2007-01-01

Physical, chemical and biological characteristics were investigated for aerobic granules and sludge flocs from three laboratory-scale sequencing batch reactors (SBRs). One reactor was operated as normal SBR (N-SBR) and two reactors were operated as granular SBRs (G-SBR1 and G-SBR2). G-SBR1 was inoculated with activated sludge and G-SBR2 with granules from the municipal wastewater plant in Garching (Germany). The following major parameters and functions were measured and compared between the three reactors: morphology, settling velocity, specific gravity (SG), sludge volume index (SVI), specific oxygen uptake rate (SOUR), distribution of the volume fraction of extracellular polymeric substances (EPS) and bacteria, organic carbon and nitrogen removal. Compared with sludge flocs, granular sludge had excellent settling properties, good solid-liquid separation, high biomass concentration, simultaneous nitrification and denitrification. Aerobic granular sludge does not have a higher microbial activity and there are some problems including higher effluent suspended solids, lower ratio of VSS/SS and no nitrification at the beginning of cultivation. Measurement with CLSM and additional image analysis showed that EPS glycoconjugates build one main fraction inside the granules. The aerobic granules from G-SBR1 prove to be heavier, smaller and have a higher microbial activity compared with G-SBR2. Furthermore, the granules were more compact, with lower SVI and less filamentous bacteria.

Methanogenic population dynamics during startup of a full-scale anaerobic sequencing batch reactor treating swine waste.

PubMed

Angenent, Largus T; Sung, Shihwu; Raskin, Lutgarde

2002-11-01

Changes in methanogenic population levels were followed during startup of a full-scale, farm-based anaerobic sequencing batch reactor (ASBR) and these changes were linked to operational and performance data. The ASBR was inoculated with anaerobic digester sludge from a municipal wastewater treatment facility. During an acclimation period of approximately 3 months, the ASBR content was diluted to maintain a total ammonia-N level of approximately 2000mg l(-1). After this acclimation period, the volatile solids loading rate was increased to its design value of 1.7g l(-1) day(-1) with a 15-day hydraulic retention time, which increased the total ammonia-N level in the ASBR to approximately 3,600 mg l(-1). The 16S ribosomal RNA (rRNA) levels of the acetate-utilizing methanogens of the genus Methanosarcina decreased from 3.8% to 1.2% (expressed as a percentage of the total 16S rRNA levels) during this period, while the 16S rRNA levels of Methanosaeta concilii remained low (below 2.2%). Methane production and reactor performance were not affected as the 16S rRNA levels of the hydrogen-utilizing methanogens of the order Methanomicrobiales increased from 2.3% to 7.0%. Hence, it is likely that during operation with high ammonia levels, the major route of methane production is through a syntrophic relationship between acetate-oxidizing bacteria and hydrogen-utilizing methanogens. Anaerobic digestion at total ammonia-N levels exceeding 3500mg l(-1) was sustainable apparently due to the acclimation of hydrogen-utilizing methanogens to high ammonia levels.

Scale-up bioprocess development for production of the antibiotic valinomycin in Escherichia coli based on consistent fed-batch cultivations.

PubMed

Li, Jian; Jaitzig, Jennifer; Lu, Ping; Süssmuth, Roderich D; Neubauer, Peter

2015-06-12

Heterologous production of natural products in Escherichia coli has emerged as an attractive strategy to obtain molecules of interest. Although technically feasible most of them are still constrained to laboratory scale production. Therefore, it is necessary to develop reasonable scale-up strategies for bioprocesses aiming at the overproduction of targeted natural products under industrial scale conditions. To this end, we used the production of the antibiotic valinomycin in E. coli as a model system for scalable bioprocess development based on consistent fed-batch cultivations. In this work, the glucose limited fed-batch strategy based on pure mineral salt medium was used throughout all scales for valinomycin production. The optimal glucose feed rate was initially detected by the use of a biocatalytically controlled glucose release (EnBase® technology) in parallel cultivations in 24-well plates with continuous monitoring of pH and dissolved oxygen. These results were confirmed in shake flasks, where the accumulation of valinomycin was highest when the specific growth rate decreased below 0.1 h(-1). This correlation was also observed for high cell density fed-batch cultivations in a lab-scale bioreactor. The bioreactor fermentation produced valinomycin with titers of more than 2 mg L(-1) based on the feeding of a concentrated glucose solution. Valinomycin production was not affected by oscillating conditions (i.e. glucose and oxygen) in a scale-down two-compartment reactor, which could mimic similar situations in industrial bioreactors, suggesting that the process is very robust and a scaling of the process to a larger industrial scale appears a realistic scenario. Valinomycin production was scaled up from mL volumes to 10 L with consistent use of the fed-batch technology. This work presents a robust and reliable approach for scalable bioprocess development and represents an example for the consistent development of a process for a heterologously expressed natural

Sliding mode control of dissolved oxygen in an integrated nitrogen removal process in a sequencing batch reactor (SBR).

PubMed

Muñoz, C; Young, H; Antileo, C; Bornhardt, C

2009-01-01

This paper presents a sliding mode controller (SMC) for dissolved oxygen (DO) in an integrated nitrogen removal process carried out in a suspended biomass sequencing batch reactor (SBR). The SMC performance was compared against an auto-tuning PI controller with parameters adjusted at the beginning of the batch cycle. A method for cancelling the slow DO sensor dynamics was implemented by using a first order model of the sensor. Tests in a lab-scale reactor showed that the SMC offers a better disturbance rejection capability than the auto-tuning PI controller, furthermore providing reasonable performance in a wide range of operation. Thus, SMC becomes an effective robust nonlinear tool to the DO control in this process, being also simple from a computational point of view, allowing its implementation in devices such as industrial programmable logic controllers (PLCs).

The development of an industrial-scale fed-batch fermentation simulation.

PubMed

Goldrick, Stephen; Ştefan, Andrei; Lovett, David; Montague, Gary; Lennox, Barry

2015-01-10

This paper describes a simulation of an industrial-scale fed-batch fermentation that can be used as a benchmark in process systems analysis and control studies. The simulation was developed using a mechanistic model and validated using historical data collected from an industrial-scale penicillin fermentation process. Each batch was carried out in a 100,000 L bioreactor that used an industrial strain of Penicillium chrysogenum. The manipulated variables recorded during each batch were used as inputs to the simulator and the predicted outputs were then compared with the on-line and off-line measurements recorded in the real process. The simulator adapted a previously published structured model to describe the penicillin fermentation and extended it to include the main environmental effects of dissolved oxygen, viscosity, temperature, pH and dissolved carbon dioxide. In addition the effects of nitrogen and phenylacetic acid concentrations on the biomass and penicillin production rates were also included. The simulated model predictions of all the on-line and off-line process measurements, including the off-gas analysis, were in good agreement with the batch records. The simulator and industrial process data are available to download at www.industrialpenicillinsimulation.com and can be used to evaluate, study and improve on the current control strategy implemented on this facility. Crown Copyright © 2014. Published by Elsevier B.V. All rights reserved.

The mechanism and design of sequencing batch reactor systems for nutrient removal--the state of the art.

PubMed

Artan, N; Wilderer, P; Orhon, D; Morgenroth, E; Ozgür, N

2001-01-01

The Sequencing Batch Reactor (SBR) process for carbon and nutrient removal is subject to extensive research, and it is finding a wider application in full-scale installations. Despite the growing popularity, however, a widely accepted approach to process analysis and modeling, a unified design basis, and even a common terminology are still lacking; this situation is now regarded as the major obstacle hindering broader practical application of the SBR. In this paper a rational dimensioning approach is proposed for nutrient removal SBRs based on scientific information on process stoichiometry and modelling, also emphasizing practical constraints in design and operation.

6. FLUX WEIGH HOPPERS AND SCALES ON THE BATCHING FLOOR ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

6. FLUX WEIGH HOPPERS AND SCALES ON THE BATCHING FLOOR OF THE FURNACE AISLE IN THE BOP SHOP LOOKING SOUTHWEST. - U.S. Steel Duquesne Works, Basic Oxygen Steelmaking Plant, Along Monongahela River, Duquesne, Allegheny County, PA

Biodegradation of industrial-strength 2,4-dichlorophenoxyacetic acid wastewaters in the presence of glucose in aerobic and anaerobic sequencing batch reactors.

PubMed

Elefsiniotis, Panagiotis; Wareham, David G

2013-01-01

This research explored the biodegradability of 2,4-dichlorophenoxyacetic acid (2,4-D) in two laboratory-scale sequencing batch reactors (SBRs) that operated under aerobic and anaerobic conditions. The potential limit of 2,4-D degradation was investigated at a hydraulic retention time of 48 h, using glucose as a supplemental substrate and increasing feed concentrations of 2,4-D; namely 100 to 700 mg/L (i.e. industrial strength) for the aerobic system and 100 to 300 mg/L for the anaerobic SBR. The results revealed that 100 mg/L of 2,4-D was completely degraded following an acclimation period of 29 d (aerobic SBR) and 70 d (anaerobic SBR). The aerobic system achieved total 2,4-D removal at feed concentrations up to 600 mg/L which appeared to be a practical limit, since a further increase to 700 mg/L impaired glucose degradation while 2,4-D biodegradation was non-existent. In all cases, glucose was consumed before the onset of 2,4-D degradation. In the anaerobic SBR, 2,4-D degradation was limited to 120 mg/L.

Cycle-time determination and process control of sequencing batch membrane bioreactors.

PubMed

Krampe, J

2013-01-01

In this paper a method to determine the cycle time for sequencing batch membrane bioreactors (SBMBRs) is introduced. One of the advantages of SBMBRs is the simplicity of adapting them to varying wastewater composition. The benefit of this flexibility can only be fully utilised if the cycle times are optimised for the specific inlet load conditions. This requires either proactive and ongoing operator adjustment or active predictive instrument-based control. Determination of the cycle times for conventional sequencing batch reactor (SBR) plants is usually based on experience. Due to the higher mixed liquor suspended solids concentrations in SBMBRs and the limited experience with their application, a new approach to calculate the cycle time had to be developed. Based on results from a semi-technical pilot plant, the paper presents an approach for calculating the cycle time in relation to the influent concentration according to the Activated Sludge Model No. 1 and the German HSG (Hochschulgruppe) Approach. The approach presented in this paper considers the increased solid contents in the reactor and the resultant shortened reaction times. This allows for an exact calculation of the nitrification and denitrification cycles with a tolerance of only a few minutes. Ultimately the same approach can be used for a predictive control strategy and for conventional SBR plants.

Biodegradation of Jet Fuel-4 (JP-4) in Sequencing Batch Reactors

DTIC Science & Technology

1992-06-01

nalw~eo %CUMENTATION PAGE__ _ _ _ _ _ _ _ _O 74S Ab -A258 020 L AW POi~W6 DATI .~ TYP AIMqm ,-& 0 U. glbs A~ I ma"&LFUN Mu BIODEGRADATION OF JET FUEL...Specific Objectives of This Proposal Are: 1. To assess the ability of C. resinae , P. chrysosporium and selected bacterial consortia to degrade individual...chemical components of JP-4. 2. To develop a sequencing batch reactor that utilizes C. resinae to degrade chemical components of JP-4 in contaminated

A Novel Bioinformatics Strategy to Analyze Microbial Big Sequence Data for Efficient Knowledge Discovery: Batch-Learning Self-Organizing Map (BLSOM).

PubMed

Iwasaki, Yuki; Abe, Takashi; Wada, Kennosuke; Wada, Yoshiko; Ikemura, Toshimichi

2013-11-20

With the remarkable increase of genomic sequence data of microorganisms, novel tools are needed for comprehensive analyses of the big sequence data available. The self-organizing map (SOM) is an effective tool for clustering and visualizing high-dimensional data, such as oligonucleotide composition on one map. By modifying the conventional SOM, we developed batch-learning SOM (BLSOM), which allowed classification of sequence fragments (e.g., 1 kb) according to phylotypes, solely depending on oligonucleotide composition. Metagenomics studies of uncultivable microorganisms in clinical and environmental samples should allow extensive surveys of genes important in life sciences. BLSOM is most suitable for phylogenetic assignment of metagenomic sequences, because fragmental sequences can be clustered according to phylotypes, solely depending on oligonucleotide composition. We first constructed oligonucleotide BLSOMs for all available sequences from genomes of known species, and by mapping metagenomic sequences on these large-scale BLSOMs, we can predict phylotypes of individual metagenomic sequences, revealing a microbial community structure of uncultured microorganisms, including viruses. BLSOM has shown that influenza viruses isolated from humans and birds clearly differ in oligonucleotide composition. Based on this host-dependent oligonucleotide composition, we have proposed strategies for predicting directional changes of virus sequences and for surveilling potentially hazardous strains when introduced into humans from non-human sources.

A Semi-Batch Reactor Experiment for the Undergraduate Laboratory

ERIC Educational Resources Information Center

Derevjanik, Mario; Badri, Solmaz; Barat, Robert

2011-01-01

This experiment and analysis offer an economic yet challenging semi-batch reactor experience. Household bleach is pumped at a controlled rate into a batch reactor containing pharmaceutical hydrogen peroxide solution. Batch temperature, product molecular oxygen, and the overall change in solution conductivity are metered. The reactor simulation…

Effects of selected pharmaceutically active compounds on treatment performance in sequencing batch reactors mimicking wastewater treatment plants operations.

PubMed

Wang, Shuyi; Gunsch, Claudia K

2011-05-01

The impact of four pharmaceutically active compounds (PhACs) introduced both individually and in mixtures was ascertained on the performance of laboratory-scale wastewater treatment sequencing batch reactors (SBRs). When introduced individually at concentrations of 0.1, 1 and 10 μM, no significant differences were observed with respect to chemical oxygen demand (COD) and ammonia removal. Microbial community analyses reveal that although similarity index values generally decreased over time with an increase in PhAC concentrations as compared to the controls, no major microbial community shifts were observed for total bacteria and ammonia-oxidizing bacteria (AOB) communities. However, when some PhACs were introduced in mixtures, they were found to both inhibit nitrification and alter AOB community structure. Ammonia removal decreased by up to 45% in the presence of 0.25 μM gemfibrozil and 0.75 μM naproxen. PhAC mixtures did not however affect COD removal performance suggesting that heterotrophic bacteria are more robust to PhACs than AOB. These results highlight that the joint action of PhACs in mixtures may have significantly different effects on nitrification than the individual PhACs. This phenomenon should be further investigated with a wider range of PhACs so that toxicity effects can more accurately be predicted. Copyright © 2011 Elsevier Ltd. All rights reserved.

In situ profiling of microbial communities in full-scale aerobic sequencing batch reactors treating winery waste in australia.

PubMed

McIlroy, Simon J; Speirs, Lachlan B M; Tucci, Joseph; Seviour, Robert J

2011-10-15

On-site aerobic sequencing batch reactor (SBR) treatment plants are implemented in many Australian wineries to treat the large volumes of associated wastewater they generate. Yet very little is known about their microbiology. This paper represents the first attempt to analyze the communities of three such systems sampled during both vintage and nonvintage operational periods using molecular methods. Alphaproteobacterial tetrad forming organisms (TFO) related to members of the genus Defluviicoccus and Amaricoccus dominated all three systems in both operational periods. Candidatus 'Alysiosphaera europaea' and Zoogloea were codominant in two communities. Production of high levels of exocellular capsular material by Zoogloea and Amaricoccus is thought to explain the poor settleability of solids in one of these plants. The dominance of these organisms is thought to result from the high COD to N/P ratios that characterize winery wastes, and it is suggested that manipulating this ratio with nutrient dosing may help control the problems they cause.

Sequencing batch reactor biofilm system for treatment of milk industry wastewater.

PubMed

Sirianuntapiboon, Suntud; Jeeyachok, Narumon; Larplai, Rarintorn

2005-07-01

A sequencing batch reactor biofilm (MSBR) system was modified from the conventional sequencing batch reactor (SBR) system by installing 2.7 m2 surface area of plastic media on the bottom of the reactor to increase the system efficiency and bio-sludge quality by increasing the bio-sludge in the system. The COD, BOD5, total kjeldahl nitrogen (TKN) and oil & grease removal efficiencies of the MSBR system, under a high organic loading of 1340 g BOD5/m3 d, were 89.3+/-0.1, 83.0+/-0.2, 59.4+/-0.8, and 82.4+/-0.4%, respectively, while they were only 87.0+/-0.2, 79.9+/-0.3, 48.7+/-1.7 and 79.3+/-10%, respectively, in the conventional SBR system. The amount of excess bio-sludge in the MSBR system was about 3 times lower than that in the conventional SBR system. The sludge volume index (SVI) of the MSBR system was lower than 100 ml/g under an organic loading of up to 1340 g BOD5/m3 d. However, the MSBR under an organic loading of 680 g BOD5/m3 d gave the highest COD, BOD5, TKN and oil & grease removal efficiencies of 97.9+/-0.0, 97.9+/-0.1, 79.3+/-1.0 and 94.8+/-0.5%, respectively, without any excess bio-sludge waste. The SVI of suspended bio-sludge in the MSBR system was only 44+/-3.4 ml/g under an organic loading of 680 g BOD5/m3 d.

Hydrolytic activities of extracellular enzymes in thermophilic and mesophilic anaerobic sequencing-batch reactors treating organic fractions of municipal solid wastes.

PubMed

Kim, Hyun-Woo; Nam, Joo-Youn; Kang, Seok-Tae; Kim, Dong-Hoon; Jung, Kyung-Won; Shin, Hang-Sik

2012-04-01

Extracellular enzymes offer active catalysis for hydrolysis of organic solid wastes in anaerobic digestion. To evidence the quantitative significance of hydrolytic enzyme activities for major waste components, track studies of thermophilic and mesophilic anaerobic sequencing-batch reactors (TASBR and MASBR) were conducted using a co-substrate of real organic wastes. During 1day batch cycle, TASBR showed higher amylase activity for carbohydrate (46%), protease activity for proteins (270%), and lipase activity for lipids (19%) than MASBR. In particular, the track study of protease identified that thermophilic anaerobes degraded protein polymers much more rapidly. Results revealed that differences in enzyme activities eventually affected acidogenic and methanogenic performances. It was demonstrated that the superior nature of enzymatic capability at thermophilic condition led to successive high-rate acidogenesis and 32% higher CH(4) recovery. Consequently, these results evidence that the coupling thermophilic digestion with sequencing-batch operation is a viable option to promote enzymatic hydrolysis of organic particulates. Copyright © 2012 Elsevier Ltd. All rights reserved.

[Improvement of municipal sewage sludge dewaterability by bioleaching: a pilot-scale study with sequence batch reaction model].

PubMed

Liu, Fen-Wu; Zhou, Li-Xiang; Zhou, Jun; Jiang, Feng; Wang, Dian-Zhan

2011-07-01

To observe the bioleaching effect on sewage sludge dewaterability, three consecutive batch bioleaching experiments were conducted through a bioleaching bio-reactor with 700 L of working volume. Subsequently, the bioleached sludge was dewatered by using chamber filter press. The results show that the 1st batch bioleaching process can be finished within 90 hours if the aeration amount was 1.2 m3/h with the 1: 15 mixing ratio of bioleached sludge to raw sludge. The pH of sludge declines from initial 6.11 to 2.33 while ORP increased from initial -134 mV to finial 507 mV. The specific resistance to filtration (SRF) of the tested sludge was decreased from original 1.00 x 10(13) m/kg to final 0.09 x 10(13) m/kg after bioleaching. For the subsequent two batch trials, the bioleaching process can be finished in 40 hours and 46 hours, respectively. Likewise, sludge SRF is also significantly decreased to 0.19 x 10(13) m/kg and 0.36 x 10(13) m/kg if the mixing ratio of bioleached sludge to fresh sludge is 1:1 although the microbial nutrient substance dosage is reduced by 25% and 50% for 2nd, and 3rd batch experiments, respectively. The harvested bioleached sludge from three batch trails is dewatered by chamber filter press with 0.3-0.4 MPa working pressure for 2 hours. It is found that the moisture of dewatered sludge cake can be reduced to 58%, and that the dewatered sludge cake is of khaki appearance and didn't emit any offensive odor. In addition, it is also observes that sludge organic matter only changed a bit from 52.9% to 48.0%, but 58% of sludge-borne Cu and 88% of sludge-borne Zn can be removed from sludge by bioleaching process. Therefore, dual goals for sludge-borne heavy metal removal and sludge dewatering of high efficiency can be achieved simultaneously through the approach mentioned above. Therefore, bioleaching technique is of great engineering application for the treatment of sewage sludge.

miBLAST: scalable evaluation of a batch of nucleotide sequence queries with BLAST

PubMed Central

Kim, You Jung; Boyd, Andrew; Athey, Brian D.; Patel, Jignesh M.

2005-01-01

A common task in many modern bioinformatics applications is to match a set of nucleotide query sequences against a large sequence dataset. Exis-ting tools, such as BLAST, are designed to evaluate a single query at a time and can be unacceptably slow when the number of sequences in the query set is large. In this paper, we present a new algorithm, called miBLAST, that evaluates such batch workloads efficiently. At the core, miBLAST employs a q-gram filtering and an index join for efficiently detecting similarity between the query sequences and database sequences. This set-oriented technique, which indexes both the query and the database sets, results in substantial performance improvements over existing methods. Our results show that miBLAST is significantly faster than BLAST in many cases. For example, miBLAST aligned 247 965 oligonucleotide sequences in the Affymetrix probe set against the Human UniGene in 1.26 days, compared with 27.27 days with BLAST (an improvement by a factor of 22). The relative performance of miBLAST increases for larger word sizes; however, it decreases for longer queries. miBLAST employs the familiar BLAST statistical model and output format, guaranteeing the same accuracy as BLAST and facilitating a seamless transition for existing BLAST users. PMID:16061938

Lactic acid production from potato peel waste by anaerobic sequencing batch fermentation using undefined mixed culture.

PubMed

Liang, Shaobo; McDonald, Armando G; Coats, Erik R

2015-11-01

Lactic acid (LA) is a necessary industrial feedstock for producing the bioplastic, polylactic acid (PLA), which is currently produced by pure culture fermentation of food carbohydrates. This work presents an alternative to produce LA from potato peel waste (PPW) by anaerobic fermentation in a sequencing batch reactor (SBR) inoculated with undefined mixed culture from a municipal wastewater treatment plant. A statistical design of experiments approach was employed using set of 0.8L SBRs using gelatinized PPW at a solids content range from 30 to 50 g L(-1), solids retention time of 2-4 days for yield and productivity optimization. The maximum LA production yield of 0.25 g g(-1) PPW and highest productivity of 125 mg g(-1) d(-1) were achieved. A scale-up SBR trial using neat gelatinized PPW (at 80 g L(-1) solids content) at the 3 L scale was employed and the highest LA yield of 0.14 g g(-1) PPW and a productivity of 138 mg g(-1) d(-1) were achieved with a 1 d SRT. Copyright © 2015 Elsevier Ltd. All rights reserved.

Coexistence of nitrifying, anammox and denitrifying bacteria in a sequencing batch reactor

PubMed Central

Langone, Michela; Yan, Jia; Haaijer, Suzanne C. M.; Op den Camp, Huub J. M.; Jetten, Mike S. M.; Andreottola, Gianni

2014-01-01

Elevated nitrogen removal efficiencies from ammonium-rich wastewaters have been demonstrated by several applications, that combine nitritation and anammox processes. Denitrification will occur simultaneously when organic carbon is also present. In this study, the activity of aerobic ammonia oxidizing, anammox and denitrifying bacteria in a full scale sequencing batch reactor, treating digester supernatants, was studied by means of batch-assays. AOB and anammox activities were maximum at pH of 8.0 and 7.8–8.0, respectively. Short term effect of nitrite on anammox activity was studied, showing nitrite up to 42 mg/L did not result in inhibition. Both denitrification via nitrate and nitrite were measured. To reduce nitrite-oxidizing activity, high NH3-N (1.9–10 mg NH3-N/L) and low nitrite (3–8 mg TNN/L) are required conditions during the whole SBR cycle. Molecular analysis showed the nitritation-anammox sludge harbored a high microbial diversity, where each microorganism has a specific role. Using ammonia monooxygenase α–subunit (amoA) gene as a marker, our analyses suggested different macro- and micro-environments in the reactor strongly affect the AOB community, allowing the development of different AOB species, such as N. europaea/eutropha and N. oligotropha groups, which improve the stability of nitritation process. A specific PCR primer set, used to target the 16S rRNA gene of anammox bacteria, confirmed the presence of the “Ca. Brocadia fulgida” type, able to grow in presence of organic matter and to tolerate high nitrite concentrations. The diversity of denitrifiers was assessed by using dissimilatory nitrite reductase (nirS) gene-based analyses, who showed denitifiers were related to different betaproteobacterial genera, such as Thauera, Pseudomonas, Dechloromonas and Aromatoleum, able to assist in forming microbial aggregates. Concerning possible secondary processes, no n-damo bacteria were found while NOB from the genus Nitrobacter was detected

U.S.-MEXICO BORDER PROGRAM ARIZONA BORDER STUDY--STANDARD OPERATING PROCEDURE FOR BATCHING OF LABORATORY DATA (UA-C-7.0)

EPA Science Inventory

The purpose of this SOP is to describe the steps involved in batching the physical laboratory data forms generated by the Arizona Border Study and slated for data entry. It applies to all physical laboratory data forms entered for this study. This procedure was followed to ensu...

Successful hydraulic strategies to start up OLAND sequencing batch reactors at lab scale

PubMed Central

Schaubroeck, Thomas; Bagchi, Samik; De Clippeleir, Haydée; Carballa, Marta; Verstraete, Willy; Vlaeminck, Siegfried E.

2012-01-01

Summary Oxygen‐limited autotrophic nitrification/denitrification (OLAND) is a one‐stage combination of partial nitritation and anammox, which can have a challenging process start‐up. In this study, start‐up strategies were tested for sequencing batch reactors (SBR), varying hydraulic parameters, i.e. volumetric exchange ratio (VER) and feeding regime, and salinity. Two sequential tests with two parallel SBR were performed, and stable removal rates > 0.4 g N l−1 day−1 with minimal nitrite and nitrate accumulation were considered a successful start‐up. SBR A and B were operated at 50% VER with 3 g NaCl l−1 in the influent, and the influent was fed over 8% and 82% of the cycle time respectively. SBR B started up in 24 days, but SBR A achieved no start‐up in 39 days. SBR C and D were fed over 65% of the cycle time at 25% VER, and salt was added only to the influent of SBR D (5 g NaCl l−1). Start‐up of both SBR C and D was successful in 9 and 32 days respectively. Reactor D developed a higher proportion of small aggregates (0.10–0.25 mm), with a high nitritation to anammox rate ratio, likely the cause of the observed nitrite accumulation. The latter was overcome by temporarily including an anoxic period at the end of the reaction phase. All systems achieved granulation and similar biomass‐specific nitrogen removal rates (141–220 mg N g−1 VSS day−1). FISH revealed a close juxtapositioning of aerobic and anoxic ammonium‐oxidizing bacteria (AerAOB and AnAOB), also in small aggregates. DGGE showed that AerAOB communities had a lower evenness than Planctomycetes communities. A higher richness of the latter seemed to be correlated with better reactor performance. Overall, the fast start‐up of SBR B, C and D suggests that stable hydraulic conditions are beneficial for OLAND while increased salinity at the tested levels is not needed for good reactor performance. PMID:22236147

Successful hydraulic strategies to start up OLAND sequencing batch reactors at lab scale.

PubMed

Schaubroeck, Thomas; Bagchi, Samik; De Clippeleir, Haydée; Carballa, Marta; Verstraete, Willy; Vlaeminck, Siegfried E

2012-05-01

Oxygen-limited autotrophic nitrification/denitrification (OLAND) is a one-stage combination of partial nitritation and anammox, which can have a challenging process start-up. In this study, start-up strategies were tested for sequencing batch reactors (SBR), varying hydraulic parameters, i.e. volumetric exchange ratio (VER) and feeding regime, and salinity. Two sequential tests with two parallel SBR were performed, and stable removal rates > 0.4 g N l(-1) day(-1) with minimal nitrite and nitrate accumulation were considered a successful start-up. SBR A and B were operated at 50% VER with 3 g NaCl l(-1) in the influent, and the influent was fed over 8% and 82% of the cycle time respectively. SBR B started up in 24 days, but SBR A achieved no start-up in 39 days. SBR C and D were fed over 65% of the cycle time at 25% VER, and salt was added only to the influent of SBR D (5 g NaCl l(-1)). Start-up of both SBR C and D was successful in 9 and 32 days respectively. Reactor D developed a higher proportion of small aggregates (0.10-0.25 mm), with a high nitritation to anammox rate ratio, likely the cause of the observed nitrite accumulation. The latter was overcome by temporarily including an anoxic period at the end of the reaction phase. All systems achieved granulation and similar biomass-specific nitrogen removal rates (141-220 mg N g(-1) VSS day(-1)). FISH revealed a close juxtapositioning of aerobic and anoxic ammonium-oxidizing bacteria (AerAOB and AnAOB), also in small aggregates. DGGE showed that AerAOB communities had a lower evenness than Planctomycetes communities. A higher richness of the latter seemed to be correlated with better reactor performance. Overall, the fast start-up of SBR B, C and D suggests that stable hydraulic conditions are beneficial for OLAND while increased salinity at the tested levels is not needed for good reactor performance. © 2012 The Authors. Microbial Biotechnology © 2012 Society for Applied Microbiology and Blackwell Publishing

Parallel steady state studies on a milliliter scale accelerate fed-batch bioprocess design for recombinant protein production with Escherichia coli.

PubMed

Schmideder, Andreas; Cremer, Johannes H; Weuster-Botz, Dirk

2016-11-01

In general, fed-batch processes are applied for recombinant protein production with Escherichia coli (E. coli). However, state of the art methods for identifying suitable reaction conditions suffer from severe drawbacks, i.e. direct transfer of process information from parallel batch studies is often defective and sequential fed-batch studies are time-consuming and cost-intensive. In this study, continuously operated stirred-tank reactors on a milliliter scale were applied to identify suitable reaction conditions for fed-batch processes. Isopropyl β-d-1-thiogalactopyranoside (IPTG) induction strategies were varied in parallel-operated stirred-tank bioreactors to study the effects on the continuous production of the recombinant protein photoactivatable mCherry (PAmCherry) with E. coli. Best-performing induction strategies were transferred from the continuous processes on a milliliter scale to liter scale fed-batch processes. Inducing recombinant protein expression by dynamically increasing the IPTG concentration to 100 µM led to an increase in the product concentration of 21% (8.4 g L -1 ) compared to an implemented high-performance production process with the most frequently applied induction strategy by a single addition of 1000 µM IPGT. Thus, identifying feasible reaction conditions for fed-batch processes in parallel continuous studies on a milliliter scale was shown to be a powerful, novel method to accelerate bioprocess design in a cost-reducing manner. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:1426-1435, 2016. © 2016 American Institute of Chemical Engineers.

Feasibility of nitrification/denitrification in a sequencing batch biofilm reactor with liquid circulation applied to post-treatment.

PubMed

Andrade do Canto, Catarina Simone; Rodrigues, José Alberto Domingues; Ratusznei, Suzana Maria; Zaiat, Marcelo; Foresti, Eugênio

2008-02-01

An investigation was performed on the biological removal of ammonium nitrogen from synthetic wastewater by the simultaneous nitrification/denitrification (SND) process, using a sequencing batch biofilm reactor (SBBR). System behavior was analyzed as to the effects of sludge type used as inoculum (autotrophic/heterotrophic), wastewater feed strategy (batch/fed-batch) and aeration strategy (continuous/intermittent). The presence of an autotrophic aerobic sludge showed to be essential for nitrification startup, despite publications stating the existence of heterotrophic organisms capable of nitrifying organic and inorganic nitrogen compounds at low dissolved oxygen concentrations. As to feed strategy, batch operation (synthetic wastewater containing 100 mg COD/L and 50 mg N-NH(4)(+)/L) followed by fed-batch (synthetic wastewater with 100 mg COD/L) during a whole cycle seemed to be the most adequate, mainly during the denitrification phase. Regarding aeration strategy, an intermittent mode, with dissolved oxygen concentration of 2.0mg/L in the aeration phase, showed the best results. Under these optimal conditions, 97% of influent ammonium nitrogen (80% of total nitrogen) was removed at a rate of 86.5 mg N-NH(4)(+)/Ld. In the treated effluent only 0.2 mg N-NO(2)(-)/L,4.6 mg N-NO(3)(-)/L and 1.0 mg N-NH(4)(+)/L remained, demonstrating the potential viability of this process in post-treatment of wastewaters containing ammonium nitrogen.

Batch test screening of industrial product/byproduct filter materials for agricultural drainage water treatment

USDA-ARS?s Scientific Manuscript database

Filter treatment may be a viable means for removing the nitrate, phosphate, and pesticides discharged with agricultural drainage waters that cause adverse environmental impacts within the U.S. on local, regional, and national scales. Laboratory batch test screening for agricultural drainage water ...

Design of Mixed Batch Reactor and Column Studies at Oak Ridge National Laboratory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Weimin; Criddle, Craig S.

2015-11-16

We (the Stanford research team) were invited as external collaborators to contribute expertise in environmental engineering and field research at the ORNL IFRC, Oak Ridge, TN, for projects carried out at the Argonne National Laboratory and funded by US DOE. Specifically, we assisted in the design of batch and column reactors using ORNL IFRC materials to ensure the experiments were relevant to field conditions. During the funded research period, we characterized ORNL IFRC groundwater and sediments in batch microcosm and column experiments conducted at ANL, and we communicated with ANL team members through email and conference calls and face-to-face meetingsmore » at the annual ERSP PI meeting and national meetings. Microcosm test results demonstrated that U(VI) in sediments was reduced to U(IV) when amended with ethanol. The reduced products were not uraninite but unknown U(IV) complexes associated with Fe. Fe(III) in solid phase was only partially reduced. Due to budget reductions at ANL, Stanford contributions ended in 2011.« less

Virus elimination in activated sludge systems: from batch tests to mathematical modeling.

PubMed

Haun, Emma; Ulbricht, Katharina; Nogueira, Regina; Rosenwinkel, Karl-Heinz

2014-01-01

A virus tool based on Activated Sludge Model No. 3 for modeling virus elimination in activated sludge systems was developed and calibrated with the results from laboratory-scale batch tests and from measurements in a municipal wastewater treatment plant (WWTP). The somatic coliphages were used as an indicator for human pathogenic enteric viruses. The extended model was used to simulate the virus concentration in batch tests and in a municipal full-scale WWTP under steady-state and dynamic conditions. The experimental and modeling results suggest that both adsorption and inactivation processes, modeled as reversible first-order reactions, contribute to virus elimination in activated sludge systems. The model should be a useful tool to estimate the number of viruses entering water bodies from the discharge of treated effluents.

Stoichiometric evaluation of partial nitritation, anammox and denitrification processes in a sequencing batch reactor and interpretation of online monitoring parameters.

PubMed

Langone, Michela; Ferrentino, Roberta; Cadonna, Maria; Andreottola, Gianni

2016-12-01

A laboratory-scale sequencing batch reactor (SBR) performing partial nitritation - anammox and denitrification was used to treat anaerobic digester effluents. The SBR cycle consisted of a short mixing filling phase followed by oxic and anoxic reaction phases. Working at 25 °C, an ammonium conversion efficiency of 96.5%, a total nitrogen removal efficiency of 88.6%, and an organic carbon removal efficiency of 63.5% were obtained at a nitrogen loading rate of 0.15 kg N m -3 d -1 , and a biodegradable organic carbon to nitrogen ratio of 0.37. The potential contribution of each biological process was evaluated by using a stoichiometric model. The nitritation contribution decreased as the temperature decreased, while the contribution from anammox depended on the wastewater type and soluble carbon to nitrogen ratio. Denitrification improved the total nitrogen removal efficiency, and it was influenced by the biodegradable organic carbon to nitrogen ratio. The characteristic patterns of conductivity, oxidation-reduction potential (ORP) and pH in the SBR cycle were well related to biological processes. Conductivity profiles were found to be directly related to the decreasing profiles of ammonium. Positive ORP values at the end of the anoxic phases were detected for total nitrogen removal efficiency of lower than 85%, and the occurrence of bending points on the ORP curves during the anoxic phases was associated with nitrite depletion by the anammox process. Copyright © 2016 Elsevier Ltd. All rights reserved.

Nitrogen removal in moving bed sequencing batch reactor using polyurethane foam cubes of various sizes as carrier materials.

PubMed

Lim, Jun-Wei; Seng, Chye-Eng; Lim, Poh-Eng; Ng, Si-Ling; Sujari, Amat-Ngilmi Ahmad

2011-11-01

The performance of moving bed sequencing batch reactors (MBSBRs) added with 8 % (v/v) of polyurethane (PU) foam cubes as carrier media in nitrogen removal was investigated in treating low COD/N wastewater. The results indicate that MBSBR with 8-mL cubes achieved the highest total nitrogen (TN) removal efficiency of 37% during the aeration period, followed by 31%, 24% and 19 % for MBSBRs with 27-, 64- and 125-mL cubes, respectively. The increased TN removal in MBSBRs was mainly due to simultaneous nitrification and denitrification (SND) process which was verified by batch studies. The relatively lower TN removal in MBSBR with larger PU foam cubes was attributed to the observation that larger PU foam cubes were not fully attached by biomass. Higher concentrations of 8-mL PU foam cubes in batch reactors yielded higher TN removal. Copyright © 2011 Elsevier Ltd. All rights reserved.

Chapter 1.1 Process Scale-Up of Cellulose Nanocrystal Production to 25 kg per Batch at the Forest Products Laboratory

Treesearch

Richard S. Reiner; Alan W. Rudie

2013-01-01

The Fiber and Chemical Sciences Research Work Unit at the Forest Products Laboratory began working out the preparation of cellulose nanocrystals in 2006, using the method of Dong, Revol, and Gray. Initial samples were provided to several scientists within the Forest Service. Continued requests for this material forced scale-up from the initial 20 g scale to kg...

Characterization of Nanoparticle Batch-To-Batch Variability

PubMed Central

Mülhopt, Sonja; Dilger, Marco; Adelhelm, Christel; Anderlohr, Christopher; Gómez de la Torre, Johan; Langevin, Dominique; Mahon, Eugene; Piella, Jordi; Puntes, Victor; Ray, Sikha; Schneider, Reinhard; Wilkins, Terry; Weiss, Carsten

2018-01-01

A central challenge for the safe design of nanomaterials (NMs) is the inherent variability of NM properties, both as produced and as they interact with and evolve in, their surroundings. This has led to uncertainty in the literature regarding whether the biological and toxicological effects reported for NMs are related to specific NM properties themselves, or rather to the presence of impurities or physical effects such as agglomeration of particles. Thus, there is a strong need for systematic evaluation of the synthesis and processing parameters that lead to potential variability of different NM batches and the reproducible production of commonly utilized NMs. The work described here represents over three years of effort across 14 European laboratories to assess the reproducibility of nanoparticle properties produced by the same and modified synthesis routes for four of the OECD priority NMs (silica dioxide, zinc oxide, cerium dioxide and titanium dioxide) as well as amine-modified polystyrene NMs, which are frequently employed as positive controls for nanotoxicity studies. For 46 different batches of the selected NMs, all physicochemical descriptors as prioritized by the OECD have been fully characterized. The study represents the most complete assessment of NMs batch-to-batch variability performed to date and provides numerous important insights into the potential sources of variability of NMs and how these might be reduced. PMID:29738461

Enhanced nitrogen removal with spent mushroom compost in a sequencing batch reactor.

PubMed

Yang, Yunlong; Tao, Xin; Lin, Ershu; Hu, Kaihui

2017-11-01

In order to remove nitrogen effectively from the wastewater with a low C/N ratio, the feasibility of using spent mushroom compost (SMC) hydrolysates as carbon sources for denitrification was investigated in a sequencing batch reactor (SBR). With SMCs supplement, the SBR performance was improved obviously within the 180days of operation. The total nitrogen removal was promoted from 46.9% to 81-89.4%, and no negative impact induced by different SMCs on the SBR system was observed. The abundance of functional genes including amoA, nirS/K, norB and nosZ in the active sludge was quantified by qPCR, and most of them elevated after SMC was fed. 16S rRNA gene high-throughput sequencing showed that the significant change in microbial community not only promoted pollutants removal but also benefited the stability of the reactor. Therefore, SMC could be an extremely promising carbon source used for nitrogen removal due to its cost-effective and efficient characteristics. Copyright © 2017 Elsevier Ltd. All rights reserved.

Critical analysis of submerged membrane sequencing batch reactor operating conditions.

PubMed

McAdam, Ewan; Judd, Simon J; Gildemeister, René; Drews, Anja; Kraume, Matthias

2005-10-01

To evaluate the Submerged Membrane Sequencing Batch Reactor process, several short-term studies were conducted to define critical flux, membrane aeration and intermittent filtration operation. Critical flux trials indicated that as mixed liquor suspended solids increased in concentration so would the propensity for membrane fouling. Consequently in order to characterise the impact of biomass concentration increase (that develops during permeate withdrawal) upon submerged microfiltration operation, two longer term studies were conducted, one with a falling hydraulic head and another with a continuous hydraulic head (as in membrane bio-reactors). Trans membrane pressure data was used to predict the maximum possible operating periods at 10 and 62 days for the falling hydraulic head and continuous hydraulic head respectively. Further analysis revealed that falling hydraulic head operation would require 21% more aeration to maintain a consistent crossflow velocity than continuous operation and would rely on pumping for full permeate withdrawal 80% earlier. This study concluded that further optimisation would be required to make this technology technically and economically viable.

Population dynamics in controlled unsteady-state systems: An application to the degradation of glyphosate in a sequencing batch reactor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Devarakonda, M.S.

1988-01-01

Control over population dynamics and organism selection in a biological waste treatment system provides an effective means of engineering process efficiency. Examples of applications of organism selection include control of filamentous organisms, biological nutrient removal, industrial waste treatment requiring the removal of specific substrates, and hazardous waste treatment. Inherently, full scale biological waste treatment systems are unsteady state systems due to the variations in the waste streams and mass flow rates of the substrates. Some systems, however, have the capacity to impose controlled selective pressures on the biological population by means of their operation. An example of such a systemmore » is the Sequencing Batch Reactor (SBR) which was the experimental system utilized in this research work. The concepts of organism selection were studied in detail for the biodegradation of a herbicide waste stream, with glyphosate as the target compound. The SBR provided a reactor configuration capable of exerting the necessary selective pressures to select and enrich for a glyphosate degrading population. Based on results for bench scale SBRs, a hypothesis was developed to explain population dynamics in glyphosate degrading systems.« less

Acceptance Test Data for Candidate AGR-5/6/7 TRISO Particle Batches BWXT Coater Batches 93165 93172 Defective IPyC Fraction and Pyrocarbon Anisotropy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Helmreich, Grant W.; Hunn, John D.; Skitt, Darren J.

2017-03-01

Coated particle fuel batches J52O-16-93165, 93166, 93168, 93169, 93170, and 93172 were produced by Babcock and Wilcox Technologies (BWXT) for possible selection as fuel for the Advanced Gas Reactor Fuel Development and Qualification (AGR) Program’s AGR-5/6/7 irradiation test in the Idaho National Laboratory (INL) Advanced Test Reactor (ATR). Some of these batches may alternately be used as demonstration coated particle fuel for other experiments. Each batch was coated in a 150-mm-diameter production-scale fluidized-bed chemical vapor deposition (CVD) furnace. Tristructural isotropic (TRISO) coatings were deposited on 425-μm-nominal-diameter spherical kernels from BWXT lot J52R-16-69317 containing a mixture of 15.5%-enriched uranium carbide andmore » uranium oxide (UCO). The TRISO coatings consisted of four consecutive CVD layers: a ~50% dense carbon buffer layer with 100-μm-nominal thickness, a dense inner pyrolytic carbon (IPyC) layer with 40-μm-nominal thickness, a silicon carbide (SiC) layer with 35-μm-nominal thickness, and a dense outer pyrolytic carbon (OPyC) layer with 40-μmnominal thickness. The TRISO-coated particle batches were sieved to upgrade the particles by removing over-sized and under-sized material, and the upgraded batches were designated by appending the letter A to the end of the batch number (e.g., 93165A).« less

Correcting for batch effects in case-control microbiome studies

PubMed Central

Gibbons, Sean M.; Duvallet, Claire

2018-01-01

High-throughput data generation platforms, like mass-spectrometry, microarrays, and second-generation sequencing are susceptible to batch effects due to run-to-run variation in reagents, equipment, protocols, or personnel. Currently, batch correction methods are not commonly applied to microbiome sequencing datasets. In this paper, we compare different batch-correction methods applied to microbiome case-control studies. We introduce a model-free normalization procedure where features (i.e. bacterial taxa) in case samples are converted to percentiles of the equivalent features in control samples within a study prior to pooling data across studies. We look at how this percentile-normalization method compares to traditional meta-analysis methods for combining independent p-values and to limma and ComBat, widely used batch-correction models developed for RNA microarray data. Overall, we show that percentile-normalization is a simple, non-parametric approach for correcting batch effects and improving sensitivity in case-control meta-analyses. PMID:29684016

Pollution prevention applications in batch manufacturing operations

NASA Astrophysics Data System (ADS)

Sykes, Derek W.; O'Shaughnessy, James

2004-02-01

Older, "low-tech" batch manufacturing operations are often fertile grounds for gains resulting from pollution prevention techniques. This paper presents a pollution prevention technique utilized for wastewater discharge permit compliance purposes at a batch manufacturer of detergents, deodorants, and floor-care products. This manufacturer generated industrial wastewater as a result of equipment rinses required after each product batch changeover. After investing a significant amount of capital on end of pip-line wastewater treatment technology designed to address existing discharge limits, this manufacturer chose to investigate alternate, low-cost approaches to address anticipated new permit limits. Mass balances using spreadsheets and readily available formulation and production data were conducted on over 300 products to determine how each individual product contributed to the total wastewater pollutant load. These mass balances indicated that 22 products accounted for over 55% of the wastewater pollutant. Laboratory tests were conducted to determine whether these same products could accept their individual changeover rinse water as make-up water in formulations without sacrificing product quality. This changeover reuse technique was then implement at the plant scale for selected products. Significant reductions in wastewater volume (25%) and wastewater pollutant loading (85+%) were realized as a direct result of this approach.

Anaerobic sequencing batch reactors for wastewater treatment: a developing technology.

PubMed

Zaiat, M; Rodrigues, J A; Ratusznei, S M; de Camargo, E F; Borzani, W

2001-01-01

This paper describes and discusses the main problems related to anaerobic batch and fed-batch processes for wastewater treatment. A critical analysis of the literature evaluated the industrial application viability and proposed alternatives to improve operation and control of this system. Two approaches were presented in order to make this anaerobic discontinuous process feasible for industrial application: (1) optimization of the operating procedures in reactors containing self-immobilized sludge as granules, and (2) design of bioreactors with inert support media for biomass immobilization.

Aquifer recharge with reclaimed water in the Llobregat Delta. Laboratory batch experiments and field test site.

NASA Astrophysics Data System (ADS)

Tobella, J.

2010-05-01

Summary Spain, as most other Mediterranean countries, faces near future water shortages, generalized pollution and loss of water dependent ecosystems. Aquifer recharge represents a promising option to become a source for indirect potable reuse purposes but presence of pathogens as well as organic and inorganic pollutants should be avoided. To this end, understanding the processes of biogeochemical degradation occurring within the aquifer during infiltration is capital. A set of laboratory batch experiments has been assembled in order to assess the behaviour of selected pesticides, drugs, estrogens, surfactant degradation products, biocides and phthalates under different redox conditions. Data collected during laboratory experiments and monitoring activities at the Sant Vicenç dels Horts test site will be used to build and calibrate a numerical model (i) of the physical-chemical-biochemical processes occurring in the batches and (ii) of multicomponent reactive transport in the unsaturated/saturated zone at the test site. Keywords Aquifer recharge, batch experiments, emerging micropollutants, infiltration, numerical model, reclaimed water, redox conditions, Soil Aquifer Treatment (SAT). 1. Introduction In Spain, the Llobregat River and aquifers, which supply water to Barcelona, have been overexploited for years and therefore, suffer from serious damages: the river dries up on summer, riparian vegetation has disappeared and seawater has intruded the aquifer. In a global context, solutions to water stress problems are urgently needed yet must be sustainable, economical and safe. Recent developments of analytical techniques detect the presence of the so-called "emerging" organic micropollutants in water and soils. Such compounds may affect living organisms when occurring in the environment at very low concentrations (microg/l or ng/l). In wastewater and drinking water treatment plants, a remarkable removal of these chemicals from water can be obtained only using

High rate psychrophilic anaerobic digestion of high solids (35%) dairy manure in sequence batch reactor.

PubMed

Saady, Noori M Cata; Massé, Daniel I

2015-06-01

Zero liquid discharge is increasingly adopted as an objective for waste treatment process. The objective of this study was to increase the feed total solids (TS) and the organic loading rate (OLR) fed to a novel psychrophilic (20°C) dry anaerobic digestion (PDAD). Duplicate laboratory-scale bioreactors were fed cow feces and wheat straw (35% TS in feed) at OLR of 6.0 g TCOD kg(-1) inoculum d(-1) during long-term operation (147 days consisting of 7 successive cycles). An overall average specific methane yield (SMY) of 151.8±7.9 N L CH4 kg(-1) VS fed with an averaged volatile solids removal of 42.4±4.3% were obtained at a volatile solids-based inoculum-to-substrate ratio (ISR) of 2.13±0.2. The operation was stable as indicated by biogas and VFAs profiles and the results were reproducible in successive cycles; a maximum SMY of 163.3±5.7 N L CH4 kg(-1) VS fed was obtained. Hydrolysis was the reaction limiting step. High rate PDAD of 35% TS dairy manure is possible in sequential batch reactor within 21 days treatment cycle length. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

Laboratory Sequence in Computational Methods for Introductory Chemistry

NASA Astrophysics Data System (ADS)

Cody, Jason A.; Wiser, Dawn C.

2003-07-01

A four-exercise laboratory sequence for introductory chemistry integrating hands-on, student-centered experience with computer modeling has been designed and implemented. The progression builds from exploration of molecular shapes to intermolecular forces and the impact of those forces on chemical separations made with gas chromatography and distillation. The sequence ends with an exploration of molecular orbitals. The students use the computers as a tool; they build the molecules, submit the calculations, and interpret the results. Because of the construction of the sequence and its placement spanning the semester break, good laboratory notebook practices are reinforced and the continuity of course content and methods between semesters is emphasized. The inclusion of these techniques in the first year of chemistry has had a positive impact on student perceptions and student learning.

[Development of laboratory sequence analysis software based on WWW and UNIX].

PubMed

Huang, Y; Gu, J R

2001-01-01

Sequence analysis tools based on WWW and UNIX were developed in our laboratory to meet the needs of molecular genetics research in our laboratory. General principles of computer analysis of DNA and protein sequences were also briefly discussed in this paper.

Biogas Production from Brewer’s Yeast Using an Anaerobic Sequencing Batch Reactor

PubMed Central

2017-01-01

Summary Renewable energy sources are becoming increasingly important in the beverage and food industries. In the brewing industry, a significant percentage of the used raw materials finishes the process as secondary resource or waste. The research on the anaerobic digestion of brewer’s yeast has been scarce until recent years. One of the reasons for this is its use as a secondary resource in the food industry and as cattle feed. Additionally, market value of brewer’s yeast is higher than its energy value. Due to the increase of energy prices, brewer’s yeast has become of interest as energy substrate despite its difficult degradability in anaerobic conditions. The anaerobic co-digestion of brewer’s yeast and anaerobically treated brewery wastewater was studied using a pilot-scale anaerobic sequencing batch reactor (ASBR) seeded with granular biomass. The experiments showed very good and stable operation with an organic loading rate of up to 8.0 kg/(m3·day), and with a maximum achieved organic loading rate of 13.6 kg/(m3·day) in a single cycle. A specific biogas productivity of over 0.430 m3/kg of the total chemical oxygen demand (COD) inserted, and total COD removal efficiencies of over 90% were achieved. This study suggests that the brewer’s yeast can be successfully digested in an ASBR without adverse effects on the biogas production from brewer’s yeast/wastewater mixtures of up to 8% (by volume). By using the brewer’s yeast in the ASBR process, the biogas production from brewery wastewater could be increased by 50%. PMID:28867948

Treatment of winery wastewater by an anaerobic sequencing batch reactor.

PubMed

Ruíz, C; Torrijos, M; Sousbie, P; Lebrato Martínez, J; Moletta, R; Delgenès, J P

2002-01-01

Treatment of winery wastewater was investigated using an anaerobic sequencing batch reactor (ASBR). Biogas production rate was monitored and permitted the automation of the bioreactor by a simple control system. The reactor was operated at an organic loading rate (ORL) around 8.6 gCOD/L.d with soluble chemical oxygen demand (COD) removal efficiency greater than 98%, hydraulic retention time (HRT) of 2.2 d and a specific organic loading rate (SOLR) of 0.96 gCOD/gVSS.d. The kinetics of COD and VFA removal were investigated for winery wastewater and for simple compounds such as ethanol, which is a major component of winery effluent, and acetate, which is the main volatile fatty acid (VFA) produced. The comparison of the profiles obtained with the 3 substrates shows that, overall, the acidification of the organic matter and the methanisation of the VFA follow zero order reactions, in the operating conditions of our study. The effect on the gas production rate resulted in two level periods separated by a sharp break when the acidification stage was finished and only the breaking down of the VFA continued.

Application of response surface methodology (RSM) for optimisation of COD, NH3-N and 2,4-DCP removal from recycled paper wastewater in a pilot-scale granular activated carbon sequencing batch biofilm reactor (GAC-SBBR).

PubMed

Muhamad, Mohd Hafizuddin; Sheikh Abdullah, Siti Rozaimah; Mohamad, Abu Bakar; Abdul Rahman, Rakmi; Hasan Kadhum, Abdul Amir

2013-05-30

In this study, the potential of a pilot-scale granular activated carbon sequencing batch biofilm reactor (GAC-SBBR) for removing chemical oxygen demand (COD), ammoniacal nitrogen (NH3-N) and 2,4-dichlorophenol (2,4-DCP) from recycled paper wastewater was assessed. For this purpose, the response surface methodology (RSM) was employed, using a central composite face-centred design (CCFD), to optimise three of the most important operating variables, i.e., hydraulic retention time (HRT), aeration rate (AR) and influent feed concentration (IFC), in the pilot-scale GAC-SBBR process for recycled paper wastewater treatment. Quadratic models were developed for the response variables, i.e., COD, NH3-N and 2,4-DCP removal, based on the high value (>0.9) of the coefficient of determination (R(2)) obtained from the analysis of variance (ANOVA). The optimal conditions were established at 750 mg COD/L IFC, 3.2 m(3)/min AR and 1 day HRT, corresponding to predicted COD, NH3-N and 2,4-DCP removal percentages of 94.8, 100 and 80.9%, respectively. Copyright © 2013 Elsevier Ltd. All rights reserved.

Anaerobic treatment of animal byproducts from slaughterhouses at laboratory and pilot scale.

PubMed

Edström, Mats; Nordberg, Ake; Thyselius, Lennart

2003-01-01

Different mixtures of animal byproducts, other slaughterhouse waste (i.e., rumen, stomach and intestinal content), food waste, and liquid manure were codigested at mesophilic conditions (37 degrees C) at laboratory and pilot scale. Animal byproducts, including blood, represent 70-80% of the total biogas potential from waste generated during slaughter of animals. The total biogas potential from waste generated during slaughter is about 1300 MJ/cattle and about 140 MJ/pig. Fed-batch digestion of pasteurized (70 degrees C, 1 h) animal byproducts resulted in a fourfold increase in biogas yield (1.14 L/g of volatile solids [VS]) compared with nonpasteurized animal byproducts (0.31 L/g of VS). Mixtures with animal byproducts representing 19-38% of the total dry matter were digested in continuous-flow stirred tank reactors at laboratory and pilot scale. Stable processes at organic loading rates (OLRs) exceeding 2.5 g of VS/(L.d) and hydraulic retention times (HRTs) less than 40 d could be obtained with total ammonia nitrogen concentrations (NH4-N + NH3-N) in the range of 4.0-5.0 g/L. After operating one process for more than 1.5 yr at total ammonia nitrogen concentrations >4 g/L, an increase in OLR to 5 g of VS/(L.d) and a decrease in HRT to 22 d was possible without accumulation of volatile fatty acids.

Kinetic study on the effect of temperature on biogas production using a lab scale batch reactor.

PubMed

Deepanraj, B; Sivasubramanian, V; Jayaraj, S

2015-11-01

In the present study, biogas production from food waste through anaerobic digestion was carried out in a 2l laboratory-scale batch reactor operating at different temperatures with a hydraulic retention time of 30 days. The reactors were operated with a solid concentration of 7.5% of total solids and pH 7. The food wastes used in this experiment were subjected to characterization studies before and after digestion. Modified Gompertz model and Logistic model were used for kinetic study of biogas production. The kinetic parameters, biogas yield potential of the substrate (B), the maximum biogas production rate (Rb) and the duration of lag phase (λ), coefficient of determination (R(2)) and root mean square error (RMSE) were estimated in each case. The effect of temperature on biogas production was evaluated experimentally and compared with the results of kinetic study. The results demonstrated that the reactor with operating temperature of 50°C achieved maximum cumulative biogas production of 7556ml with better biodegradation efficiency. Copyright © 2015 Elsevier Inc. All rights reserved.

Design and fabrication of a fixed-bed batch type pyrolysis reactor for pilot scale pyrolytic oil production in Bangladesh

NASA Astrophysics Data System (ADS)

Aziz, Mohammad Abdul; Al-khulaidi, Rami Ali; Rashid, MM; Islam, M. R.; Rashid, MAN

2017-03-01

In this research, a development and performance test of a fixed-bed batch type pyrolysis reactor for pilot scale pyrolysis oil production was successfully completed. The characteristics of the pyrolysis oil were compared to other experimental results. A solid horizontal condenser, a burner for furnace heating and a reactor shield were designed. Due to the pilot scale pyrolytic oil production encountered numerous problems during the plant’s operation. This fixed-bed batch type pyrolysis reactor method will demonstrate the energy saving concept of solid waste tire by creating energy stability. From this experiment, product yields (wt. %) for liquid or pyrolytic oil were 49%, char 38.3 % and pyrolytic gas 12.7% with an operation running time of 185 minutes.

Fed-batch anaerobic valorization of slaughterhouse by-products with mesophilic microbial consortia without methane production.

PubMed

Pessiot, J; Nouaille, R; Jobard, M; Singhania, R R; Bournilhas, A; Christophe, G; Fontanille, P; Peyret, P; Fonty, G; Larroche, C

2012-07-01

This work aimed at setting up a fully instrumented, laboratory-scale bioreactor enabling anaerobic valorization of solid substrates through hydrogen and/or volatile fatty acid (VFA) production using mixed microbial populations (consortia). The substrate used was made of meat-based wastes, especially from slaughterhouses, which are becoming available in large amounts as a consequence of the growing constraints for waste disposal from meat industry. A reconstituted microbial mesophilic consortium without Archaebacteria (methanogens), named PBr, was cultivated in a 5-L anaerobic bioreactor on slaughterhouse wastes. The experiments were carried out with sequential fed-batch operations, including liquid medium removal from the bioreactor and addition of fresh substrate. VFAs and nitrogen were the main metabolites observed, while hydrogen accumulation was very low and no methane production was evidenced. After 1,300 h of culture, yields obtained for VFAs reached 0.38 g/g dry matter. Strain composition of the microbial consortium was also characterized using molecular tools (temporal temperature gradient gel electrophoresis and gene sequencing).

Sulfamethoxazole and COD increase abundance of sulfonamide resistance genes and change bacterial community structures within sequencing batch reactors.

PubMed

Guo, Xueping; Pang, Weihai; Dou, Chunling; Yin, Daqiang

2017-05-01

The abundant microbial community in biological treatment processes in wastewater treatment plants (WWTPs) may potentially enhance the horizontal gene transfer of antibiotic resistance genes with the presence of antibiotics. A lab-scale sequencing batch reactor was designed to investigate response of sulfonamide resistance genes (sulI, sulII) and bacterial communities to various concentrations of sulfamethoxazole (SMX) and chemical oxygen demand (COD) of wastewater. The SMX concentrations (0.001 mg/L, 0.1 mg/L and 10 mg/L) decreased with treatment time and higher SMX level was more difficult to remove. The presence of SMX also significantly reduced the removal efficiency of ammonia nitrogen, affecting the normal function of WWTPs. All three concentrations of SMX raised both sulI and sulII genes with higher concentrations exhibiting greater increases. The abundance of sul genes was positive correlated with treatment time and followed the second-order reaction kinetic model. Interestingly, these two genes have rather similar activity. SulI and sulII gene abundance also performed similar response to COD. Simpson index and Shannon-Weiner index did not show changes in the microbial community diversity. However, the 16S rRNA gene cloning and sequencing results showed the bacterial community structures varied during different stages. The results demonstrated that influent antibiotics into WWTPs may facilitate selection of ARGs and affect the wastewater conventional treatment as well as the bacteria community structures. Copyright © 2017 Elsevier Ltd. All rights reserved.

High-strength N-methyl-2-pyrrolidone-containing process wastewater treatment using sequencing batch reactor and membrane bioreactor: A feasibility study.

PubMed

Loh, Chun Heng; Wu, Bing; Ge, Liya; Pan, Chaozhi; Wang, Rong

2018-03-01

N-methyl-2-pyrrolidone (NMP) is widely used as a solvent in polymeric membrane fabrication process, its elimination from the process wastewater (normally at a high concentration > 1000 mg/L) prior to discharge is essential because of environmental concern. This study investigated the feasibility of treating high-strength NMP-containing process wastewater in a sequencing batch reactor (SBR; i.e., batch feeding and intermittent aerobic/anoxic condition) and a membrane bioreactor (MBR; i.e., continuous feeding and aeration), respectively. The results showed that the SBR with the acclimated sludge was capable of removing >90% of dissolved organic carbon (DOC) and almost 98% of NMP within 2 h. In contrast, the MBR with the acclimated sludge showed a decreasing NMP removal efficiency from 100% to 40% over 15-day operation. The HPLC and LC-MS/MS analytical results showed that NMP degradation in SBR and MBR could undergo different pathways. This may be attributed to the dissimilar bacterial community compositions in the SBR and MBR as identified by 16s rRNA gene sequencing analysis. Interestingly, the NMP-degrading capability of the activated sludge derived from MBR could be recovered to >98% after they were operated at the SBR mode (batch feeding mode with intermittent aerobic/anoxic condition). This study reveals that SBR is probably a more feasible process to treat high-strength NMP-containing wastewater, but residual NMP metabolites in the SBR effluent need to be post-treated by an oxidation or adsorption process in order to achieve zero-discharge of toxic chemicals. Copyright © 2017 Elsevier Ltd. All rights reserved.

Harnessing dark fermentative hydrogen from pretreated mixture of food waste and sewage sludge under sequencing batch mode.

PubMed

Nam, Joo-Youn; Kim, Dong-Hoon; Kim, Sang-Hyoun; Lee, Wontae; Shin, Hang-Sik; Kim, Hyun-Woo

2016-04-01

Food waste and sewage sludge are the most abundant and problematic organic wastes in any society. Mixture of these two wastes may provide appropriate substrate condition for dark fermentative biohydrogen production based on synergistic mutual benefits. This work evaluates continuous hydrogen production from the cosubstrate of food waste and sewage sludge to verify mechanisms of performance improvement in anaerobic sequencing batch reactors. Volatile solid concentration and mixing ratio of food waste and sludge were adjusted to 5 % and 80:20, respectively. Five different hydraulic retention times (HRT) of 36, 42, 48, 72, and 108 h were tested using anaerobic sequencing batch reactors to find out optimal operating condition. Results show that the best performance was achieved at HRT 72 h, where the hydrogen yield, the hydrogen production rate, and hydrogen content were 62.0 mL H2/g VS, 1.0 L H2/L/day, and ~50 %, respectively. Sufficient solid retention time (143 h) and proper loading rate (8.2 g COD/L/day as carbohydrate) at HRT 72h led to the enhanced performance with better hydrogen production showing appropriate n-butyrate/acetate (B/A) ratio of 2.6. Analytical result of terminal-restriction fragment length polymorphism revealed that specific peaks associated with Clostridium sp. and Bacillus sp. were strongly related to enhanced hydrogen production from the cosubstrate of food waste and sewage sludge.

Investigation of vinegar production using a novel shaken repeated batch culture system.

PubMed

Schlepütz, Tino; Büchs, Jochen

2013-01-01

Nowadays, bioprocesses are developed or optimized on small scale. Also, vinegar industry is motivated to reinvestigate the established repeated batch fermentation process. As yet, there is no small-scale culture system for optimizing fermentation conditions for repeated batch bioprocesses. Thus, the aim of this study is to propose a new shaken culture system for parallel repeated batch vinegar fermentation. A new operation mode - the flushing repeated batch - was developed. Parallel repeated batch vinegar production could be established in shaken overflow vessels in a completely automated operation with only one pump per vessel. This flushing repeated batch was first theoretically investigated and then empirically tested. The ethanol concentration was online monitored during repeated batch fermentation by semiconductor gas sensors. It was shown that the switch from one ethanol substrate quality to different ethanol substrate qualities resulted in prolonged lag phases and durations of the first batches. In the subsequent batches the length of the fermentations decreased considerably. This decrease in the respective lag phases indicates an adaptation of the acetic acid bacteria mixed culture to the specific ethanol substrate quality. Consequently, flushing repeated batch fermentations on small scale are valuable for screening fermentation conditions and, thereby, improving industrial-scale bioprocesses such as vinegar production in terms of process robustness, stability, and productivity. Copyright © 2013 American Institute of Chemical Engineers.

Bioreactor Scalability: Laboratory-Scale Bioreactor Design Influences Performance, Ecology, and Community Physiology in Expanded Granular Sludge Bed Bioreactors

PubMed Central

Connelly, Stephanie; Shin, Seung G.; Dillon, Robert J.; Ijaz, Umer Z.; Quince, Christopher; Sloan, William T.; Collins, Gavin

2017-01-01

Studies investigating the feasibility of new, or improved, biotechnologies, such as wastewater treatment digesters, inevitably start with laboratory-scale trials. However, it is rarely determined whether laboratory-scale results reflect full-scale performance or microbial ecology. The Expanded Granular Sludge Bed (EGSB) bioreactor, which is a high-rate anaerobic digester configuration, was used as a model to address that knowledge gap in this study. Two laboratory-scale idealizations of the EGSB—a one-dimensional and a three- dimensional scale-down of a full-scale design—were built and operated in triplicate under near-identical conditions to a full-scale EGSB. The laboratory-scale bioreactors were seeded using biomass obtained from the full-scale bioreactor, and, spent water from the distillation of whisky from maize was applied as substrate at both scales. Over 70 days, bioreactor performance, microbial ecology, and microbial community physiology were monitored at various depths in the sludge-beds using 16S rRNA gene sequencing (V4 region), specific methanogenic activity (SMA) assays, and a range of physical and chemical monitoring methods. SMA assays indicated dominance of the hydrogenotrophic pathway at full-scale whilst a more balanced activity profile developed during the laboratory-scale trials. At each scale, Methanobacterium was the dominant methanogenic genus present. Bioreactor performance overall was better at laboratory-scale than full-scale. We observed that bioreactor design at laboratory-scale significantly influenced spatial distribution of microbial community physiology and taxonomy in the bioreactor sludge-bed, with 1-D bioreactor types promoting stratification of each. In the 1-D laboratory bioreactors, increased abundance of Firmicutes was associated with both granule position in the sludge bed and increased activity against acetate and ethanol as substrates. We further observed that stratification in the sludge-bed in 1-D laboratory-scale

CALIBRATION OF FULL-SCALE OZONATION SYSTEMS WITH CONSERVATIVE AND REACTIVE TRACERS

EPA Science Inventory

A full-scale ozonation reactor was characterized with respect to the overall oxidation budget by coupling laboratory kinetics with reactor hydraulics. The ozone decomposition kinetics and the ratio of the OH radical to the ozone concentration were determined in laboratory batch ...

Achieving across-laboratory replicability in psychophysical scaling

PubMed Central

Ward, Lawrence M.; Baumann, Michael; Moffat, Graeme; Roberts, Larry E.; Mori, Shuji; Rutledge-Taylor, Matthew; West, Robert L.

2015-01-01

It is well known that, although psychophysical scaling produces good qualitative agreement between experiments, precise quantitative agreement between experimental results, such as that routinely achieved in physics or biology, is rarely or never attained. A particularly galling example of this is the fact that power function exponents for the same psychological continuum, measured in different laboratories but ostensibly using the same scaling method, magnitude estimation, can vary by a factor of three. Constrained scaling (CS), in which observers first learn a standardized meaning for a set of numerical responses relative to a standard sensory continuum and then make magnitude judgments of other sensations using the learned response scale, has produced excellent quantitative agreement between individual observers’ psychophysical functions. Theoretically it could do the same for across-laboratory comparisons, although this needs to be tested directly. We compared nine different experiments from four different laboratories as an example of the level of across experiment and across-laboratory agreement achievable using CS. In general, we found across experiment and across-laboratory agreement using CS to be significantly superior to that typically obtained with conventional magnitude estimation techniques, although some of its potential remains to be realized. PMID:26191019

JOB BUILDER remote batch processing subsystem

NASA Technical Reports Server (NTRS)

Orlov, I. G.; Orlova, T. L.

1980-01-01

The functions of the JOB BUILDER remote batch processing subsystem are described. Instructions are given for using it as a component of a display system developed by personnel of the System Programming Laboratory, Institute of Space Research, USSR Academy of Sciences.

Discovery of Escherichia coli CRISPR sequences in an undergraduate laboratory.

PubMed

Militello, Kevin T; Lazatin, Justine C

2017-05-01

Clustered regularly interspaced short palindromic repeats (CRISPRs) represent a novel type of adaptive immune system found in eubacteria and archaebacteria. CRISPRs have recently generated a lot of attention due to their unique ability to catalog foreign nucleic acids, their ability to destroy foreign nucleic acids in a mechanism that shares some similarity to RNA interference, and the ability to utilize reconstituted CRISPR systems for genome editing in numerous organisms. In order to introduce CRISPR biology into an undergraduate upper-level laboratory, a five-week set of exercises was designed to allow students to examine the CRISPR status of uncharacterized Escherichia coli strains and to allow the discovery of new repeats and spacers. Students started the project by isolating genomic DNA from E. coli and amplifying the iap CRISPR locus using the polymerase chain reaction (PCR). The PCR products were analyzed by Sanger DNA sequencing, and the sequences were examined for the presence of CRISPR repeat sequences. The regions between the repeats, the spacers, were extracted and analyzed with BLASTN searches. Overall, CRISPR loci were sequenced from several previously uncharacterized E. coli strains and one E. coli K-12 strain. Sanger DNA sequencing resulted in the discovery of 36 spacer sequences and their corresponding surrounding repeat sequences. Five of the spacers were homologous to foreign (non-E. coli) DNA. Assessment of the laboratory indicates that improvements were made in the ability of students to answer questions relating to the structure and function of CRISPRs. Future directions of the laboratory are presented and discussed. © 2016 by The International Union of Biochemistry and Molecular Biology, 45(3):262-269, 2017. © 2016 The International Union of Biochemistry and Molecular Biology.

Defense Waste Processing Facility Simulant Chemical Processing Cell Studies for Sludge Batch 9

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smith, Tara E.; Newell, J. David; Woodham, Wesley H.

The Savannah River National Laboratory (SRNL) received a technical task request from Defense Waste Processing Facility (DWPF) and Saltstone Engineering to perform simulant tests to support the qualification of Sludge Batch 9 (SB9) and to develop the flowsheet for SB9 in the DWPF. These efforts pertained to the DWPF Chemical Process Cell (CPC). CPC experiments were performed using SB9 simulant (SB9A) to qualify SB9 for sludge-only and coupled processing using the nitric-formic flowsheet in the DWPF. Two simulant batches were prepared, one representing SB8 Tank 40H and another representing SB9 Tank 51H. The simulant used for SB9 qualification testing wasmore » prepared by blending the SB8 Tank 40H and SB9 Tank 51H simulants. The blended simulant is referred to as SB9A. Eleven CPC experiments were run with an acid stoichiometry ranging between 105% and 145% of the Koopman minimum acid equation (KMA), which is equivalent to 109.7% and 151.5% of the Hsu minimum acid factor. Three runs were performed in the 1L laboratory scale setup, whereas the remainder were in the 4L laboratory scale setup. Sludge Receipt and Adjustment Tank (SRAT) and Slurry Mix Evaporator (SME) cycles were performed on nine of the eleven. The other two were SRAT cycles only. One coupled flowsheet and one extended run were performed for SRAT and SME processing. Samples of the condensate, sludge, and off-gas were taken to monitor the chemistry of the CPC experiments.« less

An efficient and scalable analysis framework for variant extraction and refinement from population-scale DNA sequence data.

PubMed

Jun, Goo; Wing, Mary Kate; Abecasis, Gonçalo R; Kang, Hyun Min

2015-06-01

The analysis of next-generation sequencing data is computationally and statistically challenging because of the massive volume of data and imperfect data quality. We present GotCloud, a pipeline for efficiently detecting and genotyping high-quality variants from large-scale sequencing data. GotCloud automates sequence alignment, sample-level quality control, variant calling, filtering of likely artifacts using machine-learning techniques, and genotype refinement using haplotype information. The pipeline can process thousands of samples in parallel and requires less computational resources than current alternatives. Experiments with whole-genome and exome-targeted sequence data generated by the 1000 Genomes Project show that the pipeline provides effective filtering against false positive variants and high power to detect true variants. Our pipeline has already contributed to variant detection and genotyping in several large-scale sequencing projects, including the 1000 Genomes Project and the NHLBI Exome Sequencing Project. We hope it will now prove useful to many medical sequencing studies. © 2015 Jun et al.; Published by Cold Spring Harbor Laboratory Press.

Short-term Influence of Drilling Fluid on Ciliates from Activated Sludge in Sequencing Batch Reactors.

PubMed

Babko, Roman; Kuzmina, Tatiana; Łagód, Grzegorz; Jaromin-Gleń, Katarzyna; Danko, Yaroslav; Pawłowska, Małgorzata; Pawłowski, Artur

2017-01-01

Spent drilling muds are the liquid residues of rock drilling operations. Due to a high concentration of suspended solids and potentially detrimental chemical properties, they can negatively affect microorganisms participating in wastewater treatment processes. We evaluated the addition of a potassium-polymer drilling fluid (DF) to activated sludge in laboratory sequencing batch reactors (SBRs) for municipal wastewater treatment. Ciliate assemblage, the most dynamic component of eukaryotes in activated sludge, and which is highly sensitive to changes in the system, was evaluated. The average ciliate abundance dropped by about 51% (SBR 2; 1% DF added) and 33% (SBR 3; 3% DF added) in comparison to the control (SBR 1; wastewater only). A decrease in the total number of ciliate species during the experiment was observed, from 25 to 24 in SBR 2 and from 17 to 13 in SBR 3. Moreover, a drop in the number of dominant (>100 individuals mL) ciliate species was observed during the experiment-from eight in the control to five in SBR 2 and four in SBR 3-signaling noticeable changes in the quantitative structure of ciliate species. The species analyzed showed different responses to DF addition. The most sensitive was , which is bacteriovorus. In contrast, two predators, and , showed no reaction to DF addition. Our results indicate that addition of potassium-polymer DF, in doses of 1 to 3% of the treated wastewater volume, had no toxic effects on ciliates, but qualitative and quantitative changes in their community were observed. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

Coupled solar photo-Fenton and biological treatment for the degradation of diuron and linuron herbicides at pilot scale.

PubMed

Farré, Maria José; Maldonado, Manuel Ignacio; Gernjak, Wolfgang; Oller, Isabel; Malato, Sixto; Domènech, Xavier; Peral, José

2008-06-01

A coupled solar photo-Fenton (chemical) and biological treatment has been used to remove biorecalcitrant diuron (42 mg l(-1)) and linuron (75 mg l(-1)) herbicides from water at pilot plant scale. The chemical process has been carried out in a 82 l solar pilot plant made up by four compound parabolic collector units, and it was followed by a biological treatment performed in a 40 l sequencing batch reactor. Two Fe(II) doses (2 and 5 mg l(-1)) and sequential additions of H2O2 (20 mg l(-1)) have been used to chemically degrade the initially polluted effluent. Next, biodegradability at different oxidation states has been assessed by means of BOD/COD ratio. A reagent dose of Fe=5 mg l(-1) and H2O2=100 mg l(-1) has been required to obtain a biodegradable effluent after 100 min of irradiation time. Finally, the organic content of the photo-treated solution has been completely assimilated by a biomass consortium in the sequencing batch reactor using a total suspended solids concentration of 0.2 g l(-1) and a hydraulic retention time of 24h. Comparison between the data obtained at pilot plant scale (specially the one corresponding to the chemical step) and previously published data from a similar system performing at laboratory scale, has been carried out.

Comprehensive clone screening and evaluation of fed-batch strategies in a microbioreactor and lab scale stirred tank bioreactor system: application on Pichia pastoris producing Rhizopus oryzae lipase

PubMed Central

2014-01-01

Background In Pichia pastoris bioprocess engineering, classic approaches for clone selection and bioprocess optimization at small/micro scale using the promoter of the alcohol oxidase 1 gene (PAOX1), induced by methanol, present low reproducibility leading to high time and resource consumption. Results An automated microfermentation platform (RoboLector) was successfully tested to overcome the chronic problems of clone selection and optimization of fed-batch strategies. Different clones from Mut+P. pastoris phenotype strains expressing heterologous Rhizopus oryzae lipase (ROL), including a subset also overexpressing the transcription factor HAC1, were tested to select the most promising clones. The RoboLector showed high performance for the selection and optimization of cultivation media with minimal cost and time. Syn6 medium was better than conventional YNB medium in terms of production of heterologous protein. The RoboLector microbioreactor was also tested for different fed-batch strategies with three clones producing different lipase levels. Two mixed substrates fed-batch strategies were evaluated. The first strategy was the enzymatic release of glucose from a soluble glucose polymer by a glucosidase, and methanol addition every 24 hours. The second strategy used glycerol as co-substrate jointly with methanol at two different feeding rates. The implementation of these simple fed-batch strategies increased the levels of lipolytic activity 80-fold compared to classical batch strategies used in clone selection. Thus, these strategies minimize the risk of errors in the clone selection and increase the detection level of the desired product. Finally, the performance of two fed-batch strategies was compared for lipase production between the RoboLector microbioreactor and 5 liter stirred tank bioreactor for three selected clones. In both scales, the same clone ranking was achieved. Conclusion The RoboLector showed excellent performance in clone selection of P

Hydrodynamic Scalings: from Astrophysics to Laboratory

NASA Astrophysics Data System (ADS)

Ryutov, D. D.; Remington, B. A.

2000-05-01

A surprisingly general hydrodynamic similarity has been recently described in Refs. [1,2]. One can call it the Euler similarity because it works for the Euler equations (with MHD effects included). Although the dissipation processes are assumed to be negligible, the presence of shocks is allowed. For the polytropic medium (i.e., the medium where the energy density is proportional to the pressure), an evolution of an arbitrarily chosen 3D initial state can be scaled to another system, if a single dimensionless parameter (the Euler number) is the same for both initial states. The Euler similarity allows one to properly design laboratory experiments modeling astrophysical phenomena. We discuss several examples of such experiments related to the physics of supernovae [3]. For the problems with a single spatial scale, the condition of the smallness of dissipative processes can be adequately described in terms of the Reynolds, Peclet, and magnetic Reynolds numbers related to this scale (all three numbers must be large). However, if the system develops small-scale turbulence, dissipation may become important at these smaller scales, thereby affecting the gross behavior of the system. We analyze the corresponding constraints. We discuss also constraints imposed by the presence of interfaces between the substances with different polytropic index. Another set of similarities governs evolution of photoevaporation fronts in astrophysics. Convenient scaling laws exist in situations where the density of the ablated material is very low compared to the bulk density. We conclude that a number of hydrodynamical problems related to such objects as the Eagle Nebula can be adequately simulated in the laboratory. We discuss also possible scalings for radiative astrophysical jets (see Ref. [3] and references therein). This work was performed under the auspices of the U.S. Department of Energy by University of California Lawrence Livermore National Laboratory under contract W-7405-Eng-48

Effects of process parameters on solid self-microemulsifying particles in a laboratory scale fluid bed.

PubMed

Mukherjee, Tusharmouli; Plakogiannis, Fotios M

2012-01-01

The purpose of this study was to select the critical process parameters of the fluid bed processes impacting the quality attribute of a solid self-microemulsifying (SME) system of albendazole (ABZ). A fractional factorial design (2(4-1)) with four parameters (spray rate, inlet air temperature, inlet air flow, and atomization air pressure) was created by MINITAB software. Batches were manufactured in a laboratory top-spray fluid bed at 625-g scale. Loss on drying (LOD) samples were taken throughout each batch to build the entire moisture profiles. All dried granulation were sieved using mesh 20 and analyzed for particle size distribution (PSD), morphology, density, and flow. It was found that as spray rate increased, sauter-mean diameter (D(s)) also increased. The effect of inlet air temperature on the peak moisture which is directly related to the mean particle size was found to be significant. There were two-way interactions between studied process parameters. The main effects of inlet air flow rate and atomization air pressure could not be found as the data were inconclusive. The partial least square (PLS) regression model was found significant (P < 0.01) and predictive for optimization. This study established a design space for the parameters for solid SME manufacturing process.

Inorganic fouling mitigation by salinity cycling in batch reverse osmosis.

PubMed

Warsinger, David M; Tow, Emily W; Maswadeh, Laith A; Connors, Grace B; Swaminathan, Jaichander; Lienhard V, John H

2018-06-15

Enhanced fouling resistance has been observed in recent variants of reverse osmosis (RO) desalination which use time-varying batch or semi-batch processes, such as closed-circuit RO (CCRO) and pulse flow RO (PFRO). However, the mechanisms of batch processes' fouling resistance are not well-understood, and models have not been developed for prediction of their fouling performance. Here, a framework for predicting reverse osmosis fouling is developed by comparing the fluid residence time in batch and continuous (conventional) reverse osmosis systems to the nucleation induction times for crystallization of sparingly soluble salts. This study considers the inorganic foulants calcium sulfate (gypsum), calcium carbonate (calcite), and silica, and the work predicts maximum recovery ratios for the treatment of typical water sources using batch reverse osmosis (BRO) and continuous reverse osmosis. The prediction method is validated through comparisons to the measured time delay for CaSO 4 membrane scaling in a bench-scale, recirculating reverse osmosis unit. The maximum recovery ratio for each salt solution (CaCO 3 , CaSO 4 ) is individually predicted as a function of inlet salinity, as shown in contour plots. Next, the maximum recovery ratios of batch and conventional RO are compared across several water sources, including seawater, brackish groundwater, and RO brine. Batch RO's shorter residence times, associated with cycling from low to high salinity during each batch, enable significantly higher recovery ratios and higher salinity than in continuous RO for all cases examined. Finally, representative brackish RO brine samples were analyzed to determine the maximum possible recovery with batch RO. Overall, the induction time modeling methodology provided here can be used to allow batch RO to operate at high salinity and high recovery, while controlling scaling. The results show that, in addition to its known energy efficiency improvement, batch RO has superior inorganic

Digester performance and microbial community changes in thermophilic and mesophilic sequencing batch reactors fed with the fine sieved fraction of municipal sewage.

PubMed

Ghasimi, Dara S M; Tao, Yu; de Kreuk, Merle; Abbas, Ben; Zandvoort, Marcel H; van Lier, Jules B

2015-12-15

This study investigates the start-up and operation of bench-scale mesophilic (35 °C) and thermophilic (55 °C) anaerobic sequencing batch reactor (SBR) digesters treating the fine sieved fraction (FSF) from raw municipal sewage. FSF was sequestered from raw municipal wastewater, in the Netherlands, using a rotating belt filter equipped with a 350 micron mesh. For the given wastewater, the major component of FSF was toilet paper, which is estimated to be 10-14 kg per year per average person in the western European countries. A seven months adaptation time was allowed for the thermophilic and mesophilic digesters in order to adapt to FSF as the sole substrate with varying dry solids content of 10-25%. Different SBR cycle durations (14, 9 and 2 days) were applied for both temperature conditions to study methane production rates, volatile fatty acids (VFAs) dynamics, lag phases, as well as changes in microbial communities. The prevailing sludge in the two digesters consisted of very different bacterial and archaeal communities, with OP9 lineage and Methanothermobacter being pre-dominant in the thermophilic digester and Bacteroides and Methanosaeta dominating the mesophilic one. Eventually, decreasing the SBR cycle period, thus increasing the FSF load, resulted in improved digester performances, particularly with regard to the thermophilic digester, i.e. shortened lag phases following the batch feedings, and reduced VFA peaks. Over time, the thermophilic digester outperformed the mesophilic one with 15% increased volatile solids (VS) destruction, irrespective to lower species diversity found at high temperature. Copyright © 2015 Elsevier Ltd. All rights reserved.

Acceptance Test Data for BWXT Coated Particle Batches 93172B and 93173B—Defective IPyC and Pyrocarbon Anisotropy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hunn, John D.; Helmreich, Grant W.; Dyer, John A.

Coated particle batches J52O-16-93172B and J52O-16-93173B were produced by Babcock and Wilcox Technologies (BWXT) as part of the production campaign for the Advanced Gas Reactor Fuel Development and Qualification (AGR) Program’s AGR-5/6/7 irradiation test in the Idaho National Laboratory (INL) Advanced Test Reactor (ATR), but were not used in the final fuel composite. However, these batches may be used as demonstration production-scale coated particle fuel for other experiments. Each batch was coated in a 150-mm-diameter production-scale fluidized-bed chemical vapor deposition (CVD) furnace. Tristructural isotropic (TRISO) coatings were deposited on 425-μm-nominal-diameter spherical kernels from BWXT lot J52R-16-69317 containing a mixture ofmore » 15.5%-enriched uranium carbide and uranium oxide (UCO). The TRISO coatings consisted of four consecutive CVD layers: a ~50% dense carbon buffer layer with 100-μm-nominal thickness, a dense inner pyrolytic carbon (IPyC) layer with 40-μm-nominal thickness, a silicon carbide (SiC) layer with 35-μm-nominal thickness, and a dense outer pyrolytic carbon (OPyC) layer with 40-μm-nominal thickness. The TRISO-coated particle batches were sieved to upgrade the particles by removing over-sized and under-sized material, and the upgraded batches were designated by appending the letter A to the end of the batch number (e.g., 93172A). Secondary upgrading by sieving was performed on the A-designated batches to remove particles with missing or very-thin buffer layers that were identified during previous analysis of the individual batches for defective IPyC, as reported in the acceptance test data report for the AGR-5/6/7 production batches [Hunn et al. 2017b]. The additionally-upgraded batches were designated by appending the letter B to the end of the batch number (e.g., 93172B).« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shull, H.E.

The objective of the project was to investigate the economic feasibility of converting potato waste to fuel alcohol. The source of potato starch was Troyer Farms Potato Chips. Experimental work was carried out at both the laboratory scale and the larger pilot scale batch operation at a decommissioned waste water treatment building on campus. The laboratory scale work was considerably more extensive than originally planned, resulting in a much improved scientific work. The pilot scale facility has been completed and operated successfully. In contrast, the analysis of the economic feasibility of commercial production has not yet been completed. The projectmore » was brought to a close with the successful demonstration of the fermentation and distillation using the large scale facilities described previously. Two batches of mash were cooked using the procedures established in support of the laboratory scale work. One of the batches was fermented using the optimum values of the seven controlled factors as predicted by the laboratory scale application of the Box-Wilson design. The other batch was fermented under conditions derived out of Mr. Rouse's interpretation of his long sequence of laboratory results. He was gratified to find that his commitment to the Box-Wilson experiments was justified. The productivity of the Box-Wilson design was greater. The difference between the performance of the two fermentors (one stirred, one not) has not been established yet. Both batches were then distilled together, demonstrating the satisfactory performance of the column still. 4 references.« less

[Batch release of immunoglobulin and monoclonal antibody products].

PubMed

Gross, S

2014-10-01

The Paul-Ehrlich Institute (PEI) is an independent institution of the Federal Republic of Germany responsible for performing official experimental batch testing of sera. The institute decides about the release of each batch and performs experimental research in the field. The experimental quality control ensures the potency of the product and also the absence of harmful impurities. For release of an immunoglobulin batch the marketing authorization holder has to submit the documentation of the manufacture and the results of quality control measures together with samples of the batch to the PEI. Experimental testing is performed according to the approved specifications regarding the efficacy and safety. Since implementation of the 15th German drug law amendment, the source of antibody is not defined anymore. According to § 32 German drug law, all batches of sera need to be released by an official control laboratory. Sera are medicinal products, which contain antibodies, antibody fragments or fusion proteins with a functional antibody portion. Therefore, all batches of monoclonal antibodies and derivatives must also be released by the PEI and the marketing authorization holder has to submit a batch release application. Under certain circumstances a waiver for certain products can be issued with regard to batch release. The conditions for such a waiver apply to the majority of monoclonal antibodies.

Acceptance Test Data for BWXT Coated Particle Batch 93164A Defective IPyC Fraction and Pyrocarbon Anisotropy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Helmreich, Grant W.; Hunn, John D.; Skitt, Darren J.

2017-02-01

Coated particle fuel batch J52O-16-93164 was produced by Babcock and Wilcox Technologies (BWXT) for possible selection as fuel for the Advanced Gas Reactor Fuel Development and Qualification (AGR) Program’s AGR-5/6/7 irradiation test in the Idaho National Laboratory (INL) Advanced Test Reactor (ATR), or may be used as demonstration production-scale coated particle fuel for other experiments. The tristructural-isotropic (TRISO) coatings were deposited in a 150-mm-diameter production-scale fluidizedbed chemical vapor deposition (CVD) furnace onto 425-μm-nominal-diameter spherical kernels from BWXT lot J52L-16-69316. Each kernel contained a mixture of 15.5%-enriched uranium carbide and uranium oxide (UCO) and was coated with four consecutive CVD layers:more » a ~50% dense carbon buffer layer with 100-μm-nominal thickness, a dense inner pyrolytic carbon (IPyC) layer with 40-μm-nominal thickness, a silicon carbide (SiC) layer with 35-μm-nominal thickness, and a dense outer pyrolytic carbon (OPyC) layer with 40-μm-nominal thickness. The TRISO-coated particle batch was sieved to upgrade the particles by removing over-sized and under-sized material, and the upgraded batch was designated by appending the letter A to the end of the batch number (i.e., 93164A).« less

Leaching Behavior Of Mineral Processing Waste: Comparison Of Batch And Column Investigations

EPA Science Inventory

In this study, a comparison of laboratory batch and column experiments on metal release profile from a mineral processing waste (MPW) is presented. Batch (equilibrium) and column (dynamic) leaching tests were conducted on ground MPW at different liquid–solid ratios (LS) to determ...

Rainbow: a tool for large-scale whole-genome sequencing data analysis using cloud computing.

PubMed

Zhao, Shanrong; Prenger, Kurt; Smith, Lance; Messina, Thomas; Fan, Hongtao; Jaeger, Edward; Stephens, Susan

2013-06-27

Technical improvements have decreased sequencing costs and, as a result, the size and number of genomic datasets have increased rapidly. Because of the lower cost, large amounts of sequence data are now being produced by small to midsize research groups. Crossbow is a software tool that can detect single nucleotide polymorphisms (SNPs) in whole-genome sequencing (WGS) data from a single subject; however, Crossbow has a number of limitations when applied to multiple subjects from large-scale WGS projects. The data storage and CPU resources that are required for large-scale whole genome sequencing data analyses are too large for many core facilities and individual laboratories to provide. To help meet these challenges, we have developed Rainbow, a cloud-based software package that can assist in the automation of large-scale WGS data analyses. Here, we evaluated the performance of Rainbow by analyzing 44 different whole-genome-sequenced subjects. Rainbow has the capacity to process genomic data from more than 500 subjects in two weeks using cloud computing provided by the Amazon Web Service. The time includes the import and export of the data using Amazon Import/Export service. The average cost of processing a single sample in the cloud was less than 120 US dollars. Compared with Crossbow, the main improvements incorporated into Rainbow include the ability: (1) to handle BAM as well as FASTQ input files; (2) to split large sequence files for better load balance downstream; (3) to log the running metrics in data processing and monitoring multiple Amazon Elastic Compute Cloud (EC2) instances; and (4) to merge SOAPsnp outputs for multiple individuals into a single file to facilitate downstream genome-wide association studies. Rainbow is a scalable, cost-effective, and open-source tool for large-scale WGS data analysis. For human WGS data sequenced by either the Illumina HiSeq 2000 or HiSeq 2500 platforms, Rainbow can be used straight out of the box. Rainbow is available

Effect on orange juice of batch pasteurization in an improved pilot-scale microwave oven.

PubMed

Cinquanta, L; Albanese, D; Cuccurullo, G; Di Matteo, M

2010-01-01

The effects on orange juice batch pasteurization in an improved pilot-scale microwave (MW) oven was evaluated by monitoring pectin methyl-esterase (PME) activity, color, carotenoid compounds and vitamin C content. Trials were performed on stirred orange juice heated at different temperatures (60, 70, 75, and 85 degrees C) during batch process. MW pilot plant allowed real-time temperature control of samples using proportional integrative derivative (PID) techniques based on the infrared thermography temperature read-out. The inactivation of heat sensitive fraction of PME, that verifies orange juice pasteurization, showed a z-value of 22.1 degrees C. Carotenoid content, responsible for sensorial and nutritional quality in fresh juices, decreased by about 13% after MW pasteurization at 70 degrees C for 1 min. Total of 7 carotenoid compounds were quantified during MW heating: zeaxanthin and beta-carotene content decreased by about 26%, while no differences (P < 0.05) were found for beta-cryptoxanthin in the same trial. A slight decrease in vitamin C content was monitored after MW heating. Results showed that MW heating with a fine temperature control could result in promising stabilization treatments.

Batch Immunostaining for Large-Scale Protein Detection in the Whole Monkey Brain

PubMed Central

Zangenehpour, Shahin; Burke, Mark W.; Chaudhuri, Avi; Ptito, Maurice

2009-01-01

Immunohistochemistry (IHC) is one of the most widely used laboratory techniques for the detection of target proteins in situ. Questions concerning the expression pattern of a target protein across the entire brain are relatively easy to answer when using IHC in small brains, such as those of rodents. However, answering the same questions in large and convoluted brains, such as those of primates presents a number of challenges. Here we present a systematic approach for immunodetection of target proteins in an adult monkey brain. This approach relies on the tissue embedding and sectioning methodology of NeuroScience Associates (NSA) as well as tools developed specifically for batch-staining of free-floating sections. It results in uniform staining of a set of sections which, at a particular interval, represents the entire brain. The resulting stained sections can be subjected to a wide variety of analytical procedures in order to measure protein levels, the population of neurons expressing a certain protein. PMID:19636291

Musical Scales in Tone Sequences Improve Temporal Accuracy.

PubMed

Li, Min S; Di Luca, Massimiliano

2018-01-01

Predicting the time of stimulus onset is a key component in perception. Previous investigations of perceived timing have focused on the effect of stimulus properties such as rhythm and temporal irregularity, but the influence of non-temporal properties and their role in predicting stimulus timing has not been exhaustively considered. The present study aims to understand how a non-temporal pattern in a sequence of regularly timed stimuli could improve or bias the detection of temporal deviations. We presented interspersed sequences of 3, 4, 5, and 6 auditory tones where only the timing of the last stimulus could slightly deviate from isochrony. Participants reported whether the last tone was 'earlier' or 'later' relative to the expected regular timing. In two conditions, the tones composing the sequence were either organized into musical scales or they were random tones. In one experiment, all sequences ended with the same tone; in the other experiment, each sequence ended with a different tone. Results indicate higher discriminability of anisochrony with musical scales and with longer sequences, irrespective of the knowledge of the final tone. Such an outcome suggests that the predictability of non-temporal properties, as enabled by the musical scale pattern, can be a factor in determining the sensitivity of time judgments.

Characterization Of The As-Received Sludge Batch 9 Qualification Sample (Htf-51-15-81)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pareizs, J.

Savannah River National Laboratory (SRNL) personnel have been requested to qualify the next sludge batch (Sludge Batch 9 – SB9) for processing at the Defense Waste Processing Facility (DWPF). To accomplish this task, Savannah River Remediation (SRR) has sent SRNL a 3-L slurried sample of Tank 51H (HTF-51-15-81) to be characterized, washed, and then used in a lab-scale demonstration of the DWPF flowsheet (potentially after combining with Tank 40H sludge). This report documents the first steps of the qualification process – characterization of the as-received Tank 51H qualification sample. These results will be used to support a reprojection of SB9more » by SRR from which final Tank 51H washing, frit development, and Chemical Processing Cell (CPC) activities will be based.« less

Ethanol prefermentation of food waste in sequencing batch methane fermentation for improved buffering capacity and microbial community analysis.

PubMed

Yu, Miao; Wu, Chuanfu; Wang, Qunhui; Sun, Xiaohong; Ren, Yuanyuan; Li, Yu-You

2018-01-01

This study investigates the effects of ethanol prefermentation (EP) on methane fermentation. Yeast was added to the substrate for EP in the sequencing batch methane fermentation of food waste. An Illumina MiSeq high-throughput sequencing system was used to analyze changes in the microbial community. Methane production in the EP group (254mL/g VS) was higher than in the control group (35mL/g VS) because EP not only increased the buffering capacity of the system, but also increased hydrolytic acidification. More carbon source was converted to ethanol in the EP group than in the control group, and neutral ethanol could be converted continuously to acetic acid, which promoted the growth of Methanobacterium and Methanosarcina. As a result, the relative abundance of methane-producing bacteria was significantly higher than that of the control group. Kinetic modeling indicated that the EP group had a higher hydrolysis efficiency and shorter lag phase. Copyright © 2017 Elsevier Ltd. All rights reserved.

Effect of florfenicol on performance and microbial community of a sequencing batch biofilm reactor treating mariculture wastewater.

PubMed

Gao, Feng; Li, Zhiwei; Chang, Qingbo; Gao, Mengchun; She, Zonglian; Wu, Juan; Jin, Chunji; Zheng, Dong; Guo, Liang; Zhao, Yangguo; Wang, Sen

2018-02-01

The effects of florfenicol (FF) on the performance, microbial activity and microbial community of a sequencing batch biofilm reactor (SBBR) were evaluated in treating mariculture wastewater. The chemical oxygen demand (COD) and nitrogen removal were inhibited at high FF concentrations. The specific oxygen utilization rate (SOUR), specific ammonium oxidation rate (SAOR), specific nitrite oxidation rate (SNOR) and specific nitrate reduction rate (SNRR) were decreased with an increase in the FF concentration from 0 to 35 mg/L. The chemical compositions of loosely bound extracellular polymeric substances (LB-EPS) and tightly bound EPS (TB-EPS) could be affected with an increase in the FF concentration. The high-throughput sequencing indicated some obvious variations in the microbial community at different FF concentrations. The relative abundance of Nitrosomonas and Nitrospira showed a decreasing tendency with an increase in the FF concentration, suggesting that FF could affect the nitrification process of SBBR. Some genera capable of reducing nitrate to nitrogen gas could be inhibited by the addition of FF in the influent, such as Azospirillum and Hyphomicrobium.

Improving municipal wastewater nitrogen and phosphorous removal by feeding sludge fermentation products to sequencing batch reactor (SBR).

PubMed

Yuan, Yue; Liu, Jinjin; Ma, Bin; Liu, Ye; Wang, Bo; Peng, Yongzhen

2016-12-01

This study presents a novel strategy to improve the removal efficiency of nitrogen and phosphorus from municipal wastewater by feeding sequencing batch reactor (SBR) with sludge alkaline fermentation products as carbon sources. The performances of two SBRs treating municipal wastewater (one was fed with sludge fermentation products; F-SBR, and the other without sludge fermentation products; B-SBR) were compared. The removal efficiencies of total nitrogen (TN) and phosphorus (PO 4 3- -P) were found to be 82.9% and 96.0% in F-SBR, while the corresponding values in B-SBR were 55.9% (TN) and -6.1% (PO 4 3- -P). Illumina MiSeq sequencing indicated that ammonium-oxidizing bacteria (Nitrosomonadaceae and Nitrosomonas) and denitrifying polyphosphate accumulating organisms (Dechloromonas) were enriched in F-SBR, which resulted in NO 2 - -N accumulation and denitrifying phosphorus removal via nitrite (DPRN). Moreover, feeding of sludge fermentation products reduced 862.1mg VSS/d of sludge in the F-SBR system (volume: 10L). Copyright © 2016 Elsevier Ltd. All rights reserved.

Microalgae-activated sludge treatment of molasses wastewater in sequencing batch photo-bioreactor.

PubMed

Tsioptsias, Costas; Lionta, Gesthimani; Samaras, Petros

2017-05-01

The aim of this work was the examination of the treatment potential of molasses wastewater, by the utilization of activated sludge and microalgae. The systems used included a sequencing batch bioreactor and a similar photo-bioreactor, favoring microalgae growth. The microalgae treatment of molasses wastewater mixture resulted in a considerable reduction in the total nitrogen content. A reduction in the ammonium and nitrate content was observed in the photo-bioreactor, while the effluent's total nitrogen consisted mainly of 50% organic nitrogen. The transformation of the nitrogen forms in the photo-bioreactor was attributed to microalgae activity, resulting in the production of a better quality effluent. Lower COD removal was observed for the photo-bioreactor than the control, which however increased, by the replacement of the anoxic phase by a long aeration period. The mechanism of nitrogen removal included both the denitrification process during the anoxic stage and the microalgae activities, as the replacement of the anoxic stage resulted in low total nitrogen removal capacities. A decrease in the photobioreactor performance was observed after 35 days of operation due to biofilm formation on the light tube surface, while the operation at higher temperature accelerated microalgae growth, resulting thus in the early failure of the photoreactor.

Rainbow: a tool for large-scale whole-genome sequencing data analysis using cloud computing

PubMed Central

2013-01-01

Background Technical improvements have decreased sequencing costs and, as a result, the size and number of genomic datasets have increased rapidly. Because of the lower cost, large amounts of sequence data are now being produced by small to midsize research groups. Crossbow is a software tool that can detect single nucleotide polymorphisms (SNPs) in whole-genome sequencing (WGS) data from a single subject; however, Crossbow has a number of limitations when applied to multiple subjects from large-scale WGS projects. The data storage and CPU resources that are required for large-scale whole genome sequencing data analyses are too large for many core facilities and individual laboratories to provide. To help meet these challenges, we have developed Rainbow, a cloud-based software package that can assist in the automation of large-scale WGS data analyses. Results Here, we evaluated the performance of Rainbow by analyzing 44 different whole-genome-sequenced subjects. Rainbow has the capacity to process genomic data from more than 500 subjects in two weeks using cloud computing provided by the Amazon Web Service. The time includes the import and export of the data using Amazon Import/Export service. The average cost of processing a single sample in the cloud was less than 120 US dollars. Compared with Crossbow, the main improvements incorporated into Rainbow include the ability: (1) to handle BAM as well as FASTQ input files; (2) to split large sequence files for better load balance downstream; (3) to log the running metrics in data processing and monitoring multiple Amazon Elastic Compute Cloud (EC2) instances; and (4) to merge SOAPsnp outputs for multiple individuals into a single file to facilitate downstream genome-wide association studies. Conclusions Rainbow is a scalable, cost-effective, and open-source tool for large-scale WGS data analysis. For human WGS data sequenced by either the Illumina HiSeq 2000 or HiSeq 2500 platforms, Rainbow can be used straight out of

[Factors of the rapid startup for nitrosation in sequencing batch reactor].

PubMed

Li, Dong; Tao, Xiao-Xiao; Li, Zhan; Wang, Jun-An; Zhang, Jie

2011-08-01

The approach and factors for realizing the rapid startup of nitrosation were researched at the low level of dissolved oxygen (DO) in sequencing batch reactor (SBR). The main parameters of the reactor were controlled as follows: DO were 0.15-0.40 mg/L, pH values kept from 7.52 to 8.30, temperature maintained at 22.3-27.1 degrees C, and time of aeration was 8 hours. The purpose of rapid startup for nitrosation was achieved after 57 cycles (36 d) with the alternative influent of high and low ammonium wastewater (the mean values were 245.28 mg/L and 58.08 mg/L respectively) in a SBR, and the nitrosation rate was even 100%. Factors of accumulation of nitrite were investigated and the effects of DO and pH were analyzed during the startup for nitrosation. The results showed that it could improve the efficiency of nitrosation when DO concentration was increased appropriately. The activity of nitrite oxidizing bacteria (NOB) was recovered gradually when DO was higher than 0.72 mg/L. The key factor of controlling nitrosation reaction was the concentration of free ammonia (FA), while the final factor was the concentration of DO. pH was a desired controlling parameter to show the end of nitrification in a SBR cycle, while DO concentration did not indicate the finishing of SBR nitrification accurately because it increased rapidly before ammonia nitrogen was oxidized absolutely.

EPOS-WP16: A Platform for European Multi-scale Laboratories

NASA Astrophysics Data System (ADS)

Spiers, Chris; Drury, Martyn; Kan-Parker, Mirjam; Lange, Otto; Willingshofer, Ernst; Funiciello, Francesca; Rosenau, Matthias; Scarlato, Piergiorgio; Sagnotti, Leonardo; W16 Participants

2016-04-01

The participant countries in EPOS embody a wide range of world-class laboratory infrastructures ranging from high temperature and pressure experimental facilities, to electron microscopy, micro-beam analysis, analogue modeling and paleomagnetic laboratories. Most data produced by the various laboratory centres and networks are presently available only in limited "final form" in publications. As such many data remain inaccessible and/or poorly preserved. However, the data produced at the participating laboratories are crucial to serving society's need for geo-resources exploration and for protection against geo-hazards. Indeed, to model resource formation and system behaviour during exploitation, we need an understanding from the molecular to the continental scale, based on experimental data. This contribution will describe the work plans that the laboratories community in Europe is making, in the context of EPOS. The main objectives are: - To collect and harmonize available and emerging laboratory data on the properties and processes controlling rock system behaviour at multiple scales, in order to generate products accessible and interoperable through services for supporting research activities. - To co-ordinate the development, integration and trans-national usage of the major solid Earth Science laboratory centres and specialist networks. The length scales encompassed by the infrastructures included range from the nano- and micrometer levels (electron microscopy and micro-beam analysis) to the scale of experiments on centimetre sized samples, and to analogue model experiments simulating the reservoir scale, the basin scale and the plate scale. - To provide products and services supporting research into Geo-resources and Geo-storage, Geo-hazards and Earth System Evolution.

Elimination of the Reaction Rate "Scale Effect": Application of the Lagrangian Reactive Particle-Tracking Method to Simulate Mixing-Limited, Field-Scale Biodegradation at the Schoolcraft (MI, USA) Site

NASA Astrophysics Data System (ADS)

Ding, Dong; Benson, David A.; Fernández-Garcia, Daniel; Henri, Christopher V.; Hyndman, David W.; Phanikumar, Mantha S.; Bolster, Diogo

2017-12-01

Measured (or empirically fitted) reaction rates at groundwater remediation sites are typically much lower than those found in the same material at the batch or laboratory scale. The reduced rates are commonly attributed to poorer mixing at the larger scales. A variety of methods have been proposed to account for this scaling effect in reactive transport. In this study, we use the Lagrangian particle-tracking and reaction (PTR) method to simulate a field bioremediation experiment at the Schoolcraft, MI site. A denitrifying bacterium, Pseudomonas Stutzeri strain KC (KC), was injected to the aquifer, along with sufficient substrate, to degrade the contaminant, carbon tetrachloride (CT), under anaerobic conditions. The PTR method simulates chemical reactions through probabilistic rules of particle collisions, interactions, and transformations to address the scale effect (lower apparent reaction rates for each level of upscaling, from batch to column to field scale). In contrast to a prior Eulerian reaction model, the PTR method is able to match the field-scale experiment using the rate coefficients obtained from batch experiments.

Accelerating Aerobic Sludge Granulation by Adding Dry Sewage Sludge Micropowder in Sequencing Batch Reactors

PubMed Central

Li, Jun; Liu, Jun; Wang, Danjun; Chen, Tao; Ma, Ting; Wang, Zhihong; Zhuo, Weilong

2015-01-01

Micropowder (20–250 µm) made from ground dry waste sludge from a municipal sewage treatment plant was added in a sequencing batch reactor (R2), which was fed by synthetic wastewater with acetate as carbon source. Compared with the traditional SBR (R1), aerobic sludge granulation time was shortened 15 days in R2. Furthermore, filamentous bacteria in bulking sludge were controlled to accelerate aerobic granulation and form large granules. Correspondingly, the SVI decreased from 225 mL/g to 37 mL/g. X-ray Fluorescence (XRF) analysis demonstrated that Al and Si from the micropowder were accumulated in granules. A mechanism hypotheses for the acceleration of aerobic granulation by adding dry sludge micropowder is proposed: added micropowder acts as nuclei to induce bacterial attachment; dissolved matters from the micropowder increase abruptly the organic load for starved sludge to control overgrown filamentous bacteria as a framework for aggregation; increased friction from the movement of micropowder forces the filaments which extend outwards to shrink for shaping granules. PMID:26308025

30 CFR 14.21 - Laboratory-scale flame test apparatus.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Laboratory-scale flame test apparatus. 14.21 Section 14.21 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR TESTING... Technical Requirements § 14.21 Laboratory-scale flame test apparatus. The principal parts of the apparatus...

30 CFR 14.21 - Laboratory-scale flame test apparatus.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 30 Mineral Resources 1 2011-07-01 2011-07-01 false Laboratory-scale flame test apparatus. 14.21 Section 14.21 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR TESTING... Technical Requirements § 14.21 Laboratory-scale flame test apparatus. The principal parts of the apparatus...

ANAMMOX-like performances for nitrogen removal from ammonium-sulfate-rich wastewater in an anaerobic sequencing batch reactor.

PubMed

Prachakittikul, Pensiri; Wantawin, Chalermraj; Noophan, Pongsak Lek; Boonapatcharoen, Nimaradee

2016-01-01

Ammonium removal by the ANaerobic AMonium OXidation (ANAMMOX) process was observed through the Sulfate-Reducing Ammonium Oxidation (SRAO) process. The same concentration of ammonium (100 mg N L(-1)) was applied to two anaerobic sequencing batch reactors (AnSBRs) that were inoculated with the same activated sludge from the Vermicelli wastewater treatment process, while nitrite was fed in ANAMMOX and sulfate in SRAO reactors. In SRAO-AnSBR, in substrates that were fed with a ratio of NH4(+)/SO4(2-) at 1:0.4 ± 0.03, a hydraulic retention time (HRT) of 48 h and without sludge draining, the Ammonium Removal Rate (ARR) was 0.02 ± 0.01 kg N m(-3).d(-1). Adding specific ANAMMOX substrates to SRAO-AnSBR sludge in batch tests results in specific ammonium and nitrite removal rates of 0.198 and 0.139 g N g(-1) VSS.d, respectively, indicating that the ANAMMOX activity contributes to the removal of ammonium in the SRAO process using the nitrite that is produced from SRAO. Nevertheless, the inability of ANAMMOX to utilize sulfate to oxidize ammonium was also investigated in batch tests by augmenting enriched ANAMMOX culture in SRAO-AnSBR sludge and without nitrite supply. The time course of sulfate in a 24-hour cycle of SRAO-AnSBR showed an increase in sulfate after 6 h. For enriched SRAO culture, the uptake molar ratio of NH4(+)/SO4(2-) at 8 hours in a batch test was 1:0.82 lower than the value of 1:0.20 ± 0.09 as obtained in an SRAO-AnSBR effluent, while the stoichiometric ratio of 1:0.5 that includes the ANAMMOX reaction was in this range. After a longer operation of more than 2 years without sludge draining, the accumulation of sulfate and the reduction of ammonium removal were observed, probably due to the gradual increase in the sulfur denitrification rate and the competitive use of nitrite with ANAMMOX. The 16S rRNA gene PCR-DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis) and PCR cloning analyses resulted in the detection of the ANAMMOX

Anaerobic Digestion of Laminaria japonica Waste from Industrial Production Residues in Laboratory- and Pilot-Scale.

PubMed

Barbot, Yann Nicolas; Thomsen, Claudia; Thomsen, Laurenz; Benz, Roland

2015-09-18

The cultivation of macroalgae to supply the biofuel, pharmaceutical or food industries generates a considerable amount of organic residue, which represents a potential substrate for biomethanation. Its use optimizes the total resource exploitation by the simultaneous disposal of waste biomaterials. In this study, we explored the biochemical methane potential (BMP) and biomethane recovery of industrial Laminaria japonica waste (LJW) in batch, continuous laboratory and pilot-scale trials. Thermo-acidic pretreatment with industry-grade HCl or industrial flue gas condensate (FGC), as well as a co-digestion approach with maize silage (MS) did not improve the biomethane recovery. BMPs between 172 mL and 214 mL g(-1) volatile solids (VS) were recorded. We proved the feasibility of long-term continuous anaerobic digestion with LJW as sole feedstock showing a steady biomethane production rate of 173 mL g(-1) VS. The quality of fermentation residue was sufficient to serve as biofertilizer, with enriched amounts of potassium, sulfur and iron. We further demonstrated the upscaling feasibility of the process in a pilot-scale system where a CH₄ recovery of 189 L kg(-1) VS was achieved and a biogas composition of 55% CH₄ and 38% CO₂ was recorded.

A Model-based B2B (Batch to Batch) Control for An Industrial Batch Polymerization Process

NASA Astrophysics Data System (ADS)

Ogawa, Morimasa

This paper describes overview of a model-based B2B (batch to batch) control for an industrial batch polymerization process. In order to control the reaction temperature precisely, several methods based on the rigorous process dynamics model are employed at all design stage of the B2B control, such as modeling and parameter estimation of the reaction kinetics which is one of the important part of the process dynamics model. The designed B2B control consists of the gain scheduled I-PD/II2-PD control (I-PD with double integral control), the feed-forward compensation at the batch start time, and the model adaptation utilizing the results of the last batch operation. Throughout the actual batch operations, the B2B control provides superior control performance compared with that of conventional control methods.

Understanding variations in secondary findings reporting practices across U.S. genome sequencing laboratories.

PubMed

Ackerman, Sara L; Koenig, Barbara A

2018-01-01

Increasingly used for clinical purposes, genome and exome sequencing can generate clinically relevant information that is not directly related to the reason for testing (incidental or secondary findings). Debates about the ethical implications of secondary findings were sparked by the American College of Medical Genetics (ACMG) 2013 policy statement, which recommended that laboratories report pathogenic alterations in 56 genes. Although wide variation in laboratories' secondary findings policies has been reported, little is known about its causes. We interviewed 18 laboratory directors and genetic counselors at 10 U.S. laboratories to investigate the motivations and interests shaping secondary findings reporting policies for clinical exome sequencing. Analysis of interview transcripts and laboratory documents was informed by sociological theories of standardization. Laboratories varied widely in terms of the types of secondary findings reported, consent-form language, and choices offered to patients. In explaining their adaptation of the ACMG report, our participants weighed genetic information's clinical, moral, professional, and commercial value in an attempt to maximize benefits for patients and families, minimize the costs of sequencing and analysis, adhere to professional norms, attract customers, and contend with the uncertain clinical implications of much of the genetic information generated. Nearly all laboratories in our study voluntarily adopted ACMG's recommendations, but their actual practices varied considerably and were informed by laboratory-specific judgments about clinical utility and patient benefit. Our findings offer a compelling example of standardization as a complex process that rarely leads simply to uniformity of practice. As laboratories take on a more prominent role in decisions about the return of genetic information, strategies are needed to inform patients, families, and clinicians about the differences between laboratories' practices

Sequencing Batch Reactor (SBR) for the removal of Hg2+ and Cd2+ from synthetic petrochemical factory wastewater.

PubMed

Malakahmad, Amirhossein; Hasani, Amirhesam; Eisakhani, Mahdieh; Isa, Mohamed Hasnain

2011-07-15

Petrochemical factories which manufacture vinyl chloride monomer and poly vinyl chloride (PVC) are among the largest industries which produce wastewater contains mercury and cadmium. The objective of this research is to evaluate the performance of a lab-scale Sequencing Batch Reactor (SBR) to treat a synthetic petrochemical wastewater containing mercury and cadmium. After acclimatization of the system which lasted 60 days, the SBR was introduced to mercury and cadmium in low concentrations which then was increased gradually to 9.03±0.02 mg/L Hg and 15.52±0.02 mg/L Cd until day 110. The SBR performance was assessed by measuring Chemical Oxygen Demand, Total and Volatile Suspended Solids as well as Sludge Volume Index. At maximum concentrations of the heavy metals, the SBR was able to remove 76-90% of Hg(2+) and 96-98% of Cd(2+). The COD removal efficiency and MLVSS (microorganism population) in the SBR was affected by mercury and cadmium concentrations in influent. Different species of microorganisms such as Rhodospirilium-like bacteria, Gomphonema-like algae, and sulfate reducing-like bacteria were identified in the system. While COD removal efficiency and MLVSS concentration declined during addition of heavy metals, the appreciable performance of SBR in removal of Hg(2+) and Cd(2+) implies that the removal in SBR was not only a biological process, but also by the biosorption process of the sludge. Copyright © 2011 Elsevier B.V. All rights reserved.

Characterization of the SRNL-Washed tank 51 sludge batch 9 qualification sample

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pareizs, J. M.

2016-01-01

Savannah River National Laboratory (SRNL) personnel have been requested to qualify the next sludge batch (Sludge Batch 9 – SB9) for processing at the Defense Waste Processing Facility (DWPF). To accomplish this task, Savannah River Remediation (SRR) sent SRNL a 3-L sample of Tank 51H slurry to be characterized, washed, and then used in a lab-scale demonstration of the DWPF flowsheet (after combining with Tank 40H sludge). SRNL has washed the Tank 51H sample per the Tank Farm washing strategy as of October 20, 2015. A part of the qualification process is extensive radionuclide and chemical characterization of the SRNL-washedmore » Tank 51H slurry. This report documents the chemical characterization of the washed slurry; radiological characterization is in progress and will be documented in a separate report. The analytical results of this characterization are comparable to the Tank Farm projections. Therefore, it is recommended that SRNL use this washed slurry for the ongoing SB9 qualification activities.« less

Control of algal production in a high rate algal pond: investigation through batch and continuous experiments.

PubMed

Derabe Maobe, H; Onodera, M; Takahashi, M; Satoh, H; Fukazawa, T

2014-01-01

For decades, arid and semi-arid regions in Africa have faced issues related to water availability for drinking, irrigation and livestock purposes. To tackle these issues, a laboratory scale greywater treatment system based on high rate algal pond (HRAP) technology was investigated in order to guide the operation of the pilot plant implemented in the 2iE campus in Ouagadougou (Burkina Faso). Because of the high suspended solids concentration generally found in effluents of this system, the aim of this study is to improve the performance of HRAPs in term of algal productivity and removal. To determine the selection mechanism of self-flocculated algae, three sets of sequencing batch reactors (SBRs) and three sets of continuous flow reactors (CFRs) were operated. Despite operation with the same solids retention time and the similarity of the algal growth rate found in these reactors, the algal productivity was higher in the SBRs owing to the short hydraulic retention time of 10 days in these reactors. By using a volume of CFR with twice the volume of our experimental CFRs, the algal concentration can be controlled during operation under similar physical conditions in both reactors.

Biological treatment of thin-film transistor liquid crystal display (TFT-LCD) wastewater using aerobic and anoxic/oxic sequencing batch reactors.

PubMed

Lei, Chin-Nan; Whang, Liang-Ming; Chen, Po-Chun

2010-09-01

The amount of pollutants produced during manufacturing processes of thin-film transistor liquid crystal display (TFT-LCD) substantially increases due to an increasing production of the opto-electronic industry in Taiwan. This study presents the treatment performance of one aerobic and one anoxic/oxic (A/O) sequencing batch reactors (SBRs) treating synthetic TFT-LCD wastewater containing dimethyl sulfoxide (DMSO), monoethanolamine (MEA), and tetra-methyl ammonium hydroxide (TMAH). The long-term monitoring results for the aerobic and A/O SBRs demonstrate that stable biodegradation of DMSO, MEA, and TMAH can be achieved without any considerably adverse impacts. The ammonium released during MEA and TMAH degradation can also be completely oxidized to nitrate through nitrification in both SBRs. Batch studies on biodegradation rates for DMSO, MEA, and TMAH under anaerobic, anoxic, and aerobic conditions indicate that effective MEA degradation can be easily achieved under all three conditions examined, while efficient DMSO and TMAH degradation can be attained only under anaerobic and aerobic conditions, respectively. The potential odor problem caused by the formation of malodorous dimethyl sulfide from DMSO degradation under anaerobic conditions, however, requires insightful consideration in treating DMSO-containing wastewater. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

LABORATORY SCALE STEAM INJECTION TREATABILITY STUDIES

EPA Science Inventory

Laboratory scale steam injection treatability studies were first developed at The University of California-Berkeley. A comparable testing facility has been developed at USEPA's Robert S. Kerr Environmental Research Center. Experience has already shown that many volatile organic...

Living laboratory: whole-genome sequencing as a learning healthcare enterprise.

PubMed

Angrist, M; Jamal, L

2015-04-01

With the proliferation of affordable large-scale human genomic data come profound and vexing questions about management of such data and their clinical uncertainty. These issues challenge the view that genomic research on human beings can (or should) be fully segregated from clinical genomics, either conceptually or practically. Here, we argue that the sharp distinction between clinical care and research is especially problematic in the context of large-scale genomic sequencing of people with suspected genetic conditions. Core goals of both enterprises (e.g. understanding genotype-phenotype relationships; generating an evidence base for genomic medicine) are more likely to be realized at a population scale if both those ordering and those undergoing sequencing for diagnostic reasons are routinely and longitudinally studied. Rather than relying on expensive and lengthy randomized clinical trials and meta-analyses, we propose leveraging nascent clinical-research hybrid frameworks into a broader, more permanent instantiation of exploratory medical sequencing. Such an investment could enlighten stakeholders about the real-life challenges posed by whole-genome sequencing, such as establishing the clinical actionability of genetic variants, returning 'off-target' results to families, developing effective service delivery models and monitoring long-term outcomes. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Laboratory-scale integrated ARP filter test

DOE Office of Scientific and Technical Information (OSTI.GOV)

Poirier, M.; Burket, P.

2016-03-01

The Savannah River Site (SRS) is currently treating radioactive liquid waste with the Actinide Removal Process (ARP) and the Modular Caustic Side Solvent Extraction Unit (MCU). Recently, the low filter flux through the ARP of approximately 5 gallons per minute has limited the rate at which radioactive liquid waste can be treated. Salt Batch 6 had a lower processing rate and required frequent filter cleaning. There is a desire to understand the causes of the low filter flux and to increase ARP/MCU throughput. This task attempted to simulate the entire ARP process, including multiple batches (5), washing, chemical cleaning, andmore » blending the feed with heels and recycle streams. The objective of the tests was to determine whether one of these processes is causing excessive fouling of the crossflow or secondary filter. The authors conducted the tests with feed solutions containing 6.6 M sodium Salt Batch 6 simulant supernate with no MST.« less

College of American Pathologists' laboratory standards for next-generation sequencing clinical tests.

PubMed

Aziz, Nazneen; Zhao, Qin; Bry, Lynn; Driscoll, Denise K; Funke, Birgit; Gibson, Jane S; Grody, Wayne W; Hegde, Madhuri R; Hoeltge, Gerald A; Leonard, Debra G B; Merker, Jason D; Nagarajan, Rakesh; Palicki, Linda A; Robetorye, Ryan S; Schrijver, Iris; Weck, Karen E; Voelkerding, Karl V

2015-04-01

The higher throughput and lower per-base cost of next-generation sequencing (NGS) as compared to Sanger sequencing has led to its rapid adoption in clinical testing. The number of laboratories offering NGS-based tests has also grown considerably in the past few years, despite the fact that specific Clinical Laboratory Improvement Amendments of 1988/College of American Pathologists (CAP) laboratory standards had not yet been developed to regulate this technology. To develop a checklist for clinical testing using NGS technology that sets standards for the analytic wet bench process and for bioinformatics or "dry bench" analyses. As NGS-based clinical tests are new to diagnostic testing and are of much greater complexity than traditional Sanger sequencing-based tests, there is an urgent need to develop new regulatory standards for laboratories offering these tests. To develop the necessary regulatory framework for NGS and to facilitate appropriate adoption of this technology for clinical testing, CAP formed a committee in 2011, the NGS Work Group, to deliberate upon the contents to be included in the checklist. Results . -A total of 18 laboratory accreditation checklist requirements for the analytic wet bench process and bioinformatics analysis processes have been included within CAP's molecular pathology checklist (MOL). This report describes the important issues considered by the CAP committee during the development of the new checklist requirements, which address documentation, validation, quality assurance, confirmatory testing, exception logs, monitoring of upgrades, variant interpretation and reporting, incidental findings, data storage, version traceability, and data transfer confidentiality.

Successful treatment of high azo dye concentration wastewater using combined anaerobic/aerobic granular activated carbon-sequencing batch biofilm reactor (GAC-SBBR): simultaneous adsorption and biodegradation processes.

PubMed

Hosseini Koupaie, E; Alavi Moghaddam, M R; Hashemi, S H

2013-01-01

The application of a granular activated carbon-sequencing batch biofilm reactor (GAC-SBBR) for treatment of wastewater containing 1,000 mg/L Acid Red 18 (AR18) was investigated in this research. The treatment system consisted of a sequencing batch reactor equipped with moving GAC as biofilm support. Each treatment cycle consisted of two successive anaerobic (14 h) and aerobic (8 h) reaction phases. Removal of more than 91% chemical oxygen demand (COD) and 97% AR18 was achieved in this study. Investigation of dye decolorization kinetics showed that the dye removal was stimulated by the adsorption capacity of the GAC at the beginning of the anaerobic phase and then progressed following a first-order reaction. Based on COD analysis results, at least 77.8% of the dye total metabolites were mineralized during the applied treatment system. High-performance liquid chromatography analysis revealed that more than 97% of 1-naphthyalamine-4-sulfonate as one of the main sulfonated aromatic constituents of AR18 was removed during the aerobic reaction phase. According to the scanning electron microscopic analysis, the microbial biofilms grew in most cavities and pores of the GAC, but not on the external surfaces of the GAC.

On-site treatment of a motorway service area wastewater using a package sequencing batch reactor (SBR).

PubMed

Del Solar, J; Hudson, S; Stephenson, T

2005-01-01

A sequencing batch reactor (SBR) treating the effluent of a motorway service station in the south of England situated on a major tourist route was investigated. Wastewater from the kitchens, toilets and washrooms facilities was collected from the areas on each side of the motorway for treatment on-site. The SBR was designed for a population equivalent (p.e.) of 500, assuming an average flow of 100 m3/d, influent biochemical oxygen demand (BOD) of 300 mg/l, and influent suspended solids (SS) of 300 mg/l. Influent monitoring over 8 weeks revealed that the average flow was only 65 m3/d and the average influent BOD and SS were 480 mg/l and 473 mg/l respectively. This corresponded to a high sludge loading rate (F:M) of 0.42 d(-1) which accounted for poor performance. Therefore the cycle times were extended from 6 h to 7 h and effluent BOD improved from 79 to 27 mg/l.

Indexcov: fast coverage quality control for whole-genome sequencing.

PubMed

Pedersen, Brent S; Collins, Ryan L; Talkowski, Michael E; Quinlan, Aaron R

2017-11-01

The BAM and CRAM formats provide a supplementary linear index that facilitates rapid access to sequence alignments in arbitrary genomic regions. Comparing consecutive entries in a BAM or CRAM index allows one to infer the number of alignment records per genomic region for use as an effective proxy of sequence depth in each genomic region. Based on these properties, we have developed indexcov, an efficient estimator of whole-genome sequencing coverage to rapidly identify samples with aberrant coverage profiles, reveal large-scale chromosomal anomalies, recognize potential batch effects, and infer the sex of a sample. Indexcov is available at https://github.com/brentp/goleft under the MIT license. © The Authors 2017. Published by Oxford University Press.

Pilot-Scale Batch Alkaline Pretreatment of Corn Stover

DOE PAGES

Kuhn, Erik M.; O’Brien, Marykate H.; Ciesielski, Peter N.; ...

2015-12-18

The goal of biomass pretreatment is to increase the enzymatic digestibility of the plant cell wall polysaccharides to produce sugars for upgrading to biofuels. Alkaline pretreatment has the ability to solubilize much of the lignin in biomass while the carbohydrates remain insoluble. With an increased research focus to produce high-value products from lignin, a low molecular weight, lignin-rich stream in a biorefinery is desirable. Here, this work reports on batch alkaline pretreatment of corn stover conducted using a three-factor, two-level central composite experimental design in a pilot-scale reactor to determine the relationship between sodium hydroxide (NaOH) loading, temperature, and anthraquinonemore » (AQ) charge on solids solubilization, component yields, and enzymatic digestibility of the residual solids. Operating conditions were 100 to 140 °C, 40 to 70 mg NaOH/g dry corn stover, and 0.05% to 0.2% (w/w) AQ loading. An enzymatic hydrolysis screening study was performed at 2% cellulose loading. Empirical modeling results showed that NaOH loading and temperature are both significant factors, solubilizing 15% to 35% of the solids and up to 54% of the lignin. Enzymatic hydrolysis of the residual solids produced good monomeric glucose (>90%) and xylose (>70%) yields at the more severe pretreatment conditions. We also found that the AQ charge was not a significant factor at the conditions studied, so efforts to reduce xylan and increase lignin solubilization using this compound were not successful. Lastly, while good lignin solubilization was achieved, effectively recovering this stream remains a challenge, and demonstrating performance in continuous reactors is still needed.« less

Pilot-Scale Batch Alkaline Pretreatment of Corn Stover

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kuhn, Erik M.; O’Brien, Marykate H.; Ciesielski, Peter N.

The goal of biomass pretreatment is to increase the enzymatic digestibility of the plant cell wall polysaccharides to produce sugars for upgrading to biofuels. Alkaline pretreatment has the ability to solubilize much of the lignin in biomass while the carbohydrates remain insoluble. With an increased research focus to produce high-value products from lignin, a low molecular weight, lignin-rich stream in a biorefinery is desirable. Here, this work reports on batch alkaline pretreatment of corn stover conducted using a three-factor, two-level central composite experimental design in a pilot-scale reactor to determine the relationship between sodium hydroxide (NaOH) loading, temperature, and anthraquinonemore » (AQ) charge on solids solubilization, component yields, and enzymatic digestibility of the residual solids. Operating conditions were 100 to 140 °C, 40 to 70 mg NaOH/g dry corn stover, and 0.05% to 0.2% (w/w) AQ loading. An enzymatic hydrolysis screening study was performed at 2% cellulose loading. Empirical modeling results showed that NaOH loading and temperature are both significant factors, solubilizing 15% to 35% of the solids and up to 54% of the lignin. Enzymatic hydrolysis of the residual solids produced good monomeric glucose (>90%) and xylose (>70%) yields at the more severe pretreatment conditions. We also found that the AQ charge was not a significant factor at the conditions studied, so efforts to reduce xylan and increase lignin solubilization using this compound were not successful. Lastly, while good lignin solubilization was achieved, effectively recovering this stream remains a challenge, and demonstrating performance in continuous reactors is still needed.« less

A concise synthesis of benzimidazoles via the microwave-assisted one-pot batch reaction of amino acids up to a 10-g scale.

PubMed

Peng, Pai; Xiong, Jin-Feng; Mo, Guang-Zhen; Zheng, Jia-Li; Chen, Ren-Hong; Chen, Xiao-Yun; Wang, Zhao-Yang

2014-10-01

An efficient method for the synthesis of aminomethyl benzimidazoles is developed by using a one-pot batch reaction between amino acids and o-phenylenediamines. This reaction proceeds smoothly in an unmodified household microwave oven, even though scale-up is to 10 g. A desirable method for the quick synthesis of benzimidazoles, which are used as a kind of important intermediates in drug synthesis, is provided by the scale-up utilization of amino acid resource.

Aerobic granulation in a sequencing batch reactor (SBR) for industrial wastewater treatment.

PubMed

Inizan, M; Freval, A; Cigana, J; Meinhold, J

2005-01-01

Aerobic granulation seems to be an a attractive process for COD removal from industrial wastewater, characterised by a high content of soluble organic compounds. In order to evaluate the practical aspects of the process, comparative experimental tests are performed on synthetic and on industrial wastewater, originating from pharmaceutical industry. Two pilot plants are operated as sequencing batch bubble columns. Focus was put on the feasibility of the process for high COD removal and on its operational procedure. For both wastewaters, a rapid formation of aerobic granules is observed along with a high COD removal rate. Granule characteristics are quite similar with respect to the two types of wastewater. It seems that filamentous bacteria are part of the granule structure and that phosphorus precipitation can play an important role in granule formation. For both wastewaters similar removal performances for dissolved biodegradable COD are observed (> 95%). However, a relatively high concentration of suspended solids in the outlet deteriorates the performance with regard to total COD removal. Biomass detachment seems to play a non-negligible role in the current set-up. After a stable operational phase the variation of the pharmaceutical wastewater caused a destabilisation and loss of the granules, despite the control for balanced nutrient supply. The first results with real industrial wastewater demonstrate the feasibility of this innovative process. However, special attention has to be paid to the critical aspects such as granule stability as well as the economic competitiveness, which both will need further investigation and evaluation.

Characterization of efficient aerobic denitrifiers isolated from two different sequencing batch reactors by 16S-rRNA analysis.

PubMed

Wang, Ping; Li, Xiuting; Xiang, Mufei; Zhai, Qian

2007-06-01

By adopting two sequencing batch reactors (SBRs) A and B, nitrate as the substrate, and the intermittent aeration mode, activated sludge was domesticated to enrich aerobic denitrifiers. The pHs of reactor A were approximately 6.3 at DOs 2.2-6.1 mg/l for a carbon source of 720 mg/l COD; the pHs of reactor B were 6.8-7.8 at DOs 2.2-3.0 mg/l for a carbon source of 1500 mg/l COD. Both reactors maintained an influent nitrate concentration of 80 mg/l NO3- -N. When the total inorganic nitrogen (TIN) removal efficiency of both reactors reached 60%, aerobic denitrifier accumulation was regarded completed. By bromthymol blue (BTB) medium, 20 bacteria were isolated from the two SBRs and DNA samples of 8 of these 20 strains were amplified by PCR and processed for 16SrRNA sequencing. The obtained results were analysed by a Blast similarity search of the GenBank database, and constructing a phylogenetic tree for identification by comparison. The 8 bacteria were found to belong to the genera Pseudomonas, Delftia, Herbaspirillum and Comamonas. At present, no Delftia has been reported to be an aerobic denitrifier.

Removal of veterinary antibiotics from anaerobically digested swine wastewater using an intermittently aerated sequencing batch reactor.

PubMed

Zheng, Wei; Zhang, Zhenya; Liu, Rui; Lei, Zhongfang

2018-03-01

A lab-scale intermittently aerated sequencing batch reactor (IASBR) was applied to treat anaerobically digested swine wastewater (ADSW) to explore the removal characteristics of veterinary antibiotics. The removal rates of 11 veterinary antibiotics in the reactor were investigated under different chemical organic demand (COD) volumetric loadings, solid retention times (SRT) and ratios of COD to total nitrogen (TN) or COD/TN. Both sludge sorption and biodegradation were found to be the major contributors to the removal of veterinary antibiotics. Mass balance analysis revealed that greater than 60% of antibiotics in the influent were biodegraded in the IASBR, whereas averagely 24% were adsorbed by sludge under the condition that sludge sorption gradually reached its equilibrium. Results showed that the removal of antibiotics was greatly influenced by chemical oxygen demand (COD) volumetric loadings, which could achieve up to 85.1%±1.4% at 0.17±0.041kgCOD/m -3 /day, while dropped to 75.9%±1.3% and 49.3%±12.1% when COD volumetric loading increased to 0.65±0.032 and 1.07±0.073kgCOD/m -3 /day, respectively. Tetracyclines, the dominant antibiotics in ADSW, were removed by 87.9% in total at the lowest COD loading, of which 30.4% were contributed by sludge sorption and 57.5% by biodegradation, respectively. In contrast, sulfonamides were removed about 96.2%, almost by biodegradation. Long SRT seemed to have little obvious impact on antibiotics removal, while a shorter SRT of 30-40day could reduce the accumulated amount of antibiotics and the balanced antibiotics sorption capacity of sludge. Influent COD/TN ratio was found not a key impact factor for veterinary antibiotics removal in this work. Copyright © 2017. Published by Elsevier B.V.

Batch, design optimization, and DNA sequencing study for continuous 1,3-propanediol production from waste glycerol by a soil-based inoculum.

PubMed

Kanjilal, Baishali; Noshadi, Iman; Bautista, Eddy J; Srivastava, Ranjan; Parnas, Richard S

2015-03-01

1,3-propanediol (1,3-PD) was produced with a robust fermentation process using waste glycerol feedstock from biodiesel production and a soil-based bacterial inoculum. An iterative inoculation method was developed to achieve independence from soil and selectively breed bacterial populations capable of glycerol metabolism to 1,3-PD. The inoculum showed high resistance to impurities in the feedstock. 1,3-PD selectivity and yield in batch fermentations was optimized by appropriate nutrient compositions and pH control. The batch yield of 1,3-PD was maximized to ~0.7 mol/mol for industrial glycerol which was higher than that for pure glycerin. 16S rDNA sequencing results show a systematic selective enrichment of 1,3-PD producing bacteria with iterative inoculation and subsequent process control. A statistical design of experiments was carried out on industrial glycerol batches to optimize conditions, which were used to run two continuous flow stirred-tank reactor (CSTR) experiments over a period of >500 h each. A detailed analysis of steady states at three dilution rates is presented. Enhanced specific 1,3-PD productivity was observed with faster dilution rates due to lower levels of solvent degeneration. 1,3-PD productivity, specific productivity, and yield of 1.1 g/l hr, 1.5 g/g hr, and 0.6 mol/mol of glycerol were obtained at a dilution rate of 0.1 h(-1)which is bettered only by pure strains in pure glycerin feeds.

Anaerobic Digestion of Laminaria japonica Waste from Industrial Production Residues in Laboratory- and Pilot-Scale

PubMed Central

Barbot, Yann Nicolas; Thomsen, Claudia; Thomsen, Laurenz; Benz, Roland

2015-01-01

The cultivation of macroalgae to supply the biofuel, pharmaceutical or food industries generates a considerable amount of organic residue, which represents a potential substrate for biomethanation. Its use optimizes the total resource exploitation by the simultaneous disposal of waste biomaterials. In this study, we explored the biochemical methane potential (BMP) and biomethane recovery of industrial Laminaria japonica waste (LJW) in batch, continuous laboratory and pilot-scale trials. Thermo-acidic pretreatment with industry-grade HCl or industrial flue gas condensate (FGC), as well as a co-digestion approach with maize silage (MS) did not improve the biomethane recovery. BMPs between 172 mL and 214 mL g−1 volatile solids (VS) were recorded. We proved the feasibility of long-term continuous anaerobic digestion with LJW as sole feedstock showing a steady biomethane production rate of 173 mL g−1 VS. The quality of fermentation residue was sufficient to serve as biofertilizer, with enriched amounts of potassium, sulfur and iron. We further demonstrated the upscaling feasibility of the process in a pilot-scale system where a CH4 recovery of 189 L kg−1 VS was achieved and a biogas composition of 55% CH4 and 38% CO2 was recorded. PMID:26393620

Evaluation of a sequencing batch reactor sewage treatment rig for investigating the fate of radioactively labelled pharmaceuticals: Case study of propranolol.

PubMed

Popple, T; Williams, J B; May, E; Mills, G A; Oliver, R

2016-01-01

Pharmaceuticals are frequently detected in the aquatic environment, and have potentially damaging effects. Effluents from sewage treatment plants (STPs) are major sources of these substances. The use of sequencing batch reactor (SBR) STPs, involving cycling between aerobic and anoxic conditions to promote nitrification and denitrification, is increasing but these have yet to be understood in terms of removal of pharmaceutical residues. This study reports on the development of a laboratory rig to simulate a SBR. The rig was used to investigate the fate of radiolabelled propranolol. This is a commonly prescribed beta blocker, but with unresolved fate in STPs. The SBR rig (4.5 L) was operated on an 8 h batch cycle with settled sewage. Effective treatment was demonstrated, with clearly distinct treatment phases and evidence of nitrogen removal. Radiolabelled (14)C-propranolol was dosed into both single (closed) and continuous (flow-through) simulations over 13 SBR cycles. Radioactivity in CO2 off-gas, biomass and liquid was monitored, along with the characteristics of the sewage. This allowed apparent rate constants and coefficients for biodegradation and solid:water partitioning to be determined. Extrapolation from off-gas radioactivity measurements in the single dose 4-d study suggested that propranolol fell outside the definitions of being readily biodegradable (DegT50 = 9.1 d; 60% biodegradation at 12.0 d). During continuous dosing, 63-72% of propranolol was removed in the rig, but less than 4% of dose recovered as (14)CO2, suggesting that biodegradation was a minor process (Kbiol(M) L kg d(-1) = 22-49) and that adsorption onto solids dominated, giving rise to accumulations within biomass during the 17 d solid retention time in the SBR. Estimations of adsorption isotherm coefficients were different depending on which of three generally accepted denominators representing sorption sites was used (mixed liquor suspended solids, reactor COD or mass of waste

Towards Batched Linear Solvers on Accelerated Hardware Platforms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Haidar, Azzam; Dong, Tingzing Tim; Tomov, Stanimire

2015-01-01

As hardware evolves, an increasingly effective approach to develop energy efficient, high-performance solvers, is to design them to work on many small and independent problems. Indeed, many applications already need this functionality, especially for GPUs, which are known to be currently about four to five times more energy efficient than multicore CPUs for every floating-point operation. In this paper, we describe the development of the main one-sided factorizations: LU, QR, and Cholesky; that are needed for a set of small dense matrices to work in parallel. We refer to such algorithms as batched factorizations. Our approach is based on representingmore » the algorithms as a sequence of batched BLAS routines for GPU-contained execution. Note that this is similar in functionality to the LAPACK and the hybrid MAGMA algorithms for large-matrix factorizations. But it is different from a straightforward approach, whereby each of GPU's symmetric multiprocessors factorizes a single problem at a time. We illustrate how our performance analysis together with the profiling and tracing tools guided the development of batched factorizations to achieve up to 2-fold speedup and 3-fold better energy efficiency compared to our highly optimized batched CPU implementations based on the MKL library on a two-sockets, Intel Sandy Bridge server. Compared to a batched LU factorization featured in the NVIDIA's CUBLAS library for GPUs, we achieves up to 2.5-fold speedup on the K40 GPU.« less

Validation and Implementation of Clinical Laboratory Improvements Act-Compliant Whole-Genome Sequencing in the Public Health Microbiology Laboratory

PubMed Central

Kozyreva, Varvara K.; Truong, Chau-Linda; Greninger, Alexander L.; Crandall, John; Mukhopadhyay, Rituparna

2017-01-01

ABSTRACT Public health microbiology laboratories (PHLs) are on the cusp of unprecedented improvements in pathogen identification, antibiotic resistance detection, and outbreak investigation by using whole-genome sequencing (WGS). However, considerable challenges remain due to the lack of common standards. Here, we describe the validation of WGS on the Illumina platform for routine use in PHLs according to Clinical Laboratory Improvements Act (CLIA) guidelines for laboratory-developed tests (LDTs). We developed a validation panel comprising 10 Enterobacteriaceae isolates, 5 Gram-positive cocci, 5 Gram-negative nonfermenting species, 9 Mycobacterium tuberculosis isolates, and 5 miscellaneous bacteria. The genome coverage range was 15.71× to 216.4× (average, 79.72×; median, 71.55×); the limit of detection (LOD) for single nucleotide polymorphisms (SNPs) was 60×. The accuracy, reproducibility, and repeatability of base calling were >99.9%. The accuracy of phylogenetic analysis was 100%. The specificity and sensitivity inferred from multilocus sequence typing (MLST) and genome-wide SNP-based phylogenetic assays were 100%. The following objectives were accomplished: (i) the establishment of the performance specifications for WGS applications in PHLs according to CLIA guidelines, (ii) the development of quality assurance and quality control measures, (iii) the development of a reporting format for end users with or without WGS expertise, (iv) the availability of a validation set of microorganisms, and (v) the creation of a modular template for the validation of WGS processes in PHLs. The validation panel, sequencing analytics, and raw sequences could facilitate multilaboratory comparisons of WGS data. Additionally, the WGS performance specifications and modular template are adaptable for the validation of other platforms and reagent kits. PMID:28592550

Validation and Implementation of Clinical Laboratory Improvements Act-Compliant Whole-Genome Sequencing in the Public Health Microbiology Laboratory.

PubMed

Kozyreva, Varvara K; Truong, Chau-Linda; Greninger, Alexander L; Crandall, John; Mukhopadhyay, Rituparna; Chaturvedi, Vishnu

2017-08-01

Public health microbiology laboratories (PHLs) are on the cusp of unprecedented improvements in pathogen identification, antibiotic resistance detection, and outbreak investigation by using whole-genome sequencing (WGS). However, considerable challenges remain due to the lack of common standards. Here, we describe the validation of WGS on the Illumina platform for routine use in PHLs according to Clinical Laboratory Improvements Act (CLIA) guidelines for laboratory-developed tests (LDTs). We developed a validation panel comprising 10 Enterobacteriaceae isolates, 5 Gram-positive cocci, 5 Gram-negative nonfermenting species, 9 Mycobacterium tuberculosis isolates, and 5 miscellaneous bacteria. The genome coverage range was 15.71× to 216.4× (average, 79.72×; median, 71.55×); the limit of detection (LOD) for single nucleotide polymorphisms (SNPs) was 60×. The accuracy, reproducibility, and repeatability of base calling were >99.9%. The accuracy of phylogenetic analysis was 100%. The specificity and sensitivity inferred from multilocus sequence typing (MLST) and genome-wide SNP-based phylogenetic assays were 100%. The following objectives were accomplished: (i) the establishment of the performance specifications for WGS applications in PHLs according to CLIA guidelines, (ii) the development of quality assurance and quality control measures, (iii) the development of a reporting format for end users with or without WGS expertise, (iv) the availability of a validation set of microorganisms, and (v) the creation of a modular template for the validation of WGS processes in PHLs. The validation panel, sequencing analytics, and raw sequences could facilitate multilaboratory comparisons of WGS data. Additionally, the WGS performance specifications and modular template are adaptable for the validation of other platforms and reagent kits. Copyright © 2017 Kozyreva et al.

Environmental assessment for the proposed construction and operation of a Genome Sequencing Facility in Building 64 at Lawrence Berkeley Laboratory, Berkeley, California

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

1995-04-01

This document is an Environmental Assessment (EA) for a proposed project to modify 14,900 square feet of an existing building (Building 64) at Lawrence Berkeley Laboratory (LBL) to operate as a Genome Sequencing Facility. This EA addresses the potential environmental impacts from the proposed modifications to Building 64 and operation of the Genome Sequencing Facility. The proposed action is to modify Building 64 to provide space and equipment allowing LBL to demonstrate that the Directed DNA Sequencing Strategy can be scaled up from the current level of 750,000 base pairs per year to a facility that produces over 6,000,000 basemore » pairs per year, while still retaining its efficiency.« less

Actual waste demonstration of the nitric-glycolic flowsheet for sludge batch 9 qualification

DOE Office of Scientific and Technical Information (OSTI.GOV)

Newell, D.; Pareizs, J.; Martino, C.

For each sludge batch that is processed in the Defense Waste Processing Facility (DWPF), the Savannah River National Laboratory (SRNL) performs qualification testing to demonstrate that the sludge batch is processable. Based on the results of this actual-waste qualification and previous simulant studies, SRNL recommends implementation of the nitric-glycolic acid flowsheet in DWPF. Other recommendations resulting from this demonstration are reported in section 5.0.

Flash chemistry: flow chemistry that cannot be done in batch.

PubMed

Yoshida, Jun-ichi; Takahashi, Yusuke; Nagaki, Aiichiro

2013-11-04

Flash chemistry based on high-resolution reaction time control using flow microreactors enables chemical reactions that cannot be done in batch and serves as a powerful tool for laboratory synthesis of organic compounds and for production in chemical and pharmaceutical industries.

Semi-industrial scale (30 m3) fed-batch fermentation for the production of D-lactate by Escherichia coli strain HBUT-D15.

PubMed

Fu, Xiangmin; Wang, Yongze; Wang, Jinhua; Garza, Erin; Manow, Ryan; Zhou, Shengde

2017-02-01

D(-)-lactic acid is needed for manufacturing of stereo-complex poly-lactic acid polymer. Large scale D-lactic acid fermentation, however, has yet to be demonstrated. A genetically engineered Escherichia coli strain, HBUT-D, was adaptively evolved in a 15% calcium lactate medium for improved lactate tolerance. The resulting strain, HBUT-D15, was tested at a lab scale (7 L) by fed-batch fermentation with up to 200 g L -1 of glucose, producing 184-191 g L -1 of D-lactic acid, with a volumetric productivity of 4.38 g L -1  h -1 , a yield of 92%, and an optical purity of 99.9%. The HBUT-D15 was then evaluated at a semi-industrial scale (30 m 3 ) via fed-batch fermentation with up to 160 g L -1 of glucose, producing 146-150 g L -1 of D-lactic acid, with a volumetric productivity of 3.95-4.29 g L -1  h -1 , a yield of 91-94%, and an optical purity of 99.8%. These results are comparable to that of current industrial scale L(+)-lactic acid fermentation.

Building a Laboratory-Scale Biogas Plant and Verifying its Functionality

NASA Astrophysics Data System (ADS)

Boleman, Tomáš; Fiala, Jozef; Blinová, Lenka; Gerulová, Kristína

2011-01-01

The paper deals with the process of building a laboratory-scale biogas plant and verifying its functionality. The laboratory-scale prototype was constructed in the Department of Safety and Environmental Engineering at the Faculty of Materials Science and Technology in Trnava, of the Slovak University of Technology. The Department has already built a solar laboratory to promote and utilise solar energy, and designed SETUR hydro engine. The laboratory is the next step in the Department's activities in the field of renewable energy sources and biomass. The Department is also involved in the European Union project, where the goal is to upgrade all existed renewable energy sources used in the Department.

Energy efficiency of batch and semi-batch (CCRO) reverse osmosis desalination.

PubMed

Warsinger, David M; Tow, Emily W; Nayar, Kishor G; Maswadeh, Laith A; Lienhard V, John H

2016-12-01

As reverse osmosis (RO) desalination capacity increases worldwide, the need to reduce its specific energy consumption becomes more urgent. In addition to the incremental changes attainable with improved components such as membranes and pumps, more significant reduction of energy consumption can be achieved through time-varying RO processes including semi-batch processes such as closed-circuit reverse osmosis (CCRO) and fully-batch processes that have not yet been commercialized or modelled in detail. In this study, numerical models of the energy consumption of batch RO (BRO), CCRO, and the standard continuous RO process are detailed. Two new energy-efficient configurations of batch RO are analyzed. Batch systems use significantly less energy than continuous RO over a wide range of recovery ratios and source water salinities. Relative to continuous RO, models predict that CCRO and batch RO demonstrate up to 37% and 64% energy savings, respectively, for brackish water desalination at high water recovery. For batch RO and CCRO, the primary reductions in energy use stem from atmospheric pressure brine discharge and reduced streamwise variation in driving pressure. Fully-batch systems further reduce energy consumption by not mixing streams of different concentrations, which CCRO does. These results demonstrate that time-varying processes can significantly raise RO energy efficiency. Copyright © 2016 Elsevier Ltd. All rights reserved.

Tackling the widespread and critical impact of batch effects in high-throughput data.

PubMed

Leek, Jeffrey T; Scharpf, Robert B; Bravo, Héctor Corrada; Simcha, David; Langmead, Benjamin; Johnson, W Evan; Geman, Donald; Baggerly, Keith; Irizarry, Rafael A

2010-10-01

High-throughput technologies are widely used, for example to assay genetic variants, gene and protein expression, and epigenetic modifications. One often overlooked complication with such studies is batch effects, which occur because measurements are affected by laboratory conditions, reagent lots and personnel differences. This becomes a major problem when batch effects are correlated with an outcome of interest and lead to incorrect conclusions. Using both published studies and our own analyses, we argue that batch effects (as well as other technical and biological artefacts) are widespread and critical to address. We review experimental and computational approaches for doing so.

Biological reduction of chlorinated solvents: Batch-scale geochemical modeling

NASA Astrophysics Data System (ADS)

Kouznetsova, Irina; Mao, Xiaomin; Robinson, Clare; Barry, D. A.; Gerhard, Jason I.; McCarty, Perry L.

2010-09-01

Simulation of biodegradation of chlorinated solvents in dense non-aqueous phase liquid (DNAPL) source zones requires a model that accounts for the complexity of processes involved and that is consistent with available laboratory studies. This paper describes such a comprehensive modeling framework that includes microbially mediated degradation processes, microbial population growth and decay, geochemical reactions, as well as interphase mass transfer processes such as DNAPL dissolution, gas formation and mineral precipitation/dissolution. All these processes can be in equilibrium or kinetically controlled. A batch modeling example was presented where the degradation of trichloroethene (TCE) and its byproducts and concomitant reactions (e.g., electron donor fermentation, sulfate reduction, pH buffering by calcite dissolution) were simulated. Local and global sensitivity analysis techniques were applied to delineate the dominant model parameters and processes. Sensitivity analysis indicated that accurate values for parameters related to dichloroethene (DCE) and vinyl chloride (VC) degradation (i.e., DCE and VC maximum utilization rates, yield due to DCE utilization, decay rate for DCE/VC dechlorinators) are important for prediction of the overall dechlorination time. These parameters influence the maximum growth rate of the DCE and VC dechlorinating microorganisms and, thus, the time required for a small initial population to reach a sufficient concentration to significantly affect the overall rate of dechlorination. Self-inhibition of chlorinated ethenes at high concentrations and natural buffering provided by the sediment were also shown to significantly influence the dechlorination time. Furthermore, the analysis indicated that the rates of the competing, nonchlorinated electron-accepting processes relative to the dechlorination kinetics also affect the overall dechlorination time. Results demonstrated that the model developed is a flexible research tool that is

MendeLIMS: a web-based laboratory information management system for clinical genome sequencing.

PubMed

Grimes, Susan M; Ji, Hanlee P

2014-08-27

Large clinical genomics studies using next generation DNA sequencing require the ability to select and track samples from a large population of patients through many experimental steps. With the number of clinical genome sequencing studies increasing, it is critical to maintain adequate laboratory information management systems to manage the thousands of patient samples that are subject to this type of genetic analysis. To meet the needs of clinical population studies using genome sequencing, we developed a web-based laboratory information management system (LIMS) with a flexible configuration that is adaptable to continuously evolving experimental protocols of next generation DNA sequencing technologies. Our system is referred to as MendeLIMS, is easily implemented with open source tools and is also highly configurable and extensible. MendeLIMS has been invaluable in the management of our clinical genome sequencing studies. We maintain a publicly available demonstration version of the application for evaluation purposes at http://mendelims.stanford.edu. MendeLIMS is programmed in Ruby on Rails (RoR) and accesses data stored in SQL-compliant relational databases. Software is freely available for non-commercial use at http://dna-discovery.stanford.edu/software/mendelims/.

Optical mapping and its potential for large-scale sequencing projects.

PubMed

Aston, C; Mishra, B; Schwartz, D C

1999-07-01

Physical mapping has been rediscovered as an important component of large-scale sequencing projects. Restriction maps provide landmark sequences at defined intervals, and high-resolution restriction maps can be assembled from ensembles of single molecules by optical means. Such optical maps can be constructed from both large-insert clones and genomic DNA, and are used as a scaffold for accurately aligning sequence contigs generated by shotgun sequencing.

Computational simulation of laboratory-scale volcanic jets

NASA Astrophysics Data System (ADS)

Solovitz, S.; Van Eaton, A. R.; Mastin, L. G.; Herzog, M.

2017-12-01

Volcanic eruptions produce ash clouds that may travel great distances, significantly impacting aviation and communities downwind. Atmospheric hazard forecasting relies partly on numerical models of the flow physics, which incorporate data from eruption observations and analogue laboratory tests. As numerical tools continue to increase in complexity, they must be validated to fine-tune their effectiveness. Since eruptions are relatively infrequent and challenging to observe in great detail, analogue experiments can provide important insights into expected behavior over a wide range of input conditions. Unfortunately, laboratory-scale jets cannot easily attain the high Reynolds numbers ( 109) of natural volcanic eruption columns. Comparisons between the computational models and analogue experiments can help bridge this gap. In this study, we investigate a 3-D volcanic plume model, the Active Tracer High-resolution Atmospheric Model (ATHAM), which has been used to simulate a variety of eruptions. However, it has not been previously validated using laboratory-scale data. We conducted numerical simulations of three flows that we have studied in the laboratory: a vertical jet in a quiescent environment, a vertical jet in horizontal cross flow, and a particle-laden jet. We considered Reynolds numbers from 10,000 to 50,000, jet-to-cross flow velocity ratios of 2 to 10, and particle mass loadings of up to 25% of the exit mass flow rate. Vertical jet simulations produce Gaussian velocity profiles in the near exit region by 3 diameters downstream, matching the mean experimental profiles. Simulations of air entrainment are of the correct order of magnitude, but they show decreasing entrainment with vertical distance from the vent. Cross flow simulations reproduce experimental trajectories for the jet centerline initially, although confinement appears to impact the response later. Particle-laden simulations display minimal variation in concentration profiles between cases with

A Systems Approach towards an Intelligent and Self-Controlling Platform for Integrated Continuous Reaction Sequences**

PubMed Central

Ingham, Richard J; Battilocchio, Claudio; Fitzpatrick, Daniel E; Sliwinski, Eric; Hawkins, Joel M; Ley, Steven V

2015-01-01

Performing reactions in flow can offer major advantages over batch methods. However, laboratory flow chemistry processes are currently often limited to single steps or short sequences due to the complexity involved with operating a multi-step process. Using new modular components for downstream processing, coupled with control technologies, more advanced multi-step flow sequences can be realized. These tools are applied to the synthesis of 2-aminoadamantane-2-carboxylic acid. A system comprising three chemistry steps and three workup steps was developed, having sufficient autonomy and self-regulation to be managed by a single operator. PMID:25377747

Palm oil mill effluent and municipal wastewater co-treatment by zeolite augmented sequencing batch reactors: Turbidity removal

NASA Astrophysics Data System (ADS)

Farraji, Hossein; Zaman, Nastaein Qamaruz; Aziz, Hamidi Abdul; Sa'at, Siti Kamariah Md

2017-10-01

Palm oil mill effluent (POME) is the largest wastewater in Malaysia. Of the 60 million tons of POME produced annually, 2.4-3 million tons are total solids. Turbidity is caused by suspended solids, and 75% of total suspended solids are organic matter. Coagulation and flocculation are popular treatments for turbidity removal. Traditional commercial treatments do not meet discharge standards. This study evaluated natural zeolite and municipal wastewater (MWW)-augmented sequencing batch reactor as a microbiological digestion method for the decontamination of POME in response surface methodology. Aeration, contact time, and MWW/POME ratio were selected as response factors for turbidity removal. Results indicated that turbidity removal varied from 96.7% (MWW/POME ratio=50 %, aeration flow=0.5 L/min, and contact time=12) to 99.31% (MWW/POME ratio=80%, aeration flow 4L/min, and contact time 12 h). This study is the first to present MWW augmentation as a suitable microorganism supplier for turbidity biodegradation in high-strength agroindustrial wastewater.

Effect of magnesium oxide nanoparticles on microbial diversity and removal performance of sequencing batch reactor.

PubMed

Ma, Bingrui; Yu, Naling; Han, Yuetong; Gao, Mengchun; Wang, Sen; Li, Shanshan; Guo, Liang; She, Zonglian; Zhao, Yangguo; Jin, Chunji; Gao, Feng

2018-06-13

The performance, microbial enzymatic activity and microbial community of a sequencing batch reactor (SBR) have been explored under magnesium oxide nanoparticles (MgO NPs) stress. The NH 4 + -N removal efficiency kept relatively stable during the whole operational process. The MgO NPs at 30-60 mg/L slightly restrained the removal of chemical oxygen demand (COD), and the presence of MgO NPs also affected the denitrification and phosphorus removal. The specific oxygen uptake rate, nitrifying and denitrifying rates, phosphorus removal rate, and microbial enzymatic activities distinctly varied with the increase of MgO NPs concentration. The appearance of MgO NPs promoted more reactive oxygen species generation and lactate dehydrogenase leakage from activated sludge, suggesting that MgO NPs had obvious toxicity to activated sludge in the SBR. The protein and polysaccharide contents of extracellular polymeric substances from activated sludge increased with the increase of MgO NPs concentration. The microbial richness and diversity at different MgO NPs concentrations obviously varied at the phylum, class and genus levels due to the biological toxicity of MgO NPs. Copyright © 2018 Elsevier Ltd. All rights reserved.

Contamination level of four priority phthalates in North Indian wastewater treatment plants and their fate in sequencing batch reactor systems.

PubMed

Gani, Khalid Muzamil; Rajpal, Ankur; Kazmi, Absar Ahmad

2016-03-01

The contamination level of four phthalates in untreated and treated wastewater of fifteen wastewater treatment plants (WWTPs) and their fate in a full scale sequencing batch reactor (SBR) based WWTP was evaluated in this study. The four phthalates were diethyl phthalate (DEP), dibutyl phthalate (DBP), benzylbutyl phthalate (BBP) and diethylhexyl phthalate (DEHP). All compounds were present in untreated wastewater with DEHP being present in the highest mean concentration of 28.4 ± 5.3 μg L(-1). The concentration was in the range of 7.3 μg L(-1) (BBP) to 28.4 μg L(-1) (DEHP) in untreated wastewater and 1.3 μg L(-1) (DBP) to 2.6 μg L(-1) (DEHP) in treated wastewater. The nutrient removal process and advance tertiary treatment based WWTPs showed the highest phthalate removal efficiencies of 87% and 93%, respectively. The correlation between phthalate removal and conventional performance of WWTPs was positive. Fate analysis of these phthalates in a SBR based WWTP showed that total removal of the sum of phthalates in a primary settling tank and SBR was 84% out of which 55% is removed by biodegradation and 29% was removed by sorption to primary and secondary sludge. The percentage removal of four phthalates in primary settling tanks was 18%. Comparison of the diluted effluent DEHP concentration with its environmental quality standards showed that the dilution in an effluent receiving water body can reduce the DEHP emissions to acceptable values.

Addressing case specific biogas plant tasks: industry oriented methane yields derived from 5L Automatic Methane Potential Test Systems in batch or semi-continuous tests using realistic inocula, substrate particle sizes and organic loading.

PubMed

Kolbl, Sabina; Paloczi, Attila; Panjan, Jože; Stres, Blaž

2014-02-01

The primary aim of the study was to develop and validate an in-house upscale of Automatic Methane Potential Test System II for studying real-time inocula and real-scale substrates in batch, codigestion and enzyme enhanced hydrolysis experiments, in addition to semi-continuous operation of the developed equipment and experiments testing inoculum functional quality. The successful upscale to 5L enabled comparison of different process configurations in shorter preparation times with acceptable accuracy and high-through put intended for industrial decision making. The adoption of the same scales, equipment and methodologies in batch and semi-continuous tests mirroring those at full scale biogas plants resulted in matching methane yields between the two laboratory tests and full-scale, confirming thus the increased decision making value of the approach for industrial operations. Copyright © 2013 Elsevier Ltd. All rights reserved.

MHD scaling: from astrophysics to the laboratory

NASA Astrophysics Data System (ADS)

Ryutov, Dmitri

2000-10-01

During the last few years, considerable progress has been made in simulating astrophysical phenomena in laboratory experiments with high power lasers [1]. Astrophysical phenomena that have drawn particular interest include supernovae explosions; young supernova remnants; galactic jets; the formation of fine structures in late supernova remnants by instabilities; and the ablation driven evolution of molecular clouds illuminated by nearby bright stars, which may affect star formation. A question may arise as to what extent the laser experiments, which deal with targets of a spatial scale 0.01 cm and occur at a time scale of a few nanoseconds, can reproduce phenomena occurring at spatial scales of a million or more kilometers and time scales from hours to many years. Quite remarkably, if dissipative processes (like, e.g., viscosity, Joule dissipation, etc.) are subdominant in both systems, and the matter behaves as a polytropic gas, there exists a broad hydrodynamic similarity (the ``Euler similarity" of Ref. [2]) that allows a direct scaling of laboratory results to astrophysical phenomena. Following a review of relevant earlier work (in particular, [3]-[5]), discussion is presented of the details of the Euler similarity related to the presence of shocks and to a special case of a strong drive. After that, constraints stemming from possible development of small-scale turbulence are analyzed. Generalization of the Euler similarity to the case of a gas with spatially varying polytropic index is presented. A possibility of scaled simulations of ablation front dynamics is one more topic covered in this paper. It is shown that, with some additional constraints, a simple similarity exists. This, in particular, opens up the possibility of scaled laboratory simulation of the aforementioned ablation (photoevaporation) fronts. A nonlinear transformation [6] that establishes a duality between implosion and explosion processes is also discussed in the paper. 1. B.A. Remington et

A comparison of refuse attenuation in laboratory and field scale lysimeters.

PubMed

Youcai, Zhao; Luochun, Wang; Renhua, Hua; Dimin, Xu; Guowei, Gu

2002-01-01

For this study, small and middle scale laboratory lysimeters, and a large scale field lysimeter in situ in Shanghai Refuse Landfill, with refuse weights of 187,600 and 10,800,000 kg, respectively, were created. These lysimeters are compared in terms of leachate quality (pH, concentrations of COD, BOD and NH3-N), refuse composition (biodegradable matter and volatile solid) and surface settlement for a monitoring period of 0-300 days. The objectives of this study were to explore both the similarities and disparities between laboratory and field scale lysimeters, and to compare degradation behaviors of refuse at the intensive reaction phase in the different scale lysimeters. Quantitative relationships of leachate quality and refuse composition with placement time show that degradation behaviors of refuse seem to depend heavily on the scales of the lysimeters and the parameters of concern, especially in the starting period of 0-6 months. However, some similarities exist between laboratory and field lysimeters after 4-6 months of placement because COD and BOD concentrations in leachate in the field lysimeter decrease regularly in a parallel pattern with those in the laboratory lysimeters. NH3-N, volatile solid (VS) and biodegradable matter (BDM) also gradually decrease in parallel in this intensive reaction phase for all scale lysimeters as refuse ages. Though the concrete data are different among the different scale lysimeters, it may be considered that laboratory lysimeters with sufficient scale are basically applicable for a rough simulation of a real landfill, especially for illustrating the degradation pattern and mechanism. Settlement of refuse surface is roughly proportional to the initial refuse height.

Treatment of fruit-juice industry wastewater in a two-stage anaerobic hybrid (AH) reactor system followed by a sequencing batch reactor (SBR).

PubMed

Tawfik, A; El-Kamah, H

2012-01-01

This study has been carried out to assess the performance of a combined system consisting of an anaerobic hybrid (AH) reactor followed by a sequencing batch reactor (SBR) for treatment of fruit-juice industry wastewater at a temperature of 26 degrees C. Three experimental runs were conducted in this investigation. In the first experiment, a single-stage AH reactor was operated at a hydraulic retention time (HRT) of 10.2 h and organic loading rate (OLR) of 11.8 kg COD m(-3) d(-1). The reactor achieved a removal efficiency of 42% for chemical oxygen demand (COD), 50.8% for biochemical oxygen demand (BOD5), 50.3% for volatile fatty acids (VFA) and 56.4% for total suspended solids (TSS). In the second experiment, two AH reactors connected in series achieved a higher removal efficiency for COD (67.4%), BOD5 (77%), and TSS (71.5%) at a total HRT of 20 h and an OLR of 5.9 kg COD m(-3) d(-1). For removal of the remaining portions of COD, BOD5 and TSS from the effluent of the two-stage AH system, a sequencing batch reactor (SBR) was investigated as a post-treatment unit. The reactor achieved a substantial reduction in total COD, resulting in an average effluent concentration of 50 mg L(-1) at an HRT of 11 h and OLR of 5.3 kg COD m(-3) d(-1). Almost complete removal of total BOD5 and oil and grease was achieved, i.e. 10 mg L(-1) and 1.2 mg L(-1), respectively, remained in the final effluent of the SBR.

Design of a laboratory scale fluidized bed reactor

NASA Astrophysics Data System (ADS)

Wikström, E.; Andersson, P.; Marklund, S.

1998-04-01

The aim of this project was to construct a laboratory scale fluidized bed reactor that simulates the behavior of full scale municipal solid waste combustors. The design of this reactor is thoroughly described. The size of the laboratory scale fluidized bed reactor is 5 kW, which corresponds to a fuel-feeding rate of approximately 1 kg/h. The reactor system consists of four parts: a bed section, a freeboard section, a convector (postcombustion zone), and an air pollution control (APC) device system. The inside diameter of the reactor is 100 mm at the bed section and it widens to 200 mm in diameter in the freeboard section; the total height of the reactor is 1760 mm. The convector part consists of five identical sections; each section is 2700 mm long and has an inside diameter of 44.3 mm. The reactor is flexible regarding the placement and number of sampling ports. At the beginning of the first convector unit and at the end of each unit there are sampling ports for organic micropollutants (OMP). This makes it possible to study the composition of the flue gases at various residence times. Sampling ports for inorganic compounds and particulate matter are also placed in the convector section. All operating parameters, reactor temperatures, concentrations of CO, CO2, O2, SO2, NO, and NO2 are continuously measured and stored at selected intervals for further evaluation. These unique features enable full control over the fuel feed, air flows, and air distribution as well as over the temperature profile. Elaborate details are provided regarding the configuration of the fuel-feeding systems, the fluidized bed, the convector section, and the APC device. This laboratory reactor enables detailed studies of the formation mechanisms of OMP, such as polychlorinated dibenzo-p-dioxins (PCDDs), polychlorinated dibenzofurans (PCDFs), poly-chlorinated biphenyls (PCBs), and polychlorinated benzenes (PCBzs). With this system formation mechanisms of OMP occurring in both the combustion

Capacity planning for batch and perfusion bioprocesses across multiple biopharmaceutical facilities.

PubMed

Siganporia, Cyrus C; Ghosh, Soumitra; Daszkowski, Thomas; Papageorgiou, Lazaros G; Farid, Suzanne S

2014-01-01

Production planning for biopharmaceutical portfolios becomes more complex when products switch between fed-batch and continuous perfusion culture processes. This article describes the development of a discrete-time mixed integer linear programming (MILP) model to optimize capacity plans for multiple biopharmaceutical products, with either batch or perfusion bioprocesses, across multiple facilities to meet quarterly demands. The model comprised specific features to account for products with fed-batch or perfusion culture processes such as sequence-dependent changeover times, continuous culture constraints, and decoupled upstream and downstream operations that permit independent scheduling of each. Strategic inventory levels were accounted for by applying cost penalties when they were not met. A rolling time horizon methodology was utilized in conjunction with the MILP model and was shown to obtain solutions with greater optimality in less computational time than the full-scale model. The model was applied to an industrial case study to illustrate how the framework aids decisions regarding outsourcing capacity to third party manufacturers or building new facilities. The impact of variations on key parameters such as demand or titres on the optimal production plans and costs was captured. The analysis identified the critical ratio of in-house to contract manufacturing organization (CMO) manufacturing costs that led the optimization results to favor building a future facility over using a CMO. The tool predicted that if titres were higher than expected then the optimal solution would allocate more production to in-house facilities, where manufacturing costs were lower. Utilization graphs indicated when capacity expansion should be considered. © 2014 The Authors Biotechnology Progress published by Wiley Periodicals, Inc. on behalf of American Institute of Chemical Engineers.

Development of EnergyPlus Utility to Batch Simulate Building Energy Performance on a National Scale

DOE Office of Scientific and Technical Information (OSTI.GOV)

Valencia, Jayson F.; Dirks, James A.

2008-08-29

EnergyPlus is a simulation program that requires a large number of details to fully define and model a building. Hundreds or even thousands of lines in a text file are needed to run the EnergyPlus simulation depending on the size of the building. To manually create these files is a time consuming process that would not be practical when trying to create input files for thousands of buildings needed to simulate national building energy performance. To streamline the process needed to create the input files for EnergyPlus, two methods were created to work in conjunction with the National Renewable Energymore » Laboratory (NREL) Preprocessor; this reduced the hundreds of inputs needed to define a building in EnergyPlus to a small set of high-level parameters. The first method uses Java routines to perform all of the preprocessing on a Windows machine while the second method carries out all of the preprocessing on the Linux cluster by using an in-house built utility called Generalized Parametrics (GPARM). A comma delimited (CSV) input file is created to define the high-level parameters for any number of buildings. Each method then takes this CSV file and uses the data entered for each parameter to populate an extensible markup language (XML) file used by the NREL Preprocessor to automatically prepare EnergyPlus input data files (idf) using automatic building routines and macro templates. Using a Linux utility called “make”, the idf files can then be automatically run through the Linux cluster and the desired data from each building can be aggregated into one table to be analyzed. Creating a large number of EnergyPlus input files results in the ability to batch simulate building energy performance and scale the result to national energy consumption estimates.« less

A survey of current practices for genomic sequencing test interpretation and reporting processes in US laboratories.

PubMed

O'Daniel, Julianne M; McLaughlin, Heather M; Amendola, Laura M; Bale, Sherri J; Berg, Jonathan S; Bick, David; Bowling, Kevin M; Chao, Elizabeth C; Chung, Wendy K; Conlin, Laura K; Cooper, Gregory M; Das, Soma; Deignan, Joshua L; Dorschner, Michael O; Evans, James P; Ghazani, Arezou A; Goddard, Katrina A; Gornick, Michele; Farwell Hagman, Kelly D; Hambuch, Tina; Hegde, Madhuri; Hindorff, Lucia A; Holm, Ingrid A; Jarvik, Gail P; Knight Johnson, Amy; Mighion, Lindsey; Morra, Massimo; Plon, Sharon E; Punj, Sumit; Richards, C Sue; Santani, Avni; Shirts, Brian H; Spinner, Nancy B; Tang, Sha; Weck, Karen E; Wolf, Susan M; Yang, Yaping; Rehm, Heidi L

2017-05-01

While the diagnostic success of genomic sequencing expands, the complexity of this testing should not be overlooked. Numerous laboratory processes are required to support the identification, interpretation, and reporting of clinically significant variants. This study aimed to examine the workflow and reporting procedures among US laboratories to highlight shared practices and identify areas in need of standardization. Surveys and follow-up interviews were conducted with laboratories offering exome and/or genome sequencing to support a research program or for routine clinical services. The 73-item survey elicited multiple choice and free-text responses that were later clarified with phone interviews. Twenty-one laboratories participated. Practices highly concordant across all groups included consent documentation, multiperson case review, and enabling patient opt-out of incidental or secondary findings analysis. Noted divergence included use of phenotypic data to inform case analysis and interpretation and reporting of case-specific quality metrics and methods. Few laboratory policies detailed procedures for data reanalysis, data sharing, or patient access to data. This study provides an overview of practices and policies of experienced exome and genome sequencing laboratories. The results enable broader consideration of which practices are becoming standard approaches, where divergence remains, and areas of development in best practice guidelines that may be helpful.Genet Med advance online publication 03 Novemeber 2016.

Enhanced methane production via repeated batch bioaugmentation pattern of enriched microbial consortia.

PubMed

Yang, Zhiman; Guo, Rongbo; Xu, Xiaohui; Wang, Lin; Dai, Meng

2016-09-01

Using batch and repeated batch cultivations, this study investigated the effects of bioaugmentation with enriched microbial consortia (named as EMC) on methane production from effluents of hydrogen-producing stage of potato slurry, as well as on the indigenous bacterial community. The results demonstrated that the improved methane production and shift of the indigenous bacterial community structure were dependent on the EMC/sludge ratio and bioaugmentation patterns. The methane yield and production rate in repeated batch bioaugmentation pattern of EMC were, respectively, average 15% and 10% higher than in one-time bioaugmentation pattern of EMC. DNA-sequencing approach showed that the enhanced methane production in the repeated batch bioaugmentation pattern of EMC mainly resulted from the enriched iron-reducing bacteria and the persistence of the introduced Syntrophomonas, which led to a rapid degradation of individual VFAs to methane. The findings contributed to understanding the correlation between the bioaugmentation of microbial consortia, community shift, and methane production. Copyright © 2016 Elsevier Ltd. All rights reserved.

Outbreak Investigation Using High-Throughput Genome Sequencing within a Diagnostic Microbiology Laboratory

PubMed Central

Sherry, Norelle L.; Porter, Jessica L.; Seemann, Torsten; Watkins, Andrew; Stinear, Timothy P.

2013-01-01

Next-generation sequencing (NGS) of bacterial genomes has recently become more accessible and is now available to the routine diagnostic microbiology laboratory. However, questions remain regarding its feasibility, particularly with respect to data analysis in nonspecialist centers. To test the applicability of NGS to outbreak investigations, Ion Torrent sequencing was used to investigate a putative multidrug-resistant Escherichia coli outbreak in the neonatal unit of the Mercy Hospital for Women, Melbourne, Australia. Four suspected outbreak strains and a comparator strain were sequenced. Genome-wide single nucleotide polymorphism (SNP) analysis demonstrated that the four neonatal intensive care unit (NICU) strains were identical and easily differentiated from the comparator strain. Genome sequence data also determined that the NICU strains belonged to multilocus sequence type 131 and carried the blaCTX-M-15 extended-spectrum beta-lactamase. Comparison of the outbreak strains to all publicly available complete E. coli genome sequences showed that they clustered with neonatal meningitis and uropathogenic isolates. The turnaround time from a positive culture to the completion of sequencing (prior to data analysis) was 5 days, and the cost was approximately $300 per strain (for the reagents only). The main obstacles to a mainstream adoption of NGS technologies in diagnostic microbiology laboratories are currently cost (although this is decreasing), a paucity of user-friendly and clinically focused bioinformatics platforms, and a lack of genomics expertise outside the research environment. Despite these hurdles, NGS technologies provide unparalleled high-resolution genotyping in a short time frame and are likely to be widely implemented in the field of diagnostic microbiology in the next few years, particularly for epidemiological investigations (replacing current typing methods) and the characterization of resistance determinants. Clinical microbiologists need to

Stormwater Pollution Prevention Plan - TA-60 Asphalt Batch Plant

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sandoval, Leonard Frank

This Storm Water Pollution Prevention Plan (SWPPP) was developed in accordance with the provisions of the Clean Water Act (33 U.S.C. §§1251 et seq., as amended), and the Multi-Sector General Permit for Storm Water Discharges Associated with Industrial Activity (U.S. EPA, June 2015) issued by the U.S. Environmental Protection Agency (EPA) for the National Pollutant Discharge Elimination System (NPDES) and using the industry specific permit requirements for Sector P-Land Transportation and Warehousing as a guide. This SWPPP applies to discharges of stormwater from the operational areas of the TA-60-01 Asphalt Batch Plant at Los Alamos National Laboratory. Los Alamos Nationalmore » Laboratory (also referred to as LANL or the “Laboratory”) is owned by the Department of Energy (DOE), and is operated by Los Alamos National Security, LLC (LANS). Throughout this document, the term “facility” refers to the TA-60 Asphalt Batch Plant and associated areas. The current permit expires at midnight on June 4, 2020.« less

Unifying cancer and normal RNA sequencing data from different sources

PubMed Central

Wang, Qingguo; Armenia, Joshua; Zhang, Chao; Penson, Alexander V.; Reznik, Ed; Zhang, Liguo; Minet, Thais; Ochoa, Angelica; Gross, Benjamin E.; Iacobuzio-Donahue, Christine A.; Betel, Doron; Taylor, Barry S.; Gao, Jianjiong; Schultz, Nikolaus

2018-01-01

Driven by the recent advances of next generation sequencing (NGS) technologies and an urgent need to decode complex human diseases, a multitude of large-scale studies were conducted recently that have resulted in an unprecedented volume of whole transcriptome sequencing (RNA-seq) data, such as the Genotype Tissue Expression project (GTEx) and The Cancer Genome Atlas (TCGA). While these data offer new opportunities to identify the mechanisms underlying disease, the comparison of data from different sources remains challenging, due to differences in sample and data processing. Here, we developed a pipeline that processes and unifies RNA-seq data from different studies, which includes uniform realignment, gene expression quantification, and batch effect removal. We find that uniform alignment and quantification is not sufficient when combining RNA-seq data from different sources and that the removal of other batch effects is essential to facilitate data comparison. We have processed data from GTEx and TCGA and successfully corrected for study-specific biases, enabling comparative analysis between TCGA and GTEx. The normalized datasets are available for download on figshare. PMID:29664468

Moving from Batch to Field Using the RT3D Reactive Transport Modeling System

NASA Astrophysics Data System (ADS)

Clement, T. P.; Gautam, T. R.

2002-12-01

The public domain reactive transport code RT3D (Clement, 1997) is a general-purpose numerical code for solving coupled, multi-species reactive transport in saturated groundwater systems. The code uses MODFLOW to simulate flow and several modules of MT3DMS to simulate the advection and dispersion processes. RT3D employs the operator-split strategy which allows the code solve the coupled reactive transport problem in a modular fashion. The coupling between reaction and transport is defined through a separate module where the reaction equations are specified. The code supports a versatile user-defined reaction option that allows users to define their own reaction system through a Fortran-90 subroutine, known as the RT3D-reaction package. Further a utility code, known as BATCHRXN, allows the users to independently test and debug their reaction package. To analyze a new reaction system at a batch scale, users should first run BATCHRXN to test the ability of their reaction package to model the batch data. After testing, the reaction package can simply be ported to the RT3D environment to study the model response under 1-, 2-, or 3-dimensional transport conditions. This paper presents example problems that demonstrate the methods for moving from batch to field-scale simulations using BATCHRXN and RT3D codes. The first example describes a simple first-order reaction system for simulating the sequential degradation of Tetrachloroethene (PCE) and its daughter products. The second example uses a relatively complex reaction system for describing the multiple degradation pathways of Tetrachloroethane (PCA) and its daughter products. References 1) Clement, T.P, RT3D - A modular computer code for simulating reactive multi-species transport in 3-Dimensional groundwater aquifers, Battelle Pacific Northwest National Laboratory Research Report, PNNL-SA-28967, September, 1997. Available at: http://bioprocess.pnl.gov/rt3d.htm.

Implementation of Cloud based next generation sequencing data analysis in a clinical laboratory.

PubMed

Onsongo, Getiria; Erdmann, Jesse; Spears, Michael D; Chilton, John; Beckman, Kenneth B; Hauge, Adam; Yohe, Sophia; Schomaker, Matthew; Bower, Matthew; Silverstein, Kevin A T; Thyagarajan, Bharat

2014-05-23

The introduction of next generation sequencing (NGS) has revolutionized molecular diagnostics, though several challenges remain limiting the widespread adoption of NGS testing into clinical practice. One such difficulty includes the development of a robust bioinformatics pipeline that can handle the volume of data generated by high-throughput sequencing in a cost-effective manner. Analysis of sequencing data typically requires a substantial level of computing power that is often cost-prohibitive to most clinical diagnostics laboratories. To address this challenge, our institution has developed a Galaxy-based data analysis pipeline which relies on a web-based, cloud-computing infrastructure to process NGS data and identify genetic variants. It provides additional flexibility, needed to control storage costs, resulting in a pipeline that is cost-effective on a per-sample basis. It does not require the usage of EBS disk to run a sample. We demonstrate the validation and feasibility of implementing this bioinformatics pipeline in a molecular diagnostics laboratory. Four samples were analyzed in duplicate pairs and showed 100% concordance in mutations identified. This pipeline is currently being used in the clinic and all identified pathogenic variants confirmed using Sanger sequencing further validating the software.

Production of nattokinase by batch and fed-batch culture of Bacillus subtilis.

PubMed

Cho, Young-Han; Song, Jae Yong; Kim, Kyung Mi; Kim, Mi Kyoung; Lee, In Young; Kim, Sang Bum; Kim, Hyeon Shup; Han, Nam Soo; Lee, Bong Hee; Kim, Beom Soo

2010-09-30

Nattokinase was produced by batch and fed-batch culture of Bacillus subtilis in flask and fermentor. Effect of supplementing complex media (peptone, yeast extract, or tryptone) was investigated on the production of nattokinase. In flask culture, the highest cell growth and nattokinase activity were obtained with 50 g/L of peptone supplementation. In this condition, nattokinase activity was 630 unit/ml at 12 h. In batch culture of B. subtilis in fermentor, the highest nattokinase activity of 3400 unit/ml was obtained at 10h with 50 g/L of peptone supplementation. From the batch kinetics data, it was shown that nattokinase production was growth-associated and culture should be harvested before stationary phase for maximum nattokinase production. In fed-batch culture of B. subtilis using pH-stat feeding strategy, cell growth (optical density monitored at 600 nm) increased to ca. 100 at 22 h, which was 2.5 times higher than that in batch culture. The highest nattokinase activity was 7100 unit/ml at 19 h, which was also 2.1 times higher than that in batch culture. Copyright 2010 Elsevier B.V. All rights reserved.

Co-digestion of food waste in a municipal wastewater treatment plant: Comparison of batch tests and full-scale experiences.

PubMed

Koch, Konrad; Plabst, Markus; Schmidt, Andreas; Helmreich, Brigitte; Drewes, Jörg E

2016-01-01

The effects of co-digestion of food waste in a municipal wastewater treatment plant (WWTP) were studied in batch tests. The results obtained were compared with the mass balance of a digester at a full-scale WWTP for a one-year period without and with the addition of co-substrate. The specific methane yield calculated from the balance was 18% higher than the one in the batch tests, suggesting a stimulation of methane generation by co-digestion. It was hypothesized that this increase was caused by shifting the C/N ratio of raw sludge (8.8) to a more favourable ratio of the added food waste (17.7). In addition, potential benefits by adding food waste for energy autarky was investigated. While just 25% of the total energy demand of the plant could be recovered by biogas generation when no co-substrate was fed, this percentage has more than doubled when food waste was added at a ratio of 10% (w/w). Copyright © 2015 Elsevier Ltd. All rights reserved.

Batch and fed-batch production of butyric acid by Clostridium butyricum ZJUCB

PubMed Central

He, Guo-qing; Kong, Qing; Chen, Qi-he; Ruan, Hui

2005-01-01

The production of butyric acid by Clostridium butyricum ZJUCB at various pH values was investigated. In order to study the effect of pH on cell growth, butyric acid biosynthesis and reducing sugar consumption, different cultivation pH values ranging from 6.0 to 7.5 were evaluated in 5-L bioreactor. In controlled pH batch fermentation, the optimum pH for cell growth and butyric acid production was 6.5 with a cell yield of 3.65 g/L and butyric acid yield of 12.25 g/L. Based on these results, this study then compared batch and fed-batch fermentation of butyric acid production at pH 6.5. Maximum value (16.74 g/L) of butyric acid concentration was obtained in fed-batch fermentation compared to 12.25 g/L in batch fermentation. It was concluded that cultivation under fed-batch fermentation mode could enhance butyric acid production significantly (P<0.01) by C. butyricum ZJUCB. PMID:16252341

Organic and nitrogen removal from landfill leachate in aerobic granular sludge sequencing batch reactors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wei Yanjie; Key Laboratory of Environmental Protection in Water Transport Engineering Ministry of Communications, Tianjin Research Institute of Water Transport Engineering, Tianjin 300456; Ji Min, E-mail: jmtju@yahoo.cn

2012-03-15

Highlights: Black-Right-Pointing-Pointer Aerobic granular sludge SBR was used to treat real landfill leachate. Black-Right-Pointing-Pointer COD removal was analyzed kinetically using a modified model. Black-Right-Pointing-Pointer Characteristics of nitrogen removal at different ammonium inputs were explored. Black-Right-Pointing-Pointer DO variations were consistent with the GSBR performances at low ammonium inputs. - Abstract: Granule sequencing batch reactors (GSBR) were established for landfill leachate treatment, and the COD removal was analyzed kinetically using a modified model. Results showed that COD removal rate decreased as influent ammonium concentration increasing. Characteristics of nitrogen removal at different influent ammonium levels were also studied. When the ammonium concentration inmore » the landfill leachate was 366 mg L{sup -1}, the dominant nitrogen removal process in the GSBR was simultaneous nitrification and denitrification (SND). Under the ammonium concentration of 788 mg L{sup -1}, nitrite accumulation occurred and the accumulated nitrite was reduced to nitrogen gas by the shortcut denitrification process. When the influent ammonium increased to a higher level of 1105 mg L{sup -1}, accumulation of nitrite and nitrate lasted in the whole cycle, and the removal efficiencies of total nitrogen and ammonium decreased to only 35.0% and 39.3%, respectively. Results also showed that DO was a useful process controlling parameter for the organics and nitrogen removal at low ammonium input.« less

Methane production from food waste leachate in laboratory-scale simulated landfill.

PubMed

Behera, Shishir Kumar; Park, Jun Mo; Kim, Kyeong Ho; Park, Hung-Suck

2010-01-01

Due to the prohibition of food waste landfilling in Korea from 2005 and the subsequent ban on the marine disposal of organic sludge, including leachate generated from food waste recycling facilities from 2012, it is urgent to develop an innovative and sustainable disposal strategy that is eco-friendly, yet economically beneficial. In this study, methane production from food waste leachate (FWL) in landfill sites with landfill gas recovery facilities was evaluated in simulated landfill reactors (lysimeters) for a period of 90 d with four different inoculum-substrate ratios (ISRs) on volatile solid (VS) basis. Simultaneous biochemical methane potential batch experiments were also conducted at the same ISRs for 30 d to compare CH(4) yield obtained from lysimeter studies. Under the experimental conditions, a maximum CH(4) yield of 0.272 and 0.294 L/g VS was obtained in the batch and lysimeter studies, respectively, at ISR of 1:1. The biodegradability of FWL in batch and lysimeter experiments at ISR of 1:1 was 64% and 69%, respectively. The calculated data using the modified Gompertz equation for the cumulative CH(4) production showed good agreement with the experimental result obtained from lysimeter study. Based on the results obtained from this study, field-scale pilot test is required to re-evaluate the existing sanitary landfills with efficient leachate collection and gas recovery facilities as engineered bioreactors to treat non-hazardous liquid organic wastes for energy recovery with optimum utilization of facilities. 2010 Elsevier Ltd. All rights reserved.

Short-term Influence of Two Types of Drilling Fluids on Wastewater Treatment Rate and Eukaryotic Organisms of Activated Sludge in Sequencing Batch Reactors.

PubMed

Babko, Roman; Jaromin-Gleń, Katarzyna; Łagód, Grzegorz; Danko, Yaroslav; Kuzmina, Tatiana; Pawłowska, Małgorzata; Pawłowski, Artur

2017-07-01

This work presents the results of studies on the impact of spent drilling fluids cotreated with municipal wastewater on the rate of the wastewater treatment process and the structure of the community of eukaryotic organisms inhabiting an activated sludge. The studies were conducted under laboratory conditions in sequencing batch reactors. The effect of added polymer-potassium drilling fluid (DF1) and polymer drilling fluid (DF2) at dosages of 1 and 3% of wastewater volume on the rate of removal of total suspended solids, turbidity, chemical oxygen demand, and the content of total and ammonium nitrogen were analyzed, taking into account the values of these parameters measured at the end of each operating cycle. In addition to the impacts on the aforementioned physicochemical indices, the influence of drilling fluid on the biomass of various groups of eukaryotes in activated sludge was analyzed. The impact of the drilling fluid was highly dependent on its type and dosage. A noticeable slowdown in the rate of the wastewater treatment process and a negative effect on the organisms were observed after the addition of DF2. This effect intensified after an increase in fluid dose. However, no statistically significant negative changes were observed after the introduction of DF1. Conversely, the removal rate of some of the analyzed pollutant increased. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

Evaluation of the impact of dissolved oxygen concentration on biofilm microbial community in sequencing batch biofilm reactor.

PubMed

Wang, Jingyin; Rong, Hongwei; Zhang, Chaosheng

2018-05-01

The effect of dissolved oxygen concentration (DO) during simultaneous nitrification and denitrification (SND) was investigated in a sequencing batch biofilm reactor (SBBR). In addition, the removal rates of nitrogen and bacterial communities were investigated under different concentrations of DO (1.5, 3.5, and 4.5 mg/L). When the SND rate was 95.22%, the chemical oxygen demand and nitrogen removal was 92.22% and 84.15%, respectively, at 2.5 mg/L DO. The denitrification was inhibited by the increase of oxygen concentration. Microelectrode measurements showed that the thickness of oxygen penetration increased from 1.0 mm to 2.7 mm when the DO concentration increased from 1.5 mg/L to 5.5 mg/L. The current location of the aerobic and anaerobic layers in the biofilm was determined for analysis of the microbial community. High-throughput sequencing analysis revealed the communities of the biofilm approached similar structure and composition. Uliginosibacterium species, biofilm-forming bacteria Zoogloea species and Acinetobacter species were dominant. In the aerobic layer, phyla Betaproteobacteria and Saprospirae were predominant, the major phyla were shifted from Proteobacteria followed by Firmicutes and Bacteroidetes, which comprised 82% of the total sequences during the SND period. Anaerolineae was dominated in the anaerobic layer. The high abundance of Nitrospira in the aerobic biofilm provides evidence of the SND system performing better at ammonia oxidization. In addition, real-time PCR indicated that the amount of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) matched the Nitrospirales and Nitrosomonadales abundance well. Collectively, this study demonstrated the dynamics of key bacterial communities in the SND system were highly influenced by the DO concentration. Copyright © 2017 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Fracture induced electromagnetic emissions: extending laboratory findings by observations at the geophysical scale

NASA Astrophysics Data System (ADS)

Potirakis, Stelios M.; Contoyiannis, Yiannis; Kopanas, John; Kalimeris, Anastasios; Antonopoulos, George; Peratzakis, Athanasios; Eftaxias, Konstantinos; Nomicos, Constantinos

2014-05-01

Under natural conditions, it is practically impossible to install an experimental network on the geophysical scale using the same instrumentations as in laboratory experiments for understanding, through the states of stress and strain and their time variation, the laws that govern the friction during the last stages of EQ generation, or to monitor (much less to control) the principal characteristics of a fracture process. Fracture-induced electromagnetic emissions (EME) in a wide range of frequency bands are sensitive to the micro-structural chances. Thus, their study constitutes a nondestructive method for the monitoring of the evolution of damage process at the laboratory scale. It has been suggested that fracture induced MHz-kHz electromagnetic (EM) emissions, which emerge from a few days up to a few hours before the main seismic shock occurrence permit a real time monitoring of the damage process during the last stages of earthquake preparation, as it happens at the laboratory scale. Since the EME are produced both in the case of the laboratory scale fracture and the EQ preparation process (geophysical scale fracture) they should present similar characteristics in these two scales. Therefore, both the laboratory experimenting scientists and the experimental scientists studying the pre-earthquake EME could benefit from each- other's results. Importantly, it is noted that when studying the fracture process by means of laboratory experiments, the fault growth process normally occurs violently in a fraction of a second. However, a major difference between the laboratory and natural processes is the order-of-magnitude differences in scale (in space and time), allowing the possibility of experimental observation at the geophysical scale for a range of physical processes which are not observable at the laboratory scale. Therefore, the study of fracture-induced EME is expected to reveal more information, especially for the last stages of the fracture process, when it

Construction and fed-batch cultivation of Candida famata with enhanced riboflavin production.

PubMed

Dmytruk, Kostyantyn; Lyzak, Oleksy; Yatsyshyn, Valentyna; Kluz, Maciej; Sibirny, Vladimir; Puchalski, Czeslaw; Sibirny, Andriy

2014-02-20

Riboflavin (vitamin B2) is an essential nutrition component serving as a precursor of coenzymes FMN and FAD that are involved mostly in reactions of oxidative metabolism. Riboflavin is produced in commercial scale and is used in feed and food industries, and in medicine. The yeast Candida famata (Candida flareri) belongs to the group of so called "flavinogenic yeasts" which overproduce riboflavin under iron limitation. Three genes SEF1, RIB1 and RIB7 coding for a putative transcription factor, GTP cyclohydrolase II and riboflavin synthase, respectively were simultaneously overexpressed in the background of a non-reverting riboflavin producing mutant AF-4, obtained earlier in our laboratory using methods of classical selection (Dmytruk et al. (2011), Metabolic Engineering 13, 82-88). Cultivation conditions of the constructed strain were optimized for shake-flasks and bioreactor cultivations. The constructed strain accumulated up to 16.4g/L of riboflavin in optimized medium in a 7L laboratory bioreactor during fed-batch fermentation. Copyright © 2013 Elsevier B.V. All rights reserved.

Effect of moisture content on fed batch composting reactor of vegetable and fruit wastes.

PubMed

Jolanun, B; Tripetchkul, S; Chiemchaisri, C; Chaiprasert, P; Towprayoon, S

2005-03-01

Vegetable and fruit wastes mixed with sawdust were composted in a laboratory scale reactor by controlling the waste feeding rate at 21 kg m(-3) day(-1) and aeration rate at 10.6 l m(-3) min(-1). The effects of initial moisture content on organic matter degradation and process performance of fed batch composting were investigated. The absolute amount of removal, removal percentage, and removal rate of dry mass obtained were substantially different among the initial moisture contents. The rapid rise of moisture content and the lowest absolute amount of removal observed were achieved in the 50% condition. The initial moisture content yielding the largest absolute amount of removal in both feeding and curing stage was 30% whereas the removal percentage and rate constant of waste decomposition were highest in the 50% condition. Examined by traditional soil physics method, the moisture content at 50-55% was suitable for satisfying the degree of free air space (65-70%) of compost during the fed batch composting. Most degradable organic matter was mainly consumed in the feeding stage as indicated by a higher removal rate of dry mass in all cases. It is recommended that the initial moisture content of 30% and mode of aeration and agitation should be adopted for achieving practical fed batch composting of vegetable and fruit wastes. The study also demonstrated that the composting kinetics of vegetable and fruit wastes mixed with sawdust can be described by a first order model.

Effect of temperature and cycle length on microbial competition in PHB-producing sequencing batch reactor.

PubMed

Jiang, Yang; Marang, Leonie; Kleerebezem, Robbert; Muyzer, Gerard; van Loosdrecht, Mark C M

2011-05-01

The impact of temperature and cycle length on microbial competition between polyhydroxybutyrate (PHB)-producing populations enriched in feast-famine sequencing batch reactors (SBRs) was investigated at temperatures of 20 °C and 30 °C, and in a cycle length range of 1-18 h. In this study, the microbial community structure of the PHB-producing enrichments was found to be strongly dependent on temperature, but not on cycle length. Zoogloea and Plasticicumulans acidivorans dominated the SBRs operated at 20 °C and 30 °C, respectively. Both enrichments accumulated PHB more than 75% of cell dry weight. Short-term temperature change experiments revealed that P. acidivorans was more temperature sensitive as compared with Zoogloea. This is particularly true for the PHB degradation, resulting in incomplete PHB degradation in P. acidivorans at 20 °C. Incomplete PHB degradation limited biomass growth and allowed Zoogloea to outcompete P. acidivorans. The PHB content at the end of the feast phase correlated well with the cycle length at a constant solid retention time (SRT). These results suggest that to establish enrichment with the capacity to store a high fraction of PHB, the number of cycles per SRT should be minimized independent of the temperature.

Using relational databases for improved sequence similarity searching and large-scale genomic analyses.

PubMed

Mackey, Aaron J; Pearson, William R

2004-10-01

Relational databases are designed to integrate diverse types of information and manage large sets of search results, greatly simplifying genome-scale analyses. Relational databases are essential for management and analysis of large-scale sequence analyses, and can also be used to improve the statistical significance of similarity searches by focusing on subsets of sequence libraries most likely to contain homologs. This unit describes using relational databases to improve the efficiency of sequence similarity searching and to demonstrate various large-scale genomic analyses of homology-related data. This unit describes the installation and use of a simple protein sequence database, seqdb_demo, which is used as a basis for the other protocols. These include basic use of the database to generate a novel sequence library subset, how to extend and use seqdb_demo for the storage of sequence similarity search results and making use of various kinds of stored search results to address aspects of comparative genomic analysis.

SOBA: sequence ontology bioinformatics analysis.

PubMed

Moore, Barry; Fan, Guozhen; Eilbeck, Karen

2010-07-01

The advent of cheaper, faster sequencing technologies has pushed the task of sequence annotation from the exclusive domain of large-scale multi-national sequencing projects to that of research laboratories and small consortia. The bioinformatics burden placed on these laboratories, some with very little programming experience can be daunting. Fortunately, there exist software libraries and pipelines designed with these groups in mind, to ease the transition from an assembled genome to an annotated and accessible genome resource. We have developed the Sequence Ontology Bioinformatics Analysis (SOBA) tool to provide a simple statistical and graphical summary of an annotated genome. We envisage its use during annotation jamborees, genome comparison and for use by developers for rapid feedback during annotation software development and testing. SOBA also provides annotation consistency feedback to ensure correct use of terminology within annotations, and guides users to add new terms to the Sequence Ontology when required. SOBA is available at http://www.sequenceontology.org/cgi-bin/soba.cgi.

Improved Mannanase Production from Penicillium occitanis by Fed-Batch Fermentation Using Acacia Seeds

PubMed Central

Blibech, Monia; Ellouz Ghorbel, Raoudha; Chaari, Fatma; Dammak, Ilyes; Bhiri, Fatma; Neifar, Mohamed; Ellouz Chaabouni, Semia

2011-01-01

By applying a fed-batch strategy, production of Penicillium occitanis mannanases could be almost doubled as compared to a batch cultivation on acacia seeds (76 versus 41 U/mL). Also, a 10-fold increase of enzyme activities was observed from shake flask fermentation to the fed-batch fermentation. These production levels were 3-fold higher than those obtained on coconut meal. The high mannanase production using acacia seeds powder as inducer substrate showed the suitability of this culture process for industrial-scale development. PMID:23724314

Respirometric response and microbial succession of nitrifying sludge to m-cresol pulses in a sequencing batch reactor.

PubMed

Ordaz, Alberto; Sánchez, Mariana; Rivera, Rodrigo; Rojas, Rafael; Zepeda, Alejandro

2017-02-01

A nitrifying consortium was kinetically, stoichiometrically and molecularly characterized via the in situ pulse respirometric method and pyrosequencing analysis before and after the addition of m-cresol (25 mg C L -1 ) in a sequencing batch reactor (SBR). Five important kinetic and stoichiometric parameters were determined: the maximum oxygen uptake rate, the maximum nitrification rate, the oxidation yield, the biomass growth yield, and the substrate affinity constant. An inhibitory effect was observed in the nitrification process with a recovery of this by up to eight SBR cycles after m-cresol was added to the system. However, full recovery of the nitrification process was not observed, as the maximum oxygen uptake rate was 25% lower than that of the previous operation without m-cresol addition. Furthermore, the pyrosequencing analyses of the nitrifying consortium after the addition of only two pulses of 25 mg C L -1 m-cresol showed an important microbial community change represented by a decrease in the nitrifying populations and an increase in the populations degrading phenolic compounds.

Simultaneous removal of aniline, nitrogen and phosphorus in aniline-containing wastewater treatment by using sequencing batch reactor.

PubMed

Jiang, Yu; Wang, Hongyu; Shang, Yu; Yang, Kai

2016-05-01

The high removal efficiencies of traditional biological aniline-degrading systems always lead to accumulation of ammonium. In this study, simultaneous removal of aniline, nitrogen and phosphorus in a single sequencing batch reactor was achieved by using anaerobic/aerobic/anoxic (A/O/A) operational process. The removal efficiencies of COD, NH4(+)-N, TN, TP were over 95.80%, 83.03%, 87.13%, 90.95%, respectively in most cases with 250mgL(-1) of initial aniline at 6h cycle when DO was 5.5±0.5mgL(-1). Aniline was able to be completely degraded when initial concentrations were less than 750mgL(-1). When DO increased, the removal rate of NH4(+)-N and TP slightly increased along with the moderate decrease of removal efficiencies of TN. The variation of HRT had obvious influence on removal performance of pollutants. The system showed high removal efficiencies of aniline, COD and nutrients during the variation of operating conditions, which might contribute to disposal of aniline-rich industrial wastewater. Copyright © 2016 Elsevier Ltd. All rights reserved.

Integrating sequencing batch reactor with bio-electrochemical treatment for augmenting remediation efficiency of complex petrochemical wastewater.

PubMed

Yeruva, Dileep Kumar; Jukuri, Srinivas; Velvizhi, G; Naresh Kumar, A; Swamy, Y V; Venkata Mohan, S

2015-01-01

The present study evaluates the sequential integration of two advanced biological treatment methods viz., sequencing batch reactor (SBR) and bioelectrochemical treatment systems (BET) for the treatment of real-field petrochemical wastewater (PCW). Initially two SBR reactors were operated in aerobic (SBR(Ae)) and anoxic (SBR(Ax)) microenvironments with an organic loading rate (OLR) of 9.68 kg COD/m(3)-day. Relatively, SBR(Ax) showed higher substrate degradation (3.34 kg COD/m(3)-day) compared to SBR(Ae) (2.9 kg COD/m(3)-day). To further improve treatment efficiency, the effluents from SBR process were fed to BET reactors. BET(Ax) depicted higher SDR (1.92 kg COD/m(3)-day) with simultaneous power generation (17.12 mW/m(2)) followed by BET(Ae) (1.80 kg COD/m(3)-day; 14.25 mW/m(2)). Integrating both the processes documented significant improvement in COD removal efficiency due to the flexibility of combining multiple microenvironments sequentially. Results were supported with GC-MS and FTIR, which confirmed the increment in biodegradability of wastewater. Copyright © 2015 Elsevier Ltd. All rights reserved.

Comparison of batch cultivation strategies for cost-effective biomass production of Micractinium inermum NLP-F014 using a blended wastewater medium.

PubMed

Park, Seonghwan; Kim, Jeongmi; Park, Younghyun; Son, Suyoung; Cho, Sunja; Kim, Changwon; Lee, Taeho

2017-06-01

Two competitive strategies, fed-batch and sequencing-batch cultivation, were compared in cost-effective biomass production of a high lipid microalgae, Micractinium inermum NLP-F014 using a blended wastewater medium. For fed-batch cultivations, additional nutrient was supplemented at day 2 (FB1) or consecutively added at day 2 and 4 (FB2). Through inoculum size test, 1.0g-DCWL -1 was selected for the sequencing-batch cultivation (SB) where about 65% of culture was replaced with fresh medium every 2days. Both fed-batch cultivations showed the maximum biomass productivity of 0.95g-DCWL -1 d -1 , while average biomass productivity in SB was slightly higher as 0.96±0.08g-DCWL -1 d -1 . Furthermore, remained concentrations of organics (426mg-CODL -1 ), total nitrogen (15.4mg-NL -1 ) and phosphorus (0.6mg-PL -1 ) in SB were much lower than those of fed-batch conditions. The results suggested that SB could be a promising strategy to cultivate M. inermum NLP-F014 with the blended wastewater medium. Copyright © 2017 Elsevier Ltd. All rights reserved.

Capacity Planning for Batch and Perfusion Bioprocesses Across Multiple Biopharmaceutical Facilities

PubMed Central

Siganporia, Cyrus C; Ghosh, Soumitra; Daszkowski, Thomas; Papageorgiou, Lazaros G; Farid, Suzanne S

2014-01-01

Production planning for biopharmaceutical portfolios becomes more complex when products switch between fed-batch and continuous perfusion culture processes. This article describes the development of a discrete-time mixed integer linear programming (MILP) model to optimize capacity plans for multiple biopharmaceutical products, with either batch or perfusion bioprocesses, across multiple facilities to meet quarterly demands. The model comprised specific features to account for products with fed-batch or perfusion culture processes such as sequence-dependent changeover times, continuous culture constraints, and decoupled upstream and downstream operations that permit independent scheduling of each. Strategic inventory levels were accounted for by applying cost penalties when they were not met. A rolling time horizon methodology was utilized in conjunction with the MILP model and was shown to obtain solutions with greater optimality in less computational time than the full-scale model. The model was applied to an industrial case study to illustrate how the framework aids decisions regarding outsourcing capacity to third party manufacturers or building new facilities. The impact of variations on key parameters such as demand or titres on the optimal production plans and costs was captured. The analysis identified the critical ratio of in-house to contract manufacturing organization (CMO) manufacturing costs that led the optimization results to favor building a future facility over using a CMO. The tool predicted that if titres were higher than expected then the optimal solution would allocate more production to in-house facilities, where manufacturing costs were lower. Utilization graphs indicated when capacity expansion should be considered. © 2013 The Authors Biotechnology Progress published by Wiley Periodicals, Inc. on behalf of American Institute of Chemical Engineers Biotechnol. Prog., 30:594–606, 2014 PMID:24376262

Effect of metal ions and petrochemicals on bioremediation of chlorpyrifos in aerobic sequencing batch bioreactor (ASBR).

PubMed

Khalid, Saira; Hashmi, Imran; Jamal Khan, Sher; Qazi, Ishtiaq A; Nasir, Habib

2016-10-01

Application of chlorpyrifos (CP) has increased its environmental concentration. Increasing CP concentration has increased chances of adverse health effects. Its removal from environment has attained researcher's attention. CP degrading bacterial strains were isolated from wastewater and agricultural soil. Finally, selected five bacterial strains were identified using 16S rRNA nucleotide sequence analysis as Pseudomonas kilonensis SRK1, Serratia marcescens SRK2, Bacillus pumilus SRK4, Achromobacter xylosoxidans SRK5, and Klebsiella sp. T13. Interaction studies among bacterial strains demonstrated possibility for development of five membered bacterial consortium. Biodegradation potential of bacterial consortium was investigated in the presence of petrochemicals and trace metals. About 98 % CP removal was observed in sequencing batch reactors at inoculum level, 10 %; pH, 7; CP concentration, 400 mgL -1 , and HRT, 48 h. Experimental data has shown an excellent fit to first order growth model. Among all petrochemicals only toluene (in low concentration) has stimulatory effect on biodegradation of CP. Addition of petrochemicals (benzene, toluene, and xylene) in high concentration (100 mg L -1 ) inhibited bacterial activity and decreased CP removal. At low concentration i.e., 1 mg L -1 of inorganic contaminants (Cu, Hg, and Zn) >96 % degradation was observed. Addition of Cu(II) in low concentration has stimulated CP removal efficiency. Hg(II) in all concentrations has strongly inhibited biodegradation rate except at 1 mgL -1 . In simulated pesticide, wastewater CP removal efficiency decreased to 77.5 %. Outcomes of study showed that both type and concentration of petrochemicals and trace metals influenced biodegradation of CP.

Competitive adsorption and selectivity sequence of heavy metals by chicken bone-derived biochar: Batch and column experiment.

PubMed

Park, Jong-Hwan; Cho, Ju-Sik; Ok, Yong Sik; Kim, Seong-Heon; Kang, Se-Won; Choi, Ik-Won; Heo, Jong-Soo; DeLaune, Ronald D; Seo, Dong-Cheol

2015-01-01

The objective of this research was to evaluate adsorption of heavy metals in single- and ternary-metal forms onto chicken bone biochar (CBB). Competitive sorption of heavy metals by CBB has never been reported previously. The maximum adsorption capacities of metals by CBB were in the order of Cu (130 mg g(-1)) > Cd (109 mg g(-1)) > Zn (93 mg g(-1)) in the single-metal adsorption isotherm and Cu (108 mg g(-1)) > Cd (54 mg g(-1)) ≥ Zn (44 mg g(-1)) in the ternary-metal adsorption isotherm. Cu was the most retained cation, whereas Zn could be easily exchanged and substituted by Cu. Batch experimental data best fit the Langmuir model rather than the Freundlich isotherms. In the column experiments, the total adsorbed amounts of the metals were in the following order of Cu (210 mg g(-1)) > Cd (192 mg g(-1)) > Zn (178) in single-metal conditions, and Cu (156) > Cd (123) > Zn (92) in ternary-metal conditions. Results from both the batch and column experiments indicate that competitive adsorption among metals increases the mobility of these metals. Especially, Zn in single-metal conditions lost it adsorption capacity most significantly. Based on the 3D simulation graphs of heavy metals, adsorption patterns under single adsorption condition were different than under competitive adsorption condition. Results from both the batch and column experiments show that competitive adsorption among metals increases the mobility of these metals. The maximum metal adsorption capacity of the metals in the column experiments was higher than that in the batch experiment indicating other metal retention mechanisms rather than adsorption may be involved. Therefore, both column and batch experiments are needed for estimating retention capacities and removal efficiencies of metals in CBB.

Large-Scale Biomonitoring of Remote and Threatened Ecosystems via High-Throughput Sequencing

PubMed Central

Gibson, Joel F.; Shokralla, Shadi; Curry, Colin; Baird, Donald J.; Monk, Wendy A.; King, Ian; Hajibabaei, Mehrdad

2015-01-01

Biodiversity metrics are critical for assessment and monitoring of ecosystems threatened by anthropogenic stressors. Existing sorting and identification methods are too expensive and labour-intensive to be scaled up to meet management needs. Alternately, a high-throughput DNA sequencing approach could be used to determine biodiversity metrics from bulk environmental samples collected as part of a large-scale biomonitoring program. Here we show that both morphological and DNA sequence-based analyses are suitable for recovery of individual taxonomic richness, estimation of proportional abundance, and calculation of biodiversity metrics using a set of 24 benthic samples collected in the Peace-Athabasca Delta region of Canada. The high-throughput sequencing approach was able to recover all metrics with a higher degree of taxonomic resolution than morphological analysis. The reduced cost and increased capacity of DNA sequence-based approaches will finally allow environmental monitoring programs to operate at the geographical and temporal scale required by industrial and regulatory end-users. PMID:26488407

Characterising and correcting batch variation in an automated direct infusion mass spectrometry (DIMS) metabolomics workflow.

PubMed

Kirwan, J A; Broadhurst, D I; Davidson, R L; Viant, M R

2013-06-01

Direct infusion mass spectrometry (DIMS)-based untargeted metabolomics measures many hundreds of metabolites in a single experiment. While every effort is made to reduce within-experiment analytical variation in untargeted metabolomics, unavoidable sources of measurement error are introduced. This is particularly true for large-scale multi-batch experiments, necessitating the development of robust workflows that minimise batch-to-batch variation. Here, we conducted a purpose-designed, eight-batch DIMS metabolomics study using nanoelectrospray (nESI) Fourier transform ion cyclotron resonance mass spectrometric analyses of mammalian heart extracts. First, we characterised the intrinsic analytical variation of this approach to determine whether our existing workflows are fit for purpose when applied to a multi-batch investigation. Batch-to-batch variation was readily observed across the 7-day experiment, both in terms of its absolute measurement using quality control (QC) and biological replicate samples, as well as its adverse impact on our ability to discover significant metabolic information within the data. Subsequently, we developed and implemented a computational workflow that includes total-ion-current filtering, QC-robust spline batch correction and spectral cleaning, and provide conclusive evidence that this workflow reduces analytical variation and increases the proportion of significant peaks. We report an overall analytical precision of 15.9%, measured as the median relative standard deviation (RSD) for the technical replicates of the biological samples, across eight batches and 7 days of measurements. When compared against the FDA guidelines for biomarker studies, which specify an RSD of <20% as an acceptable level of precision, we conclude that our new workflows are fit for purpose for large-scale, high-throughput nESI DIMS metabolomics studies.

Beyond-laboratory-scale prediction for channeling flows through subsurface rock fractures with heterogeneous aperture distributions revealed by laboratory evaluation

NASA Astrophysics Data System (ADS)

Ishibashi, Takuya; Watanabe, Noriaki; Hirano, Nobuo; Okamoto, Atsushi; Tsuchiya, Noriyoshi

2015-01-01

The present study evaluates aperture distributions and fluid flow characteristics for variously sized laboratory-scale granite fractures under confining stress. As a significant result of the laboratory investigation, the contact area in fracture plane was found to be virtually independent of scale. By combining this characteristic with the self-affine fractal nature of fracture surfaces, a novel method for predicting fracture aperture distributions beyond laboratory scale is developed. Validity of this method is revealed through reproduction of the results of laboratory investigation and the maximum aperture-fracture length relations, which are reported in the literature, for natural fractures. The present study finally predicts conceivable scale dependencies of fluid flows through joints (fractures without shear displacement) and faults (fractures with shear displacement). Both joint and fault aperture distributions are characterized by a scale-independent contact area, a scale-dependent geometric mean, and a scale-independent geometric standard deviation of aperture. The contact areas for joints and faults are approximately 60% and 40%. Changes in the geometric means of joint and fault apertures (µm), em, joint and em, fault, with fracture length (m), l, are approximated by em, joint = 1 × 102 l0.1 and em, fault = 1 × 103 l0.7, whereas the geometric standard deviations of both joint and fault apertures are approximately 3. Fluid flows through both joints and faults are characterized by formations of preferential flow paths (i.e., channeling flows) with scale-independent flow areas of approximately 10%, whereas the joint and fault permeabilities (m2), kjoint and kfault, are scale dependent and are approximated as kjoint = 1 × 10-12 l0.2 and kfault = 1 × 10-8 l1.1.

EFFECTS OF LARVAL STOCKING DENSITY ON LABORATORY-SCALE AND COMMERICAL-SCALE PRODUCTION OF SUMMER FLOUNDER, PARALICHTHYS DENTATUS

EPA Science Inventory

Three experiments investigating larval stocking densities of summer flounder from hatch to metamorphosis, Paralichthys dentatus, were conducted at laboratory-scale (75-L aquaria) and at commercial scale (1,000-L tanks). Experiments 1 and 2 at commercial scale tested the densities...

Stormwater Pollution Prevention Plan TA-60 Asphalt Batch Plant Revision 2: January 2017

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sandoval, Leonard Frank

The Stormwater Pollution Prevention Team (PPT) is applicable to operations at the Technical Area (TA)- 60 Asphalt Batch Plant (ABP) located on Eniwetok Drive/Sigma Mesa, in Los Alamos County, New Mexico at Los Alamos National Laboratory (LANL).

Estimating Animal Abundance in Ground Beef Batches Assayed with Molecular Markers

PubMed Central

Hu, Xin-Sheng; Simila, Janika; Platz, Sindey Schueler; Moore, Stephen S.; Plastow, Graham; Meghen, Ciaran N.

2012-01-01

Estimating animal abundance in industrial scale batches of ground meat is important for mapping meat products through the manufacturing process and for effectively tracing the finished product during a food safety recall. The processing of ground beef involves a potentially large number of animals from diverse sources in a single product batch, which produces a high heterogeneity in capture probability. In order to estimate animal abundance through DNA profiling of ground beef constituents, two parameter-based statistical models were developed for incidence data. Simulations were applied to evaluate the maximum likelihood estimate (MLE) of a joint likelihood function from multiple surveys, showing superiority in the presence of high capture heterogeneity with small sample sizes, or comparable estimation in the presence of low capture heterogeneity with a large sample size when compared to other existing models. Our model employs the full information on the pattern of the capture-recapture frequencies from multiple samples. We applied the proposed models to estimate animal abundance in six manufacturing beef batches, genotyped using 30 single nucleotide polymorphism (SNP) markers, from a large scale beef grinding facility. Results show that between 411∼1367 animals were present in six manufacturing beef batches. These estimates are informative as a reference for improving recall processes and tracing finished meat products back to source. PMID:22479559

System for Informatics in the Molecular Pathology Laboratory: An Open-Source End-to-End Solution for Next-Generation Sequencing Clinical Data Management.

PubMed

Kang, Wenjun; Kadri, Sabah; Puranik, Rutika; Wurst, Michelle N; Patil, Sushant A; Mujacic, Ibro; Benhamed, Sonia; Niu, Nifang; Zhen, Chao Jie; Ameti, Bekim; Long, Bradley C; Galbo, Filipo; Montes, David; Iracheta, Crystal; Gamboa, Venessa L; Lopez, Daisy; Yourshaw, Michael; Lawrence, Carolyn A; Aisner, Dara L; Fitzpatrick, Carrie; McNerney, Megan E; Wang, Y Lynn; Andrade, Jorge; Volchenboum, Samuel L; Furtado, Larissa V; Ritterhouse, Lauren L; Segal, Jeremy P

2018-04-24

Next-generation sequencing (NGS) diagnostic assays increasingly are becoming the standard of care in oncology practice. As the scale of an NGS laboratory grows, management of these assays requires organizing large amounts of information, including patient data, laboratory processes, genomic data, as well as variant interpretation and reporting. Although several Laboratory Information Systems and/or Laboratory Information Management Systems are commercially available, they may not meet all of the needs of a given laboratory, in addition to being frequently cost-prohibitive. Herein, we present the System for Informatics in the Molecular Pathology Laboratory, a free and open-source Laboratory Information System/Laboratory Information Management System for academic and nonprofit molecular pathology NGS laboratories, developed at the Genomic and Molecular Pathology Division at the University of Chicago Medicine. The System for Informatics in the Molecular Pathology Laboratory was designed as a modular end-to-end information system to handle all stages of the NGS laboratory workload from test order to reporting. We describe the features of the system, its clinical validation at the Genomic and Molecular Pathology Division at the University of Chicago Medicine, and its installation and testing within a different academic center laboratory (University of Colorado), and we propose a platform for future community co-development and interlaboratory data sharing. Copyright © 2018. Published by Elsevier Inc.

Performance evaluation and microbial community of a sequencing batch biofilm reactor (SBBR) treating mariculture wastewater at different chlortetracycline concentrations.

PubMed

Zheng, Dong; Chang, Qingbo; Gao, Mengchun; She, Zonglian; Jin, Chunji; Guo, Liang; Zhao, Yangguo; Wang, Sen; Wang, Xuejiao

2016-11-01

The effects of chlortetracycline (CTC) on the performance, microbial activity, extracellular polymeric substances (EPS) and microbial community of a sequencing batch biofilm reactor (SBBR) were investigated in treating mariculture wastewater. Low CTC concentration (less than 6 mg/L) had no obvious effect on the SBBR performance, whereas high CTC concentration could inhibit the chemical oxygen demand (COD) and nitrogen removal of the SBBR. The microbial activity of the biofilm in the SBBR decreased with the increase of CTC concentration from 0 to 35 mg/L. The protein (PN) contents were always higher than the PS contents in both loosely bound EPS (LB-EPS) and tightly bound EPS (TB-EPS) at different CTC concentrations. The chemical compositions of LB-EPS and TB-EPS had obvious variations with the increase of CTC concentration from 0 to 35 mg/L. The high-throughput sequencing revealed the effects of CTC on the microbial communities of the biofilm at phylum, class and genus level. The relative abundances of some genera displayed a decreasing tendency with the increase of CTC concentration from 0 to 35 mg/L, such as Nitrospira, Paracoccus, Hyphomicrobium, Azospirillum. However, the relative abundances of the genera Flavobacterium, Aequorivita, Buchnera, Azonexus and Thioalbus increased with the increase of CTC concentration. Copyright © 2016 Elsevier Ltd. All rights reserved.

Mesophilic and thermophilic anaerobic co-digestion of abattoir wastewater and fruit and vegetable waste in anaerobic sequencing batch reactors.

PubMed

Bouallagui, Hassib; Rachdi, Boutheina; Gannoun, Hana; Hamdi, Moktar

2009-06-01

Anaerobic co-digestion of fruit and vegetable waste (FVW) and abattoir wastewater (AW) was investigated using anaerobic sequencing batch reactors (ASBRs). The effects of hydraulic retention time (HRT) and temperature variations on digesters performances were examined. At both 20 and 10 days biogas production for co-digestion was greater thanks to the improved balance of nutrients. The high specific gas productions for the different digestion processes were 0.56, 0.61 and 0.85 l g(-1) total volatile solids (TVS) removal for digesters treating AW, FVW and AW + FVW, respectively. At an HRT of 20 days, biogas production rates from thermophilic digesters were higher on average than from mesophilic AW, FVW and AW + FVW digestion by 28.5, 44.5 and 25%, respectively. However, at 10 days of HRT results showed a decrease of biogas production rate for AW and AW + FVW digestion processes due to the high amount of free ammonia at high organic loading rate (OLR).

Methanol metabolism and archaeal community changes in a bioelectrochemical anaerobic digestion sequencing batch reactor with copper-coated graphite cathode.

PubMed

Park, Jungyu; Lee, Beom; Shi, Peng; Kwon, Hyejeong; Jeong, Sang Mun; Jun, Hangbae

2018-07-01

In this study, the metabolism of methanol and changes in an archaeal community were examined in a bioelectrochemical anaerobic digestion sequencing batch reactor with a copper-coated graphite cathode (BEAD-SBR Cu ). Copper-coated graphite cathode produced methanol from food waste. The BEAD-SBR Cu showed higher methanol removal and methane production than those of the anaerobic digestion (AD)-SBR. The methane production and pH of the BEAD-SBR Cu were stable even under a high organic loading rate (OLR). The hydrogenotrophic methanogens increased from 32.2 to 60.0%, and the hydrogen-dependent methylotrophic methanogens increased from 19.5 to 37.7% in the bulk of BEAD-SBR Cu at high OLR. Where methanol was directly injected as a single substrate into the BEAD-SBR Cu , the main metabolism of methane production was hydrogenotrophic methanogenesis using carbon dioxide and hydrogen released by the oxidation of methanol on the anode through bioelectrochemical reactions. Copyright © 2018 Elsevier Ltd. All rights reserved.

Bioaggregate of photo-fermentative bacteria for enhancing continuous hydrogen production in a sequencing batch photobioreactor

NASA Astrophysics Data System (ADS)

Xie, Guo-Jun; Liu, Bing-Feng; Wang, Rui-Qing; Ding, Jie; Ren, Hong-Yu; Zhou, Xu; Ren, Nan-Qi

2015-11-01

Hydrogen recovery through solar-driven biomass conversion by photo-fermentative bacteria (PFB) has been regarded as a promising way for sustainable energy production. However, a considerable fraction of organic substrate was consumed for the growth of PFB as biocatalysts, furthermore, these PFB were continuously washed out from the photobioreactor in continuous operation because of their poor flocculation. In this work, PFB bioaggregate induced by L-cysteine was applied in a sequencing batch photobioreactor to enhance continuous hydrogen production and reduce biomass washout. The effects of the hydraulic retention time (HRT), influent concentration and light intensity on hydrogen production of the photobioreactor were investigated. The maximum hydrogen yield (3.35 mol H2/mol acetate) and production rate (1044 ml/l/d) were obtained at the HRT of 96 h, influent concentration of 3.84 g COD/l, and light intensity of 200 W/m2. With excellent settling ability, biomass accumulated in the photobioreactor and reached 2.15 g/l under the optimum conditions. Structural analysis of bioaggregate showed that bacterial cells were covered and tightly linked together by extracellular polymeric substances, and formed a stable structure. Therefore, PFB bioaggregate induced by L-cysteine is an efficient strategy to improve biomass retention capacity of the photobioreactor and enhance hydrogen recovery efficiency from organic wastes.

BioPig: a Hadoop-based analytic toolkit for large-scale sequence data.

PubMed

Nordberg, Henrik; Bhatia, Karan; Wang, Kai; Wang, Zhong

2013-12-01

The recent revolution in sequencing technologies has led to an exponential growth of sequence data. As a result, most of the current bioinformatics tools become obsolete as they fail to scale with data. To tackle this 'data deluge', here we introduce the BioPig sequence analysis toolkit as one of the solutions that scale to data and computation. We built BioPig on the Apache's Hadoop MapReduce system and the Pig data flow language. Compared with traditional serial and MPI-based algorithms, BioPig has three major advantages: first, BioPig's programmability greatly reduces development time for parallel bioinformatics applications; second, testing BioPig with up to 500 Gb sequences demonstrates that it scales automatically with size of data; and finally, BioPig can be ported without modification on many Hadoop infrastructures, as tested with Magellan system at National Energy Research Scientific Computing Center and the Amazon Elastic Compute Cloud. In summary, BioPig represents a novel program framework with the potential to greatly accelerate data-intensive bioinformatics analysis.

Influence of Al(III) on biofilm and its extracellular polymeric substances in sequencing batch biofilm reactors.

PubMed

Hu, Xuewei; Yang, Lei; Lai, Xinke; Yao, Qi; Chen, Kai

2017-10-03

This paper presented the influence of Al(III) on biodegradability, micromorphology, composition and functional groups characteristics of the biofilm extracellular polymeric substances (EPS) during different growth phases. The sequencing batch biofilm reactors were developed to cultivate biofilms under different Al(III) dosages. The results elucidated that Al(III) affected biofilm development adversely at the beginning of biofilm growth, but promoted the biofilm mass and improved the biofilm activity with the growth of the biofilm. The micromorphological observation indicated that Al(III) led to a reduction of the filaments and promotion of the EPS secretion in growth phases of the biofilm, also Al(III) could promote microorganisms to form larger colonies for mature biofilm. Then, the analysis of EPS contents and components suggested that Al(III) could increase the protein (PN) of tightly bound EPS (TB-EPS) which alleviated the metal toxicity inhibition on the biofilm during the initial phases of biofilm growth. The biofilm could gradually adapt to the inhibition caused by Al(III) at the biofilm maturation moment. Finally, through the Fourier transform infrared spectroscopy, it was found that Al(III) was beneficial for the proliferation and secretion of TB-EPS functional groups, especially the functional groups of protein and polysaccharides.

Performance of a sequencing-batch membrane bioreactor (SMBR) with an automatic control strategy treating high-strength swine wastewater.

PubMed

Sui, Qianwen; Jiang, Chao; Yu, Dawei; Chen, Meixue; Zhang, Junya; Wang, Yawei; Wei, Yuansong

2018-01-15

Due to high-strength of organic matters, nutrients and pathogen, swine wastewater is a major source of pollution to rural environment and surface water. A sequencing-batch membrane bioreactor (SMBR) system with an automatic control strategy was developed for high-strength swine wastewater treatment. Short-cut nitrification and denitrification (SND) was achieved at nitrite accumulation rate of 83.6%, with removal rates of COD, NH 4 + -N and TN at 95%, 99% and 93%, respectively, at reduced HRT of 6.0 d and TN loading rate of 0.02kgN/(kgVSS d). With effective membrane separation, the reduction of total bacteria (TB) and putative pathogen were 2.77 logs and 1%, respectively. The shift of microbial community was well responded to controlling parameters. During the SND process, ammonia oxidizing bacteria (AOB) (Nitrosomonas, Nitrosospira) and nitrite oxidizing bacteria (NOB) (Nitrospira) were enriched by 52 times and reduced by 2 times, respectively. The denitrifiers (Thauera) were well enriched and the diversity was enhanced. Copyright © 2017. Published by Elsevier B.V.

Operation and model description of a sequencing batch reactor treating reject water for biological nitrogen removal via nitrite.

PubMed

Dosta, J; Galí, A; Benabdallah El-Hadj, T; Macé, S; Mata-Alvarez, J

2007-08-01

The aim of this study was the operation and model description of a sequencing batch reactor (SBR) for biological nitrogen removal (BNR) from a reject water (800-900 mg NH(4)(+)-NL(-1)) from a municipal wastewater treatment plant (WWTP). The SBR was operated with three cycles per day, temperature 30 degrees C, SRT 11 days and HRT 1 day. During the operational cycle, three alternating oxic/anoxic periods were performed to avoid alkalinity restrictions. Oxygen supply and working pH range were controlled to achieve the BNR via nitrite, which makes the process more economical. Under steady state conditions, a total nitrogen removal of 0.87 kg N (m(3)day)(-1) was reached. A four-step nitrogen removal model was developed to describe the process. This model enlarges the IWA activated sludge models for a more detailed description of the nitrogen elimination processes and their inhibitions. A closed intermittent-flow respirometer was set up for the estimation of the most relevant model parameters. Once calibrated, model predictions reproduced experimental data accurately.

NHEXAS PHASE I ARIZONA STUDY--STANDARD OPERATING PROCEDURE FOR BATCHING OF LAB DATA (UA-C-7.0)

EPA Science Inventory

The purpose of this SOP is to describe the steps involved in batching the physical laboratory data forms generated by NHEXAS Arizona and slated for data entry at the primary NHEXAS Arizona office. It applies to all physical laboratory data forms entered at this site. This proced...

Pair-barcode high-throughput sequencing for large-scale multiplexed sample analysis.

PubMed

Tu, Jing; Ge, Qinyu; Wang, Shengqin; Wang, Lei; Sun, Beili; Yang, Qi; Bai, Yunfei; Lu, Zuhong

2012-01-25

The multiplexing becomes the major limitation of the next-generation sequencing (NGS) in application to low complexity samples. Physical space segregation allows limited multiplexing, while the existing barcode approach only permits simultaneously analysis of up to several dozen samples. Here we introduce pair-barcode sequencing (PBS), an economic and flexible barcoding technique that permits parallel analysis of large-scale multiplexed samples. In two pilot runs using SOLiD sequencer (Applied Biosystems Inc.), 32 independent pair-barcoded miRNA libraries were simultaneously discovered by the combination of 4 unique forward barcodes and 8 unique reverse barcodes. Over 174,000,000 reads were generated and about 64% of them are assigned to both of the barcodes. After mapping all reads to pre-miRNAs in miRBase, different miRNA expression patterns are captured from the two clinical groups. The strong correlation using different barcode pairs and the high consistency of miRNA expression in two independent runs demonstrates that PBS approach is valid. By employing PBS approach in NGS, large-scale multiplexed pooled samples could be practically analyzed in parallel so that high-throughput sequencing economically meets the requirements of samples which are low sequencing throughput demand.

Nitrate removal from high strength nitrate-bearing wastes in granular sludge sequencing batch reactors.

PubMed

Krishna Mohan, Tulasi Venkata; Renu, Kadali; Nancharaiah, Yarlagadda Venkata; Satya Sai, Pedapati Murali; Venugopalan, Vayalam Purath

2016-02-01

A 6-L sequencing batch reactor (SBR) was operated for development of granular sludge capable of denitrification of high strength nitrates. Complete and stable denitrification of up to 5420 mg L(-1) nitrate-N (2710 mg L(-1) nitrate-N in reactor) was achieved by feeding simulated nitrate waste at a C/N ratio of 3. Compact and dense denitrifying granular sludge with relatively stable microbial community was developed during reactor operation. Accumulation of large amounts of nitrite due to incomplete denitrification occurred when the SBR was fed with 5420 mg L(-1) NO3-N at a C/N ratio of 2. Complete denitrification could not be achieved at this C/N ratio, even after one week of reactor operation as the nitrite levels continued to accumulate. In order to improve denitrification performance, the reactor was fed with nitrate concentrations of 1354 mg L(-1), while keeping C/N ratio at 2. Subsequently, nitrate concentration in the feed was increased in a step-wise manner to establish complete denitrification of 5420 mg L(-1) NO3-N at a C/N ratio of 2. The results show that substrate concentration plays an important role in denitrification of high strength nitrate by influencing nitrite accumulation. Complete denitrification of high strength nitrates can be achieved at lower substrate concentrations, by an appropriate acclimatization strategy. Copyright © 2015 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Nitrogen Removal over Nitrite by Aeration Control in Aerobic Granular Sludge Sequencing Batch Reactors

PubMed Central

Lochmatter, Samuel; Maillard, Julien; Holliger, Christof

2014-01-01

This study investigated the potential of aeration control for the achievement of N-removal over nitrite with aerobic granular sludge in sequencing batch reactors. N-removal over nitrite requires less COD, which is particularly interesting if COD is the limiting parameter for nutrient removal. The nutrient removal performances for COD, N and P have been analyzed as well as the concentration of nitrite-oxidizing bacteria in the granular sludge. Aeration phase length control combined with intermittent aeration or alternate high-low DO, has proven to be an efficient way to reduce the nitrite-oxidizing bacteria population and hence achieve N-removal over nitrite. N-removal efficiencies of up to 95% were achieved for an influent wastewater with COD:N:P ratios of 20:2.5:1. The total N-removal rate was 0.18 kgN·m−3·d−1. With N-removal over nitrate the N-removal was only 74%. At 20 °C, the nitrite-oxidizing bacteria concentration decreased by over 95% in 60 days and it was possible to switch from N-removal over nitrite to N-removal over nitrate and back again. At 15 °C, the nitrite-oxidizing bacteria concentration decreased too but less, and nitrite oxidation could not be completely suppressed. However, the combination of aeration phase length control and high-low DO was also at 15 °C successful to maintain the nitrite pathway despite the fact that the maximum growth rate of nitrite-oxidizing bacteria at temperatures below 20 °C is in general higher than the one of ammonium-oxidizing bacteria. PMID:25006970

EPOS-WP16: A coherent and collaborative network of Solid Earth Multi-scale laboratories

NASA Astrophysics Data System (ADS)

Calignano, Elisa; Rosenau, Matthias; Lange, Otto; Spiers, Chris; Willingshofer, Ernst; Drury, Martyn; van Kan-Parker, Mirjam; Elger, Kirsten; Ulbricht, Damian; Funiciello, Francesca; Trippanera, Daniele; Sagnotti, Leonardo; Scarlato, Piergiorgio; Tesei, Telemaco; Winkler, Aldo

2017-04-01

Laboratory facilities are an integral part of Earth Science research. The diversity of methods employed in such infrastructures reflects the multi-scale nature of the Earth system and is essential for the understanding of its evolution, for the assessment of geo-hazards and for the sustainable exploitation of geo-resources. In the frame of EPOS (European Plate Observing System), the Working Package 16 represents a developing community of European Geoscience Multi-scale laboratories. The participant and collaborating institutions (Utrecht University, GFZ, RomaTre University, INGV, NERC, CSIC-ICTJA, CNRS, LMU, C4G-UBI, ETH, CNR*) embody several types of laboratory infrastructures, engaged in different fields of interest of Earth Science: from high temperature and pressure experimental facilities, to electron microscopy, micro-beam analysis, analogue tectonic and geodynamic modelling and paleomagnetic laboratories. The length scales encompassed by these infrastructures range from the nano- and micrometre levels (electron microscopy and micro-beam analysis) to the scale of experiments on centimetres-sized samples, and to analogue model experiments simulating the reservoir scale, the basin scale and the plate scale. The aim of WP16 is to provide two services by the year 2019: first, providing virtual access to data from laboratories (data service) and, second, providing physical access to laboratories (transnational access, TNA). Regarding the development of a data service, the current status is such that most data produced by the various laboratory centres and networks are available only in limited "final form" in publications, many data remain inaccessible and/or poorly preserved. Within EPOS the TCS Multi-scale laboratories is collecting and harmonizing available and emerging laboratory data on the properties and process controlling rock system behaviour at all relevant scales, in order to generate products accessible and interoperable through services for supporting

[Genome-scale sequence data processing and epigenetic analysis of DNA methylation].

PubMed

Wang, Ting-Zhang; Shan, Gao; Xu, Jian-Hong; Xue, Qing-Zhong

2013-06-01

A new approach recently developed for detecting cytosine DNA methylation (mC) and analyzing the genome-scale DNA methylation profiling, is called BS-Seq which is based on bisulfite conversion of genomic DNA combined with next-generation sequencing. The method can not only provide an insight into the difference of genome-scale DNA methylation among different organisms, but also reveal the conservation of DNA methylation in all contexts and nucleotide preference for different genomic regions, including genes, exons, and repetitive DNA sequences. It will be helpful to under-stand the epigenetic impacts of cytosine DNA methylation on the regulation of gene expression and maintaining silence of repetitive sequences, such as transposable elements. In this paper, we introduce the preprocessing steps of DNA methylation data, by which cytosine (C) and guanine (G) in the reference sequence are transferred to thymine (T) and adenine (A), and cytosine in reads is transferred to thymine, respectively. We also comprehensively review the main content of the DNA methylation analysis on the genomic scale: (1) the cytosine methylation under the context of different sequences; (2) the distribution of genomic methylcytosine; (3) DNA methylation context and the preference for the nucleotides; (4) DNA- protein interaction sites of DNA methylation; (5) degree of methylation of cytosine in the different structural elements of genes. DNA methylation analysis technique provides a powerful tool for the epigenome study in human and other species, and genes and environment interaction, and founds the theoretical basis for further development of disease diagnostics and therapeutics in human.

Identification of oxidative coupling products of xylenols arising from laboratory-scale phytoremediation.

PubMed

Poerschmann, J; Schultze-Nobre, L; Ebert, R U; Górecki, T

2015-01-01

Oxidative coupling reactions take place during the passage of xylenols through a laboratory-scale helophyte-based constructed wetland system. Typical coupling product groups including tetramethyl-[1,1'-biphenyl] diols and tetramethyl diphenylether monools as stable organic intermediates could be identified by a combination of pre-chromatographic derivatization and GC/MS analysis. Structural assignment of individual analytes was performed by an increment system developed by Zenkevich to pre-calculate retention sequences. The most abundant analyte turned out to be 3,3',5,5'-tetramethyl-[1,1'-biphenyl]-4,4'-diol, which can be formed by a combination of radicals based on 2,6-xylenol or by an attack of a 2,6-xylenol-based radical on 2,6-xylenol. Organic intermediates originating from oxidative coupling could also be identified in anaerobic constructed wetland systems. This finding suggested the presence of (at least partly) oxic conditions in the rhizosphere. Copyright © 2014 Elsevier Ltd. All rights reserved.

Fate of estrone in laboratory-scale constructed wetlands

USDA-ARS?s Scientific Manuscript database

A horizontal, subsurface, laboratory-scale constructed wetland (CW) consisting of four cells in series was used to determine the attenuation of the steroid hormone estrone (E1) present in animal wastewater. Liquid swine manure diluted 1:80 with farm pond water and dosed with [14C]E1 flowed through ...

Performance and microbial community dynamics of electricity-assisted sequencing batch reactor (SBR) for treatment of saline petrochemical wastewater.

PubMed

Liu, Jiaxin; Shi, Shengnan; Ji, Xiangyu; Jiang, Bei; Xue, Lanlan; Li, Meidi; Tan, Liang

2017-07-01

High-salinity wastewater is often difficult to treat by common biological technologies due to salinity stress on the bacterial community. Electricity-assisted anaerobic technologies have significantly enhanced the treatment performance by alleviating the impact of salinity stress on the bacterial community, but electricity-assisted aerobic technologies have less been reported. Herein, a novel bio-electrochemistry system has been designed and operated in which a pair of stainless iron mesh-graphite plate electrodes were installed into a sequencing batch reactor (SBR, designated as S1) to strengthen the performance of saline petrochemical wastewater under aerobic conditions. The removal efficiency of phenol and chemical oxygen demand (COD) in S1 were 94.1 and 91.2%, respectively, on day 45, which was clearly higher than the removal efficiency of a single SBR (S2) and an electrochemical reactor (S3), indicating that a coupling effect existed between the electrochemical process and biodegradation. A certain amount of salinity (≤8000 mg/L) could enhance the treatment performance in S1 but weaken that in S2. Illumina sequencing revealed that microbial communities in S1 on days 45 and 91 were richer and more diverse than in S2, which suggests that electrical stimulation could enhance the diversity and richness of the microbial community, and reduce the negative effect of salinity on the microorganisms and enrich some salt-adapted microorganisms, thus improve the ability of S1 to respond to salinity stress. This novel bio-electrochemistry system was shown to be an alternative technology for the high saline petrochemical wastewater.

Impact of selected non-steroidal anti-inflammatory pharmaceuticals on microbial community assembly and activity in sequencing batch reactors

PubMed Central

Jiang, Cong; Hu, Haidong; Ma, Haijun; Gao, Xingsheng; Ren, Hongqiang

2017-01-01

This study covers three widely detected non-steroidal anti-inflammatory pharmaceuticals (NSAIDs), diclofenac (DCF), ibuprofen (IBP) and naproxen (NPX), as NSAIDs pollutants. The objective is to evaluate the impact of NSAIDs at their environmental concentrations on microbial community assembly and activity. The exposure experiments were conducted under three conditions (5 μg L-1 DCF, 5 μg L-1 DCF+5 μg L-1 IBP and 5 μg L-1 DCF+5 μg L-1 IBP+ 5 μg L-1 NPX) in sequencing batch reactors (SBRs) for 130 days. Removals of COD and NH4+-N were not affected but total nitrogen (TN) removal decreased. IBP and NPX had the high removal efficiencies (79.96% to 85.64%), whereas DCF was more persistent (57.24% to 64.12%). In addition, the decreased removals of TN remained the same under the three conditions (p > 0.05). The results of oxidizing enzyme activities, live cell percentages and extracellular polymeric substances (EPS) indicated that NSAIDs damaged the cell walls or microorganisms and the mixtures of the three NSAIDs increased the toxicity. The increased Shannon-Wiener diversity index suggested that bacterial diversity was increased with the addition of selected NSAIDs. Bacterial ribosomal RNA small subunit (16S) gene sequencing results indicated that Actinobacteria and Bacteroidetes were enriched, while Micropruina and Nakamurella decreased with the addition of NSAIDs. The enrichment of Actinobacteria and Bacteroidetes indicated that both of them might have the ability to degrade NSAIDs and thereby could adapt well with the presence of NSAIDs. PMID:28640897

Impact of selected non-steroidal anti-inflammatory pharmaceuticals on microbial community assembly and activity in sequencing batch reactors.

PubMed

Jiang, Cong; Geng, Jinju; Hu, Haidong; Ma, Haijun; Gao, Xingsheng; Ren, Hongqiang

2017-01-01

This study covers three widely detected non-steroidal anti-inflammatory pharmaceuticals (NSAIDs), diclofenac (DCF), ibuprofen (IBP) and naproxen (NPX), as NSAIDs pollutants. The objective is to evaluate the impact of NSAIDs at their environmental concentrations on microbial community assembly and activity. The exposure experiments were conducted under three conditions (5 μg L-1 DCF, 5 μg L-1 DCF+5 μg L-1 IBP and 5 μg L-1 DCF+5 μg L-1 IBP+ 5 μg L-1 NPX) in sequencing batch reactors (SBRs) for 130 days. Removals of COD and NH4+-N were not affected but total nitrogen (TN) removal decreased. IBP and NPX had the high removal efficiencies (79.96% to 85.64%), whereas DCF was more persistent (57.24% to 64.12%). In addition, the decreased removals of TN remained the same under the three conditions (p > 0.05). The results of oxidizing enzyme activities, live cell percentages and extracellular polymeric substances (EPS) indicated that NSAIDs damaged the cell walls or microorganisms and the mixtures of the three NSAIDs increased the toxicity. The increased Shannon-Wiener diversity index suggested that bacterial diversity was increased with the addition of selected NSAIDs. Bacterial ribosomal RNA small subunit (16S) gene sequencing results indicated that Actinobacteria and Bacteroidetes were enriched, while Micropruina and Nakamurella decreased with the addition of NSAIDs. The enrichment of Actinobacteria and Bacteroidetes indicated that both of them might have the ability to degrade NSAIDs and thereby could adapt well with the presence of NSAIDs.

The stability of accumulating nitrite from Swine wastewater in a sequencing batch reactor.

PubMed

Wang, Liang; Zhu, Jun; Miller, Curtis

2011-02-01

Shortcut nitrification is the first step of shortcut nitrogen removal from swine wastewater. Stably obtaining an effluent with a significant amount of nitrite is the premise for the subsequent shortcut denitrification. In this paper, the stability of nitrite accumulation was investigated using a 1.5-day hydraulic retention time in a 10-L (working volume) activated sludge sequencing batch reactor (SBR) with an 8-h cycle consisted of 4 h 38 min aerobic feeding, 1 h 22 min aerobic reaction, 30 min settling, 24 min withdrawal, and 1 h 6 min idle. The nitrite production stability was tested using four different ammonium loading rates, 0.075, 0.062, 0.053, and 0.039 g NH(4)-N/g (mixed liquid suspended solid, MLSS) day in a 2-month running period. The total inorganic nitrogen composition in the effluent was not affected when the ammonium load was between 0.053 and 0.075 g NH(4)-N/g MLSS · day (64% NO(2)-N, 16% NO(3)-N, and 20% NH(4)-N). Under 0.039 g NH(4)-N/g MLSS · day, more NO(2)-N was transformed to NO(3)-N with an effluent of 60% NO(2)-N, 20% NO(3)-N, and 20% NH(4)-N. The reducing load test was able to show the relationship between a declining free nitrous acid (FNA) concentration and the decreasing nitrite production, indicating that the inhibition of FNA on nitrite oxidizing bacteria depends on its levels and an ammonium loading rate around 0.035 g NH(4)-N/g MLSS · day is the lower threshold for producing a nitrite dominance effluent in the activated sludge SBR under the current settings.

Enrichment of denitrifying methane-oxidizing microorganisms using up-flow continuous reactors and batch cultures.

PubMed

Hatamoto, Masashi; Kimura, Masafumi; Sato, Takafumi; Koizumi, Masato; Takahashi, Masanobu; Kawakami, Shuji; Araki, Nobuo; Yamaguchi, Takashi

2014-01-01

Denitrifying anaerobic methane oxidizing (DAMO) microorganisms were enriched from paddy field soils using continuous-flow and batch cultures fed with nitrate or nitrite as a sole electron acceptor. After several months of cultivation, the continuous-flow cultures using nitrite showed remarkable simultaneous methane oxidation and nitrite reduction and DAMO bacteria belonging to phylum NC10 were enriched. A maximum volumetric nitrite consumption rate of 70.4±3.4 mg-N·L(-1)·day(-1) was achieved with very short hydraulic retention time of 2.1 hour. In the culture, about 68% of total microbial cells were bacteria and no archaeal cells were detected by fluorescence in situ hybridization. In the nitrate-fed continuous-flow cultures, 58% of total microbial cells were bacteria while archaeal cells accounted for 7% of total cell numbers. Phylogenetic analysis of pmoA gene sequence showed that enriched DAMO bacteria in the continuous-flow cultivation had over 98% sequence similarity to DAMO bacteria in the inoculum. In contrast, for batch culture, the enriched pmoA gene sequences had 89-91% sequence similarity to DAMO bacteria in the inoculum. These results indicate that electron acceptor and cultivation method strongly affect the microbial community structures of DAMO consortia.

The Babushka Concept--An Instructional Sequence to Enhance Laboratory Learning in Science Education

ERIC Educational Resources Information Center

Gårdebjer, Sofie; Larsson, Anette; Adawi, Tom

2017-01-01

This paper deals with a novel method for improving the traditional "verification" laboratory in science education. Drawing on the idea of integrated instructional units, we describe an instructional sequence which we call the Babushka concept. This concept consists of three integrated instructional units: a start-up lecture, a laboratory…

Regime Shift and Microbial Dynamics in a Sequencing Batch Reactor for Nitrification and Anammox Treatment of Urine ▿†

PubMed Central

Bürgmann, Helmut; Jenni, Sarina; Vazquez, Francisco; Udert, Kai M.

2011-01-01

The microbial population and physicochemical process parameters of a sequencing batch reactor for nitrogen removal from urine were monitored over a 1.5-year period. Microbial community fingerprinting (automated ribosomal intergenic spacer analysis), 16S rRNA gene sequencing, and quantitative PCR on nitrogen cycle functional groups were used to characterize the microbial population. The reactor combined nitrification (ammonium oxidation)/anammox with organoheterotrophic denitrification. The nitrogen elimination rate initially increased by 400%, followed by an extended period of performance degradation. This phase was characterized by accumulation of nitrite and nitrous oxide, reduced anammox activity, and a different but stable microbial community. Outwashing of anammox bacteria or their inhibition by oxygen or nitrite was insufficient to explain reactor behavior. Multiple lines of evidence, e.g., regime-shift analysis of chemical and physical parameters and cluster and ordination analysis of the microbial community, indicated that the system had experienced a rapid transition to a new stable state that led to the observed inferior process rates. The events in the reactor can thus be interpreted to be an ecological regime shift. Constrained ordination indicated that the pH set point controlling cycle duration, temperature, airflow rate, and the release of nitric and nitrous oxides controlled the primarily heterotrophic microbial community. We show that by combining chemical and physical measurements, microbial community analysis and ecological theory allowed extraction of useful information about the causes and dynamics of the observed process instability. PMID:21724875

Study of the diversity of microbial communities in a sequencing batch reactor oxic-settling-anaerobic process and its modified process.

PubMed

Sun, Lianpeng; Chen, Jianfan; Wei, Xiange; Guo, Wuzhen; Lin, Meishan; Yu, Xiaoyu

2016-05-01

To further reveal the mechanism of sludge reduction in the oxic-settling-anaerobic (OSA) process, the polymerase chain reaction - denaturing gradient gel electrophoresis protocol was used to study the possible difference in the microbial communities between a sequencing batch reactor (SBR)-OSA process and its modified process, by analyzing the change in the diversity of the microbial communities in each reactor of both systems. The results indicated that the structure of the microbial communities in aerobic reactors of the 2 processes was very different, but the predominant microbial populations in anaerobic reactors were similar. The predominant microbial population in the aerobic reactor of the SBR-OSA belonged to Burkholderia cepacia, class Betaproteobacteria, while those of the modified process belonged to the classes Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. These 3 types of microbes had a cryptic growth characteristic, which was the main cause of a greater sludge reduction efficiency achieved by the modified process.

Enhancing the performance of sequencing batch reactors by adding crushed date seeds to remove high concentrations of 2,4-dinitrophenol.

PubMed

Al-Mutairi, Nayef Z

2011-11-01

Wastewater treatment systems using simultaneous adsorption and biodegradation processes have been successful in treating toxic pollutants present in industrial wastewater. The goal of this investigation was to assess the effectiveness of date seeds in reducing the toxic effects of 2,4-dinitrophenol (DNP) on activated sludge microorganisms. Two identical sequencing batch reactors (SBRs) (4-L glass vessel), each with a 3.5-L working volume, were used. The initial DNP concentrations in the reactor were 50, 75, 100, 250, and 500 mg/L. The reactor amended with date seeds was capable of degrading DNP at significantly greater rates (11 +/- 2.5 mg/L x h) than the control SBR (4 +/- 1.2 mg/L x h) at a 95% confidence level. Date seeds can be added to the mixed liquor of activated sludge treatment plants to remove high concentrations of DNP from wastewater, to protect the treatment plant against toxic components in the influent and enhance the settling characteristics of the mixed liquor.

Nitrile bioconversion by Microbacterium imperiale CBS 498-74 resting cells in batch and ultrafiltration membrane bioreactors.

PubMed

Cantarella, M; Cantarella, L; Gallifuoco, A; Spera, A

2006-03-01

The biohydration of acrylonitrile, propionitrile and benzonitrile catalysed by the NHase activity contained in resting cells of Microbacterium imperiale CBS 498-74 was operated at 5, 10 and 20 degrees C in laboratory-scale batch and membrane bioreactors. The bioreactions were conducted in buffered medium (50 mM Na(2)HPO(4)/NaH(2)PO(4), pH 7.0) in the presence of distilled water or tap-water, to simulate a possible end-pipe biotreatment process. The integral bioreactor performances were studied with a cell loading (dry cell weight; DCW) varying from 0.1 mg(DCW) per reactor to 16 mg(DCW) per reactor, in order to realize near 100% bioconversion of acrylonitrile, propionitrile and benzonitrile without consistent loss of NHase activity.

Performance and membrane fouling of a step-fed submerged membrane sequencing batch reactor treating swine biogas digestion slurry.

PubMed

Han, Zhiying; Chen, Shixia; Lin, Xiaochang; Yu, Hongjun; Duan, Li'an; Ye, Zhangying; Jia, Yanbo; Zhu, Songming; Liu, Dezhao

2018-01-02

To identify the performance of step-fed submerged membrane sequencing batch reactor (SMSBR) treating swine biogas digestion slurry and to explore the correlation between microbial metabolites and membrane fouling within this novel reactor, a lab-scale step-fed SMSBR was operated under nitrogen loading rate of 0.026, 0.052 and 0.062 g NH 4 + -N (gVSS·d) -1 . Results show that the total removal efficiencies for NH 4 + -N, total nitrogen and chemical oxygen demand in the reactor (>94%, >89% and >97%, respectively) were high during the whole experiment. However, the cycle removal efficiency of NH 4 + -N decreased significantly when the nitrogen loading rate was increased to 0.062 g NH 4 + -N (gVSS·d) -1 . The total removal efficiency of total phosphorus in the step-fed SMSBR was generally higher than 75%, though large fluctuations were observed during the experiments. In addition, the concentrations of microbial metabolites, i.e., soluble microbial products (SMP) and extracellular polymeric substances (EPS) from activated sludge increased as nitrogen loading rate increased, both showing quadratic equation correlations with viscosity of the mixed liquid in the step-fed SMSBR (both R 2 > 0.90). EPS content was higher than SMP content, while protein (PN) was detected as the main component in both SMP and EPS. EPS PN was found to be well correlated with transmembrane pressure, membrane flux and the total membrane fouling resistance. Furthermore, the three-dimensional excitation-emission matrix fluorescence spectroscopy results suggested the tryptophan-like protein as one of the main contributors to the membrane fouling. Overall, this study showed that the step-fed SMSBR could be used to treat swine digestion slurry at nitrogen loading rate of 0.052 g NH 4 + -N (gVSS·d) -1 , and the control strategy of membrane fouling should be developed based on reducing the tryptophan-like PN in EPS.

New Experimental Technique for Nodularity and Mg Fading Control in Compacted Graphite Iron Production on Laboratory Scale

NASA Astrophysics Data System (ADS)

Hernando, Juan Carlos; Domeij, Björn; González, Daniel; Amieva, José Manuel; Diószegi, Attila

2017-11-01

The narrow production window for compacted graphite iron material (CGI) drastically reduces the possibilities to produce it in small batches outside an industrial environment. This fact hinders laboratory-scale investigations on CGI solidification. This work presents a solution to that issue by introducing an experimental technique to produce graphitic cast iron of the main three families. Samples of a base hypereutectic spheroidal graphite iron (SGI) were re-melted in a resistance furnace under Ar atmosphere. Varying the holding time at 1723 K (1450 °C), graphitic irons ranging from spheroidal to lamellar were produced. Characterization of the graphite morphology evolution, in terms of nodularity as a function of holding time, is presented. The nodularity decay for the SGI region suggests a linear correlation with the holding time. In the CGI region, nodularity deterioration shows a slower rate, concluding with the sudden appearance of lamellar graphite. The fading process of magnesium, showing agreement with previous researchers, is described by means of empirical relations as a function of holding time and nodularity. The results on nodularity fade and number of nodules per unit area fade suggest that both phenomena occur simultaneously during the fading process of magnesium.

Pair-barcode high-throughput sequencing for large-scale multiplexed sample analysis

PubMed Central

2012-01-01

Background The multiplexing becomes the major limitation of the next-generation sequencing (NGS) in application to low complexity samples. Physical space segregation allows limited multiplexing, while the existing barcode approach only permits simultaneously analysis of up to several dozen samples. Results Here we introduce pair-barcode sequencing (PBS), an economic and flexible barcoding technique that permits parallel analysis of large-scale multiplexed samples. In two pilot runs using SOLiD sequencer (Applied Biosystems Inc.), 32 independent pair-barcoded miRNA libraries were simultaneously discovered by the combination of 4 unique forward barcodes and 8 unique reverse barcodes. Over 174,000,000 reads were generated and about 64% of them are assigned to both of the barcodes. After mapping all reads to pre-miRNAs in miRBase, different miRNA expression patterns are captured from the two clinical groups. The strong correlation using different barcode pairs and the high consistency of miRNA expression in two independent runs demonstrates that PBS approach is valid. Conclusions By employing PBS approach in NGS, large-scale multiplexed pooled samples could be practically analyzed in parallel so that high-throughput sequencing economically meets the requirements of samples which are low sequencing throughput demand. PMID:22276739

Recent volcanic history of Irazu volcano, Costa Rica: alternation and mixing of two magma batches, and pervasive mixing

USGS Publications Warehouse

Alvarado, Guillermo E.; Carr, Michael J.; Turrin, Brent D.; Swisher, Carl C.; Schmincke, Hans-Ulrich; Hudnut, Kenneth W.

2006-01-01

40Ar/39Ar dates, field observations, and geochemical data are reported for Irazú volcano, Costa Rica. Volcanism dates back to at least 854 ka, but has been episodic with lava shield construction peaks at ca. 570 ka and 136–0 ka. The recent volcanic record on Irazú volcano comprises lava flows and a variety of Strombolian and phreatomagmatic deposits, with a long-term trend toward more hydrovolcanic deposits. Banded scorias and hybridized rocks reflect ubiquitous magma mixing and commingling. Two distinct magma batches have been identified. One magma type or batch, Haya, includes basalt with higher high field strength (HFS) and rare-earth element contents, suggesting a lower degree melt of a subduction modified mantle source. The second batch, Sapper, has greater enrichment of large ion lithophile elements (LILE) relative to HFS elements and rare-earth elements, suggesting a higher subduction signature. The recent volcanic history at Irazú records two and one half sequences of the following pattern: eruptions of the Haya batch; eruptions of the Sapper batch; and finally, an unusually clear unconformity, indicating a pause in eruptions. In the last two sequences, strongly hybridized magma erupted after the eruption of the Haya batch. The continuing presence of two distinct magma batches requires two active magma chambers. The common occurrence of hybrids is evidence for a small, nearer to the surface chamber for mixing the two batches. Estimated pre-eruptive temperatures based on two-pyroxene geothermometry range from ∼1000–1176 °C in basalts to 922 °C in hornblende andesites. Crystallization occurred mainly between 4.6 and 3 kb as measured by different geobarometers. Hybridized rocks show intermediate pressures and temperatures. High silica magma occurs in very small volumes as banded scorias but not as lava flows. Although eruptions at Irazú are not often very explosive, the pervasiveness of magma mixing presents the danger of larger, more explosive

Characterization of seismic properties across scales: from the laboratory- to the field scale

NASA Astrophysics Data System (ADS)

Grab, Melchior; Quintal, Beatriz; Caspari, Eva; Maurer, Hansruedi; Greenhalgh, Stewart

2016-04-01

When exploring geothermal systems, the main interest is on factors controlling the efficiency of the heat exchanger. This includes the energy state of the pore fluids and the presence of permeable structures building part of the fluid transport system. Seismic methods are amongst the most common exploration techniques to image the deep subsurface in order to evaluate such a geothermal heat exchanger. They make use of the fact that a seismic wave caries information on the properties of the rocks in the subsurface through which it passes. This enables the derivation of the stiffness and the density of the host rock from the seismic velocities. Moreover, it is well-known that the seismic waveforms are modulated while propagating trough the subsurface by visco-elastic effects due to wave induced fluid flow, hence, delivering information about the fluids in the rock's pore space. To constrain the interpretation of seismic data, that is, to link seismic properties with the fluid state and host rock permeability, it is common practice to measure the rock properties of small rock specimens in the laboratory under in-situ conditions. However, in magmatic geothermal systems or in systems situated in the crystalline basement, the host rock is often highly impermeable and fluid transport predominately takes place in fracture networks, consisting of fractures larger than the rock samples investigated in the laboratory. Therefore, laboratory experiments only provide the properties of relatively intact rock and an up-scaling procedure is required to characterize the seismic properties of large rock volumes containing fractures and fracture networks and to study the effects of fluids in such fractured rock. We present a technique to parameterize fractured rock volumes as typically encountered in Icelandic magmatic geothermal systems, by combining laboratory experiments with effective medium calculations. The resulting models can be used to calculate the frequency-dependent bulk

An Integer Batch Scheduling Model for a Single Machine with Simultaneous Learning and Deterioration Effects to Minimize Total Actual Flow Time

NASA Astrophysics Data System (ADS)

Yusriski, R.; Sukoyo; Samadhi, T. M. A. A.; Halim, A. H.

2016-02-01

In the manufacturing industry, several identical parts can be processed in batches, and setup time is needed between two consecutive batches. Since the processing times of batches are not always fixed during a scheduling period due to learning and deterioration effects, this research deals with batch scheduling problems with simultaneous learning and deterioration effects. The objective is to minimize total actual flow time, defined as a time interval between the arrival of all parts at the shop and their common due date. The decision variables are the number of batches, integer batch sizes, and the sequence of the resulting batches. This research proposes a heuristic algorithm based on the Lagrange Relaxation. The effectiveness of the proposed algorithm is determined by comparing the resulting solutions of the algorithm to the respective optimal solution obtained from the enumeration method. Numerical experience results show that the average of difference among the solutions is 0.05%.

SIMILARITY PROPERTIES AND SCALING LAWS OF RADIATION HYDRODYNAMIC FLOWS IN LABORATORY ASTROPHYSICS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Falize, E.; Bouquet, S.; Michaut, C., E-mail: emeric.falize@cea.fr

The spectacular recent development of modern high-energy density laboratory facilities which concentrate more and more energy in millimetric volumes allows the astrophysical community to reproduce and to explore, in millimeter-scale targets and during very short times, astrophysical phenomena where radiation and matter are strongly coupled. The astrophysical relevance of these experiments can be checked from the similarity properties and especially scaling law establishment, which constitutes the keystone of laboratory astrophysics. From the radiating optically thin regime to the so-called optically thick radiative pressure regime, we present in this paper, for the first time, a complete analysis of the main radiatingmore » regimes that we encountered in laboratory astrophysics with the same formalism based on Lie group theory. The use of the Lie group method appears to be a systematic method which allows us to construct easily and systematically the scaling laws of a given problem. This powerful tool permits us to unify the recent major advances on scaling laws and to identify new similarity concepts that we discuss in this paper, and suggests important applications for present and future laboratory astrophysics experiments. All these results enable us to demonstrate theoretically that astrophysical phenomena in such radiating regimes can be explored experimentally thanks to powerful facilities. Consequently, the results presented here are a fundamental tool for the high-energy density laboratory astrophysics community in order to quantify the astrophysics relevance and justify laser experiments. Moreover, relying on Lie group theory, this paper constitutes the starting point of any analysis of the self-similar dynamics of radiating fluids.« less

Biological treatment of produced water in a sequencing batch reactor by a consortium of isolated halophilic microorganisms.

PubMed

Pendashteh, A R; Fakhru'l-Razi, A; Chuah, T G; Radiah, A B Dayang; Madaeni, S S; Zurina, Z A

2010-10-01

Produced water or oilfield wastewater is the largest volume ofa waste stream associated with oil and gas production. The aim of this study was to investigate the biological pretreatment of synthetic and real produced water in a sequencing batch reactor (SBR) to remove hydrocarbon compounds. The SBR was inoculated with isolated tropical halophilic microorganisms capable of degrading crude oil. A total sequence of 24 h (60 min filling phase; 21 h aeration; 60 min settling and 60 min decant phase) was employed and studied. Synthetic produced water was treated with various organic loading rates (OLR) (0.9 kg COD m(-3) d(-1), 1.8 kg COD m(-3) d(-1) and 3.6 kg COD m(-3) d(-1)) and different total dissolved solids (TDS) concentration (35,000 mg L(-1), 100,000 mg L(-1), 150,000 mg L(-1), 200,000 mg L(-1) and 250,000 mg L(-1)). It was found that with an OLR of 0.9 kg COD m(-3) d(-1) and 1.8 kg COD m(-3) d(-1), average oil and grease (O&G) concentrations in the effluent were 7 mg L(-1) and 12 mg L(-1), respectively. At TDS concentration of 35,000 mg L(-1) and at an OLR of 1.8 kg COD m(-3)d(-1), COD and O&G removal efficiencies were more than 90%. However, with increase in salt content to 250,000 mg L(-1), COD and O&G removal efficiencies decreased to 74% and 63%, respectively. The results of biological treatment of real produced water showed that the removal rates of the main pollutants of wastewater, such as COD, TOC and O&G, were above 81%, 83%, and 85%, respectively.

Effect of salinity on extracellular polymeric substances of activated sludge from an anoxic-aerobic sequencing batch reactor.

PubMed

Wang, Zichao; Gao, Mengchun; Wang, Zhe; She, Zonglian; Chang, Qingbo; Sun, Changqing; Zhang, Jian; Ren, Yun; Yang, Ning

2013-11-01

The effect of salinity on extracellular polymeric substances (EPS) of activated sludge was investigated in an anoxic-aerobic sequencing batch reactor (SBR). The contents of loosely bound EPS (LB-EPS) and tightly bound EPS (TB-EPS) were positively correlated with the salinity. The polysaccharide (PS) and protein (PN) contents in both LB-EPS and TB-EPS increased with the increase of salinity. With the increase of salinity from 0.5% to 6%, the PN/PS ratios in LB-EPS and TB-EPS decreased from 4.8 to 0.9 and from 2.9 to 1.4, respectively. The four fluorescence peaks in both LB-EPS and TB-EPS identified by three-dimensional excitation-emission matrix fluorescence spectroscopy are attributed to PN-like substances and humic acid-like substances. The Fourier transform infrared spectra of the LB-EPS and TB-EPS appeared to be very similar, but the differences across the spectra were apparent in terms of the relative intensity of some bands with the increase of salinity. The sludge volume index showed a linear correlation with LB-EPS (R(2)=0.9479) and TB-EPS (R(2)=0.9355) at different salinities, respectively. Copyright © 2013 Elsevier Ltd. All rights reserved.

[Pilot-scale cultivation of Spirulina plantensis with digested piggery wastewater ].

PubMed

Guo, Qing-qing; Liu, Rui; Luo, Jin-fei; Wang, Gen-rong; Chen, Lii-jun; Liu, Xiao

2014-09-01

The swine waste pretreated with coagulation sedimentation was used for the outdoor pilot-scale cultivation of Spirulina platensis isolated from digested piggery wastewater (DPW) in a raceway pond. The growth of S. platensis and removal of nitrogen/ phosphorus were studied, moreover, the conversion efficiency of total nitrogen (TN) or total phosphorus (TP) from DPW to S. platensis was calculated. On this basis, the existing problems and countermeasures during outdoor pilot-scale culture were analyzed and summarized combined with the laboratory research. We conducted 6 batches culture experiments, only 3 of which could reach the S. platensis harvest requirements (D560 >0. 8). Meanwhile, the 3 successful batches achieved removal of COD, ammonia nitrogen, TN, TP with corresponding 28. 6% -48. 5% , 0.4% -48. 5% , 41. 8% -48. 6% , 14. 3% -94. 5% , and the conversion efficiency of TN or TP from DPW to S. platensis reached 12. 1% -98. 5% , 21.2% -83.7% , respectively. High concentration of ammonia nitrogen and insect attack of remaining egg hatching in the pretreated swine waste were the main factors to cause the slow-growing of the 3 batches of S. platensis. Therefore, it is highly necessary for the removal of ammonia nitrogen with biological treatment technology and insect eggs with membrane to achieve a stable high productivity.

Results Of Initial Analyses Of The Salt (Macro) Batch 9 Tank 21H Qualification Samples

DOE Office of Scientific and Technical Information (OSTI.GOV)

Peters, T.

2015-10-08

Savannah River National Laboratory (SRNL) analyzed samples from Tank 21H in support of qualification of Interim Salt Disposition Project (ISDP) Salt (Macro) Batch 9 for processing through the Actinide Removal Process (ARP) and the Modular Caustic-Side Solvent Extraction Unit (MCU). This document reports the initial results of the analyses of samples of Tank 21H. Analysis of the Tank 21H Salt (Macro) Batch 9 composite sample indicates that the material does not display any unusual characteristics. Further results on the chemistry and other tests will be issued in the future.

SeqReporter: automating next-generation sequencing result interpretation and reporting workflow in a clinical laboratory.

PubMed

Roy, Somak; Durso, Mary Beth; Wald, Abigail; Nikiforov, Yuri E; Nikiforova, Marina N

2014-01-01

A wide repertoire of bioinformatics applications exist for next-generation sequencing data analysis; however, certain requirements of the clinical molecular laboratory limit their use: i) comprehensive report generation, ii) compatibility with existing laboratory information systems and computer operating system, iii) knowledgebase development, iv) quality management, and v) data security. SeqReporter is a web-based application developed using ASP.NET framework version 4.0. The client-side was designed using HTML5, CSS3, and Javascript. The server-side processing (VB.NET) relied on interaction with a customized SQL server 2008 R2 database. Overall, 104 cases (1062 variant calls) were analyzed by SeqReporter. Each variant call was classified into one of five report levels: i) known clinical significance, ii) uncertain clinical significance, iii) pending pathologists' review, iv) synonymous and deep intronic, and v) platform and panel-specific sequence errors. SeqReporter correctly annotated and classified 99.9% (859 of 860) of sequence variants, including 68.7% synonymous single-nucleotide variants, 28.3% nonsynonymous single-nucleotide variants, 1.7% insertions, and 1.3% deletions. One variant of potential clinical significance was re-classified after pathologist review. Laboratory information system-compatible clinical reports were generated automatically. SeqReporter also facilitated quality management activities. SeqReporter is an example of a customized and well-designed informatics solution to optimize and automate the downstream analysis of clinical next-generation sequencing data. We propose it as a model that may envisage the development of a comprehensive clinical informatics solution. Copyright © 2014 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

Fuel cell performance of palladium-platinum core-shell electrocatalysts synthesized in gram-scale batches

DOE Office of Scientific and Technical Information (OSTI.GOV)

Khateeb, Siddique; Su, Dong; Guerreo, Sandra

This article presents the performance of palladium-platinum core-shell catalysts (Pt/Pd/C) for oxygen reduction synthesized in gram-scale batches in both liquid cells and polymer-electrolyte membrane fuel cells. Core-shell catalyst synthesis and characterization, ink fabrication, and cell assembly details are discussed. The Pt mass activity of the Pt/Pd core-shell catalyst was 0.95 A mg –1 at 0.9 V measured in liquid cells (0.1 M HClO4), which was 4.8 times higher than a commercial Pt/C catalyst. The performances of Pt/Pd/C and Pt/C in large single cells (315 cm 2) were assessed under various operating conditions. The core-shell catalyst showed consistently higher performance thanmore » commercial Pt/C in fuel cell testing. A 20–60 mV improvement across the whole current density range was observed on air. Sensitivities to temperature, humidity, and gas composition were also investigated and the core-shell catalyst showed a consistent benefit over Pt under all conditions. However, the 4.8 times activity enhancement predicated by liquid cell measurements was not fully realized in fuel cells.« less

Fuel cell performance of palladium-platinum core-shell electrocatalysts synthesized in gram-scale batches

DOE PAGES

Khateeb, Siddique; Su, Dong; Guerreo, Sandra; ...

2016-05-03

This article presents the performance of palladium-platinum core-shell catalysts (Pt/Pd/C) for oxygen reduction synthesized in gram-scale batches in both liquid cells and polymer-electrolyte membrane fuel cells. Core-shell catalyst synthesis and characterization, ink fabrication, and cell assembly details are discussed. The Pt mass activity of the Pt/Pd core-shell catalyst was 0.95 A mg –1 at 0.9 V measured in liquid cells (0.1 M HClO4), which was 4.8 times higher than a commercial Pt/C catalyst. The performances of Pt/Pd/C and Pt/C in large single cells (315 cm 2) were assessed under various operating conditions. The core-shell catalyst showed consistently higher performance thanmore » commercial Pt/C in fuel cell testing. A 20–60 mV improvement across the whole current density range was observed on air. Sensitivities to temperature, humidity, and gas composition were also investigated and the core-shell catalyst showed a consistent benefit over Pt under all conditions. However, the 4.8 times activity enhancement predicated by liquid cell measurements was not fully realized in fuel cells.« less

Comparison of batch and column tests for the elution of artificial turf system components.

PubMed

Krüger, O; Kalbe, U; Berger, W; Nordhauβ, K; Christoph, G; Walzel, H-P

2012-12-18

Synthetic athletic tracks and turf areas for outdoor sporting grounds may release contaminants due to the chemical composition of some components. A primary example is that of zinc from reused scrap tires (main constituent, styrene butadiene rubber, SBR), which might be harmful to the environment. Thus, methods for the risk assessment of those materials are required. Laboratory leaching methods like batch and column tests are widely used to examine the soil-groundwater pathway. We tested several components for artificial sporting grounds with batch tests at a liquid to solid (LS) ratio of 2 L/kg and column tests with an LS up to 26.5 L/kg. We found a higher zinc release in the batch test eluates for all granules, ranging from 15% higher to 687% higher versus data from column tests for SBR granules. Accompanying parameters, especially the very high turbidity of one ethylene propylene diene monomer rubber (EPDM) or thermoplastic elastomer (TPE) eluates, reflect the stronger mechanical stress of batch testing. This indicates that batch test procedures might not be suitable for the risk assessment of synthetic sporting ground components. Column tests, on the other hand, represent field conditions more closely and allow for determination of time-dependent contaminants release.

Sequence Diversity, Intersubgroup Relationships, and Origins of the Mouse Leukemia Gammaretroviruses of Laboratory and Wild Mice.

PubMed

Bamunusinghe, Devinka; Naghashfar, Zohreh; Buckler-White, Alicia; Plishka, Ronald; Baliji, Surendranath; Liu, Qingping; Kassner, Joshua; Oler, Andrew J; Hartley, Janet; Kozak, Christine A

2016-04-01

Mouse leukemia viruses (MLVs) are found in the common inbred strains of laboratory mice and in the house mouse subspecies ofMus musculus Receptor usage and envelope (env) sequence variation define three MLV host range subgroups in laboratory mice: ecotropic, polytropic, and xenotropic MLVs (E-, P-, and X-MLVs, respectively). These exogenous MLVs derive from endogenous retroviruses (ERVs) that were acquired by the wild mouse progenitors of laboratory mice about 1 million years ago. We analyzed the genomes of seven MLVs isolated from Eurasian and American wild mice and three previously sequenced MLVs to describe their relationships and identify their possible ERV progenitors. The phylogenetic tree based on the receptor-determining regions ofenvproduced expected host range clusters, but these clusters are not maintained in trees generated from other virus regions. Colinear alignments of the viral genomes identified segmental homologies to ERVs of different host range subgroups. Six MLVs show close relationships to a small xenotropic ERV subgroup largely confined to the inbred mouse Y chromosome.envvariations define three E-MLV subtypes, one of which carries duplications of various sizes, sequences, and locations in the proline-rich region ofenv Outside theenvregion, all E-MLVs are related to different nonecotropic MLVs. These results document the diversity in gammaretroviruses isolated from globally distributedMussubspecies, provide insight into their origins and relationships, and indicate that recombination has had an important role in the evolution of these mutagenic and pathogenic agents. Laboratory mice carry mouse leukemia viruses (MLVs) of three host range groups which were acquired from their wild mouse progenitors. We sequenced the complete genomes of seven infectious MLVs isolated from geographically separated Eurasian and American wild mice and compared them with endogenous germ line retroviruses (ERVs) acquired early in house mouse evolution. We did this

Conversion of H2 and CO2 to CH4 and acetate in fed-batch biogas reactors by mixed biogas community: a novel route for the power-to-gas concept.

PubMed

Szuhaj, Márk; Ács, Norbert; Tengölics, Roland; Bodor, Attila; Rákhely, Gábor; Kovács, Kornél L; Bagi, Zoltán

2016-01-01

Applications of the power-to-gas principle for the handling of surplus renewable electricity have been proposed. The feasibility of using hydrogenotrophic methanogens as CH4 generating catalysts has been demonstrated. Laboratory and scale-up experiments have corroborated the benefits of the CO2 mitigation via biotechnological conversion of H2 and CO2 to CH4. A major bottleneck in the process is the gas-liquid mass transfer of H2. Fed-batch reactor configuration was tested at mesophilic temperature in laboratory experiments in order to improve the contact time and H2 mass transfer between the gas and liquid phases. Effluent from an industrial biogas facility served as biocatalyst. The bicarbonate content of the effluent was depleted after some time, but the addition of stoichiometric CO2 sustained H2 conversion for an extended period of time and prevented a pH shift. The microbial community generated biogas from the added α-cellulose substrate with concomitant H2 conversion, but the organic substrate did not facilitate H2 consumption. Fed-batch operational mode allowed a fourfold increase in volumetric H2 load and a 6.5-fold augmentation of the CH4 formation rate relative to the CSTR reactor configuration. Acetate was the major by-product of the reaction. Fed-batch reactors significantly improve the efficiency of the biological power-to-gas process. Besides their storage function, biogas fermentation effluent reservoirs can serve as large-scale bio CH4 reactors. On the basis of this recognition, a novel concept is proposed, which merges biogas technology with other means of renewable electricity production for improved efficiency and sustainability.

A comparison of relative toxicity rankings by some small-scale laboratory tests

NASA Technical Reports Server (NTRS)

Hilado, C. J.; Cumming, H. J.

1977-01-01

Small-scale laboratory tests for fire toxicity, suitable for use in the average laboratory hood, are needed for screening and ranking materials on the basis of relative toxicity. The performance of wool, cotton, and aromatic polyamide under several test procedures is presented.

Batched matrix computations on hardware accelerators based on GPUs

DOE PAGES

Haidar, Azzam; Dong, Tingxing; Luszczek, Piotr; ...

2015-02-09

Scientific applications require solvers that work on many small size problems that are independent from each other. At the same time, the high-end hardware evolves rapidly and becomes ever more throughput-oriented and thus there is an increasing need for an effective approach to develop energy-efficient, high-performance codes for these small matrix problems that we call batched factorizations. The many applications that need this functionality could especially benefit from the use of GPUs, which currently are four to five times more energy efficient than multicore CPUs on important scientific workloads. This study, consequently, describes the development of the most common, one-sidedmore » factorizations, Cholesky, LU, and QR, for a set of small dense matrices. The algorithms we present together with their implementations are, by design, inherently parallel. In particular, our approach is based on representing the process as a sequence of batched BLAS routines that are executed entirely on a GPU. Importantly, this is unlike the LAPACK and the hybrid MAGMA factorization algorithms that work under drastically different assumptions of hardware design and efficiency of execution of the various computational kernels involved in the implementation. Thus, our approach is more efficient than what works for a combination of multicore CPUs and GPUs for the problems sizes of interest of the application use cases. The paradigm where upon a single chip (a GPU or a CPU) factorizes a single problem at a time is not at all efficient in our applications’ context. We illustrate all of these claims through a detailed performance analysis. With the help of profiling and tracing tools, we guide our development of batched factorizations to achieve up to two-fold speedup and three-fold better energy efficiency as compared against our highly optimized batched CPU implementations based on MKL library. Finally, the tested system featured two sockets of Intel Sandy Bridge CPUs and we

Room-Temperature C-H Functionalization Sequence under Benchtop Conditions for the Undergraduate Chemistry Laboratory

ERIC Educational Resources Information Center

Chen, Shuming

2018-01-01

An iridium(III)-mediated C-H functionalization sequence involving a concerted cyclometalation-deprotonation/migratory insertion pathway is reported for the undergraduate chemistry laboratory. The air- and water-stable iridacycle intermediates are readily isolated and characterized by NMR spectroscopy. Both steps of the experiment are performed at…

Long-term effects of nickel oxide nanoparticles on performance, microbial enzymatic activity, and microbial community of a sequencing batch reactor.

PubMed

Wang, Sen; Li, Zhiwei; Gao, Mengchun; She, Zonglian; Guo, Liang; Zheng, Dong; Zhao, Yangguo; Ma, Bingrui; Gao, Feng; Wang, Xuejiao

2017-02-01

The nitrogen and phosphorus removal, microbial enzymatic activity, and microbial community of a sequencing batch reactor (SBR) were evaluated under long-term exposure to nickel oxide nanoparticles (NiO NPs). High NiO NP concentration (over 5 mg L -1 ) affected the removal of chemical oxygen demand, nitrogen, and phosphorus. The presence of NiO NP inhibited the microbial enzymatic activities and reduced the nitrogen and phosphorus removal rates of activated sludge. The microbial enzymatic activities of the activated sludge showed a similar variation trend to the nitrogen and phosphorus removal rates with the increase in NiO NP concentration from 0 to 60 mg L -1 . The Ni content in the effluent and activated sludge showed an increasing trend with the increase in NiO NP concentration. Some NiO NPs were absorbed on the sludge surface or penetrate the cell membrane into the interior of microbial cells in the activated sludge. NiO NP facilitated the increase in reactive oxygen species by disturbing the balance between the oxidation and anti-oxidation processes, and the variation in lactate dehydrogenase demonstrated that NiO NP could destroy the cytomembrane and cause variations in the microbial morphology and physiological function. High-throughput sequencing demonstrated that the microbial community of SBR had some obvious changes at 0-60 mg L -1 NiO NPs at the phyla, class and genus levels. Copyright © 2016 Elsevier Ltd. All rights reserved.

Operation optimization of a photo-sequencing batch reactor for wastewater treatment: Study on influencing factors and impact on symbiotic microbial ecology.

PubMed

Ye, Jianfeng; Liang, Junyu; Wang, Liang; Markou, Giorgos; Jia, Qilong

2018-03-01

Wastewater treatment technology with better energy efficiency and recyclability is in urgent demand. Photo-Sequencing batch reactor (SBR), which introduces microalgae into conventional SBR, is considered to have more potential for resource recycling. In this study, a photo-SBR was evaluated through the manipulation of several key operational parameters, i.e., aeration strength, light supply intensity and time per cycle, and solid retention time (SRT). The algal-bacterial symbiotic system had the potential of removing COD, NH 4 + -N and TN with limited aeration, representing the advantage of energy-saving by low aeration requirement. Maintaining appropriate proportion of microalgae in the symbiotic system is critical for good system performance. Introducing microalgae into conventional SBR has obvious impact on the original microbial ecology. When the concentration of microalgae is too high (>4.60 mg Chl/L), the inhibition on certain phyla of bacteria, e.g., Bacteroidetes and Actinobacteria, would become prominent and not conducive to the stable operation. Copyright © 2017 Elsevier Ltd. All rights reserved.

Laboratory and pilot-scale bioremediation of pentaerythritol tetranitrate (PETN) contaminated soil.

PubMed

Zhuang, Li; Gui, Lai; Gillham, Robert W; Landis, Richard C

2014-01-15

PETN (pentaerythritol tetranitrate), a munitions constituent, is commonly encountered in munitions-contaminated soils, and pose a serious threat to aquatic organisms. This study investigated anaerobic remediation of PETN-contaminated soil at a site near Denver Colorado. Both granular iron and organic carbon amendments were used in both laboratory and pilot-scale tests. The laboratory results showed that, with various organic carbon amendments, PETN at initial concentrations of between 4500 and 5000mg/kg was effectively removed within 84 days. In the field trial, after a test period of 446 days, PETN mass removal of up to 53,071mg/kg of PETN (80%) was achieved with an organic carbon amendment (DARAMEND) of 4% by weight. In previous laboratory studies, granular iron has shown to be highly effective in degrading PETN. However, for both the laboratory and pilot-scale tests, granular iron was proven to be ineffective. This was a consequence of passivation of the iron surfaces caused by the very high concentrations of nitrate in the contaminated soil. This study indicated that low concentration of organic carbon was a key factor limiting bioremediation of PETN in the contaminated soil. Furthermore, the addition of organic carbon amendments such as the DARAMEND materials or brewers grain, proved to be highly effective in stimulating the biodegradation of PETN and could provide the basis for full-scale remediation of PETN-contaminated sites. Copyright © 2013 Elsevier B.V. All rights reserved.

Scheduling algorithm for flow shop with two batch-processing machines and arbitrary job sizes

NASA Astrophysics Data System (ADS)

Cheng, Bayi; Yang, Shanlin; Hu, Xiaoxuan; Li, Kai

2014-03-01

This article considers the problem of scheduling two batch-processing machines in flow shop where the jobs have arbitrary sizes and the machines have limited capacity. The jobs are processed in batches and the total size of jobs in each batch cannot exceed the machine capacity. Once a batch is being processed, no interruption is allowed until all the jobs in it are completed. The problem of minimising makespan is NP-hard in the strong sense. First, we present a mathematical model of the problem using integer programme. We show the scale of feasible solutions of the problem and provide optimality properties. Then, we propose a polynomial time algorithm with running time in O(nlogn). The jobs are first assigned in feasible batches and then scheduled on machines. For the general case, we prove that the proposed algorithm has a performance guarantee of 4. For the special case where the processing times of each job on the two machines satisfy p 1 j = ap 2 j , the performance guarantee is ? for a > 0.

Replicating the microbial community and water quality performance of full-scale slow sand filters in laboratory-scale filters.

PubMed

Haig, Sarah-Jane; Quince, Christopher; Davies, Robert L; Dorea, Caetano C; Collins, Gavin

2014-09-15

Previous laboratory-scale studies to characterise the functional microbial ecology of slow sand filters have suffered from methodological limitations that could compromise their relevance to full-scale systems. Therefore, to ascertain if laboratory-scale slow sand filters (L-SSFs) can replicate the microbial community and water quality production of industrially operated full-scale slow sand filters (I-SSFs), eight cylindrical L-SSFs were constructed and were used to treat water from the same source as the I-SSFs. Half of the L-SSFs sand beds were composed of sterilized sand (sterile) from the industrial filters and the other half with sand taken directly from the same industrial filter (non-sterile). All filters were operated for 10 weeks, with the microbial community and water quality parameters sampled and analysed weekly. To characterize the microbial community phyla-specific qPCR assays and 454 pyrosequencing of the 16S rRNA gene were used in conjunction with an array of statistical techniques. The results demonstrate that it is possible to mimic both the water quality production and the structure of the microbial community of full-scale filters in the laboratory - at all levels of taxonomic classification except OTU - thus allowing comparison of LSSF experiments with full-scale units. Further, it was found that the sand type composing the filter bed (non-sterile or sterile), the water quality produced, the age of the filters and the depth of sand samples were all significant factors in explaining observed differences in the structure of the microbial consortia. This study is the first to the authors' knowledge that demonstrates that scaled-down slow sand filters can accurately reproduce the water quality and microbial consortia of full-scale slow sand filters. Copyright © 2014 Elsevier Ltd. All rights reserved.

Collaborative study for the establishment of erythropoietin BRP batch 4.

PubMed

Burns, C; Bristow, A F; Daas, A; Costanzo, A

2015-01-01

The European Pharmacopoeia (Ph. Eur.) Biological Reference Preparation (BRP) for erythropoietin (EPO) is used as a working standard for potency determination of EPO preparations by in vivo bioassay as prescribed in the Ph. Eur. monograph Erythropoietin concentrated solution (1316). The BRP batch 3 was calibrated in 2006 and its stocks are depleted. The European Directorate for the Quality of Medicines & HealthCare (EDQM) thus initiated a project to calibrate a replacement batch in International Units against the WHO 3(rd) International Standard (IS) for Erythropoietin, recombinant, for bioassay (11/170). A Ph. Eur. Chemical Reference Substance (CRS) was established recently for use as reference in some of the physicochemical tests prescribed in the monograph. Therefore, the EPO BRP batch 4 was only calibrated for the normocythaemic and polycythaemic mouse in vivo bioassays described in the Assay section of the Ph. Eur. monograph (1316). The collaborative study involved seven laboratories from Europe, the USA and South America. The results confirmed that the candidate BRP (cBRP) is suitable for use as a reference preparation in the potency determination of EPO medicinal products by bioassay (using the normocythaemic or polycythaemic mouse methods). The outcome of the study enabled the Ph. Eur. Commission to establish the proposed standard as erythropoietin BRP batch 4 in November 2014 for use as a reference preparation solely for the polycythaemic and normocythaemic mouse bioassay, with an assigned potency of 13 000 IU/vial. Furthermore, the potency of BRP3 was confirmed during the study, thus warranting a good continuity of the IU.

27 CFR 19.748 - Dump/batch records.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Dump/batch records. 19.748... OF THE TREASURY LIQUORS DISTILLED SPIRITS PLANTS Records and Reports Processing Account § 19.748 Dump/batch records. (a) Format of dump/batch records. Proprietor's dump/batch records shall contain, as...

A sequential treatment of intermediate tropical landfill leachate using a sequencing batch reactor (SBR) and coagulation.

PubMed

Yong, Zi Jun; Bashir, Mohammed J K; Ng, Choon Aun; Sethupathi, Sumathi; Lim, Jun-Wei

2018-01-01

The increase in landfill leachate generation is due to the increase of municipal solid waste (MSW) as global development continues. Landfill leachate has constantly been the most challenging issue in MSW management as it contains high amount of organic and inorganic compounds that might cause pollution to water resources. Biologically treated landfill leachate often fails to fulfill the regulatory discharge standards. Thus, to prevent environmental pollution, many landfill leachate treatment plants involve multiple stages treatment process. The Papan Landfill in Perak, Malaysia currently has no proper leachate treatment system. In the current study, sequential treatment via sequencing batch reactor (SBR) followed by coagulation was used to treat chemical oxygen demand (COD), ammoniacal nitrogen (NH 3 -N), total suspended solids (TSS), and colour from raw landfill leachate. SBR optimum aeration rate, L/min, optimal pH and dosage (g/L) of Alum for coagulation as a post-treatment were determined. The two-step sequential treatment by SBR followed by coagulation (Alum) achieved a removal efficiency of 84.89%, 94.25%, 91.82% and 85.81% for COD, NH 3 -N, TSS and colour, respectively. Moreover, the two-stage treatment process achieved 95.0% 95.0%, 95.3%, 100.0%, 87.2%, 62.9%, 50.0%, 41.3%, 41.2, 34.8, and 22.9 removals of Cadmium, Lead, Copper, Selenium, Barium, Iron, Silver, Nickel, Zinc, Arsenic, and Manganese, respectively. Copyright © 2017 Elsevier Ltd. All rights reserved.

Scaling Property of Period-n-Tupling Sequences in One-Dimensional Mappings

NASA Astrophysics Data System (ADS)

Zeng, Wan-Zhen; Hao, Bai-Lin; Wang, Guang-Rui; Chen, Shi-Gang

1984-05-01

We calculated the universal scaling function g(x) and the scaling factor α as well as the convergence rate δ for periodtripling, -quadrapling and-quintupling sequences of RL, RL^2, RLR^2, RL2 R and RL^3 types. The superstable periods are closely connected to a set of polynomial P_n defined recursively by the original mapping. Some notable properties of these polynomials are studied. Several approaches to solving the renormalization group equation and estimating the scaling factors are suggested.

Dynamic control of nutrient-removal from industrial wastewater in a sequencing batch reactor, using common and low-cost online sensors.

PubMed

Dries, Jan

2016-01-01

On-line control of the biological treatment process is an innovative tool to cope with variable concentrations of chemical oxygen demand and nutrients in industrial wastewater. In the present study we implemented a simple dynamic control strategy for nutrient-removal in a sequencing batch reactor (SBR) treating variable tank truck cleaning wastewater. The control system was based on derived signals from two low-cost and robust sensors that are very common in activated sludge plants, i.e. oxidation reduction potential (ORP) and dissolved oxygen. The amount of wastewater fed during anoxic filling phases, and the number of filling phases in the SBR cycle, were determined by the appearance of the 'nitrate knee' in the profile of the ORP. The phase length of the subsequent aerobic phases was controlled by the oxygen uptake rate measured online in the reactor. As a result, the sludge loading rate (F/M ratio), the volume exchange rate and the SBR cycle length adapted dynamically to the activity of the activated sludge and the actual characteristics of the wastewater, without affecting the final effluent quality.

Cloud-based bioinformatics workflow platform for large-scale next-generation sequencing analyses

PubMed Central

Liu, Bo; Madduri, Ravi K; Sotomayor, Borja; Chard, Kyle; Lacinski, Lukasz; Dave, Utpal J; Li, Jianqiang; Liu, Chunchen; Foster, Ian T

2014-01-01

Due to the upcoming data deluge of genome data, the need for storing and processing large-scale genome data, easy access to biomedical analyses tools, efficient data sharing and retrieval has presented significant challenges. The variability in data volume results in variable computing and storage requirements, therefore biomedical researchers are pursuing more reliable, dynamic and convenient methods for conducting sequencing analyses. This paper proposes a Cloud-based bioinformatics workflow platform for large-scale next-generation sequencing analyses, which enables reliable and highly scalable execution of sequencing analyses workflows in a fully automated manner. Our platform extends the existing Galaxy workflow system by adding data management capabilities for transferring large quantities of data efficiently and reliably (via Globus Transfer), domain-specific analyses tools preconfigured for immediate use by researchers (via user-specific tools integration), automatic deployment on Cloud for on-demand resource allocation and pay-as-you-go pricing (via Globus Provision), a Cloud provisioning tool for auto-scaling (via HTCondor scheduler), and the support for validating the correctness of workflows (via semantic verification tools). Two bioinformatics workflow use cases as well as performance evaluation are presented to validate the feasibility of the proposed approach. PMID:24462600

Adaptive Batch Mode Active Learning.

PubMed

Chakraborty, Shayok; Balasubramanian, Vineeth; Panchanathan, Sethuraman

2015-08-01

Active learning techniques have gained popularity to reduce human effort in labeling data instances for inducing a classifier. When faced with large amounts of unlabeled data, such algorithms automatically identify the exemplar and representative instances to be selected for manual annotation. More recently, there have been attempts toward a batch mode form of active learning, where a batch of data points is simultaneously selected from an unlabeled set. Real-world applications require adaptive approaches for batch selection in active learning, depending on the complexity of the data stream in question. However, the existing work in this field has primarily focused on static or heuristic batch size selection. In this paper, we propose two novel optimization-based frameworks for adaptive batch mode active learning (BMAL), where the batch size as well as the selection criteria are combined in a single formulation. We exploit gradient-descent-based optimization strategies as well as properties of submodular functions to derive the adaptive BMAL algorithms. The solution procedures have the same computational complexity as existing state-of-the-art static BMAL techniques. Our empirical results on the widely used VidTIMIT and the mobile biometric (MOBIO) data sets portray the efficacy of the proposed frameworks and also certify the potential of these approaches in being used for real-world biometric recognition applications.

Sequence and batch language programs and alarm-related ``C`` programs for the 242-A MCS. Revision 2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Berger, J.F.

1995-03-01

A Distributive Process Control system was purchased by Project B-534, ``242-A Evaporator/Crystallizer Upgrades``. This control system, called the Monitor and Control System (MCS), was installed in the 242-A Evaporator located in the 200 East Area. The purpose of the MCS is to monitor and control the Evaporator and monitor a number of alarms and other signals from various Tank Farm facilities. Applications software for the MCS was developed by the Waste Treatment Systems Engineering (WTSE) group of Westinghouse. The standard displays and alarm scheme provide for control and monitoring, but do not directly indicate the signal location or depict themore » overall process. To do this, WTSE developed a second alarm scheme which uses special programs, annunciator keys, and process graphics. The special programs are written in two languages; Sequence and Batch Language (SABL), and ``C`` language. The WTSE-developed alarm scheme works as described below: SABL relates signals and alarms to the annunciator keys, called SKID keys. When an alarm occurs, a SABL program causes a SKID key to flash, and if the alarm is of yellow or white priority then a ``C`` program turns on an audible horn (the D/3 system uses a different audible horn for the red priority alarms). The horn and flashing key draws the attention of the operator.« less

Powdered ZELIAC augmented sequencing batch reactors (SBR) process for co-treatment of landfill leachate and domestic wastewater.

PubMed

Mojiri, Amin; Aziz, Hamidi Abdul; Zaman, Nastaein Q; Aziz, Shuokr Qarani; Zahed, Mohammad Ali

2014-06-15

Sequencing batch reactor (SBR) is one of the various methods of biological treatments used for treating wastewater and landfill leachate. This study investigated the treatment of landfill leachate and domestic wastewater by adding a new adsorbent (powdered ZELIAC; PZ) to the SBR technique. ZELIAC consists of zeolite, activated carbon, lime stone, rice husk ash, and Portland cement. The response surface methodology and central composite design were used to elucidate the nature of the response surface in the experimental design and describe the optimum conditions of the independent variables, including aeration rate (L/min), contact time (h), and ratio of leachate to wastewater mixture (%; v/v), as well as their responses (dependent variables). Appropriate conditions of operating variables were also optimized to predict the best value of responses. To perform an adequate analysis of the aerobic process, four dependent parameters, namely, chemical oxygen demand (COD), color, ammonia-nitrogen (NH3-N), and phenols, were measured as responses. The results indicated that the PZ-SBR showed higher performance in removing certain pollutants compared with SBR. Given the optimal conditions of aeration rate (1.74 L/min), leachate to wastewater ratio (20%), and contact time (10.31 h) for the PZ-SBR, the removal efficiencies for color, NH3-N, COD, and phenols were 84.11%, 99.01%, 72.84%, and 61.32%, respectively. Copyright © 2014 Elsevier Ltd. All rights reserved.

The proximal-to-distal sequence in upper-limb motions on multiple levels and time scales.

PubMed

Serrien, Ben; Baeyens, Jean-Pierre

2017-10-01

The proximal-to-distal sequence is a phenomenon that can be observed in a large variety of motions of the upper limbs in both humans and other mammals. The mechanisms behind this sequence are not completely understood and motor control theories able to explain this phenomenon are currently incomplete. The aim of this narrative review is to take a theoretical constraints-led approach to the proximal-to-distal sequence and provide a broad multidisciplinary overview of relevant literature. This sequence exists at multiple levels (brain, spine, muscles, kinetics and kinematics) and on multiple time scales (motion, motor learning and development, growth and possibly even evolution). We hypothesize that the proximodistal spatiotemporal direction on each time scale and level provides part of the organismic constraints that guide the dynamics at the other levels and time scales. The constraint-led approach in this review may serve as a first onset towards integration of evidence and a framework for further experimentation to reveal the dynamics of the proximal-to-distal sequence. Copyright © 2017 Elsevier B.V. All rights reserved.

Passive flux meter measurement of water and nutrient flux in saturated porous media: bench-scale laboratory tests.

PubMed

Cho, Jaehyun; Annable, Michael D; Jawitz, James W; Hatfield, Kirk

2007-01-01

The passive nutrient flux meter (PNFM) is introduced for simultaneous measurement of both water and nutrient flux through saturated porous media. The PNFM comprises a porous sorbent pre-equilibrated with a suite of alcohol tracers, which have different partitioning coefficients. Water flux was estimated based on the loss of loaded resident tracers during deployment, while nutrient flux was quantified based on the nutrient solute mass captured on the sorbent. An anionic resin, Lewatit 6328 A, was used as a permeable sorbent and phosphate (PO4(3-)) was the nutrient studied. The phosphate sorption capacity of the resin was measured in batch equilibration tests as 56 mg PO4(3-) g(-1), which was determined to be adequate capacity to retain PO4(3-) loads intercepted over typical PNFM deployment periods in most natural systems. The PNFM design was validated with bench-scale laboratory tests for a range of 9.8 to 28.3 cm d(-1) Darcy velocities and 6 to 43 h deployment durations. Nutrient and water fluxes measured by the PNFM averaged within 6 and 12% of the applied values, respectively, indicating that the PNFM shows promise as a tool for simultaneous measurement of water and nutrient fluxes.

Rapid formation and pollutant removal ability of aerobic granules in a sequencing batch airlift reactor at low temperature.

PubMed

Jiang, Yu; Shang, Yu; Wang, Hongyu; Yang, Kai

2016-12-01

The start-up of an aerobic granular sludge (AGS) reactor at low temperature was more difficult than at ambient temperature.The rapid formation and characteristics of AGS in a sequencing batch airlift reactor at low temperature were investigated. The nutrient removal ability of the system was also evaluated. It was found that compact granules with clear boundary were formed within 10 days and steady state was achieved within 25 days. The settling properties of sludge were improved with the increasing secretion of extracellular polymeric substances and removal performances of pollutants were enhanced along with granulation. The average removal efficiencies of COD, NH4(+)-N, total nitrogen (TN), total phosphorus (TP) after aerobic granules maturing were over 90.9%, 94.7%, 75.4%, 80.2%, respectively. The rise of temperature had little impact on pollutant biodegradation while the variation of dissolved oxygen caused obvious changes in TN and TP removal rates. COD concentrations of effluents were below 30 mg l(-1) in most cycles of operation with a wide range of organic loading rates (0.6-3.0 kg COD m(-3) d(-1)). The rapid granulation and good performance of pollutant reduction by the system might provide an alternate for wastewater treatment in cold regions.

Enhancing nitrogen removal from low carbon to nitrogen ratio wastewater by using a novel sequencing batch biofilm reactor.

PubMed

Zou, Jinte; Li, Jun; Ni, Yongjiong; Wei, Su

2016-12-01

Removing nitrogen from wastewater with low chemical oxygen demand/total nitrogen (COD/TN) ratio is a difficult task due to the insufficient carbon source available for denitrification. Therefore, in the present work, a novel sequencing batch biofilm reactor (NSBBR) was developed to enhance the nitrogen removal from wastewater with low COD/TN ratio. The NSBBR was divided into two units separated by a vertical clapboard. Alternate feeding and aeration was performed in the two units, which created an anoxic unit with rich substrate content and an aeration unit deficient in substrate simultaneously. Therefore, the utilization of the influent carbon source for denitrification was increased, leading to higher TN removal compared to conventional SBBR (CSBBR) operation. The results show that the CSBBR removed up to 76.8%, 44.5% and 10.4% of TN, respectively, at three tested COD/TN ratios (9.0, 4.8 and 2.5). In contrast, the TN removal of the NSBBR could reach 81.9%, 60.5% and 26.6%, respectively, at the corresponding COD/TN ratios. Therefore, better TN removal performance could be achieved in the NSBBR, especially at low COD/TN ratios (4.8 and 2.5). Furthermore, it is easy to upgrade a CSBBR into an NSBBR in practice. Copyright © 2016. Published by Elsevier B.V.

Medication waste reduction in pediatric pharmacy batch processes.

PubMed

Toerper, Matthew F; Veltri, Michael A; Hamrock, Eric; Mollenkopf, Nicole L; Holt, Kristen; Levin, Scott

2014-04-01

To inform pediatric cart-fill batch scheduling for reductions in pharmaceutical waste using a case study and simulation analysis. A pre and post intervention and simulation analysis was conducted during 3 months at a 205-bed children's center. An algorithm was developed to detect wasted medication based on time-stamped computerized provider order entry information. The algorithm was used to quantify pharmaceutical waste and associated costs for both preintervention (1 batch per day) and postintervention (3 batches per day) schedules. Further, simulation was used to systematically test 108 batch schedules outlining general characteristics that have an impact on the likelihood for waste. Switching from a 1-batch-per-day to a 3-batch-per-day schedule resulted in a 31.3% decrease in pharmaceutical waste (28.7% to 19.7%) and annual cost savings of $183,380. Simulation results demonstrate how increasing batch frequency facilitates a more just-in-time process that reduces waste. The most substantial gains are realized by shifting from a schedule of 1 batch per day to at least 2 batches per day. The simulation exhibits how waste reduction is also achievable by avoiding batch preparation during daily time periods where medication administration or medication discontinuations are frequent. Last, the simulation was used to show how reducing batch preparation time per batch provides some, albeit minimal, opportunity to decrease waste. The case study and simulation analysis demonstrate characteristics of batch scheduling that may support pediatric pharmacy managers in redesign toward minimizing pharmaceutical waste.

Cadmium removal using Cladophora in batch, semi-batch and flow reactors.

PubMed

Sternberg, Steven P K; Dorn, Ryan W

2002-02-01

This study presents the results of using viable algae to remove cadmium from a synthetic wastewater. In batch and semi-batch tests, a local strain of Cladophora algae removed 80-94% of the cadmium introduced. The flow experiments that followed were conducted using non-local Cladophora parriaudii. Results showed that the alga removed only 12.7(+/-6.4)% of the cadmium introduced into the reactor. Limited removal was the result of insufficient algal quantities and poor contact between the algae and cadmium solution.

Efficient arachidonic acid-rich oil production by Mortierella alpina through a repeated fed-batch fermentation strategy.

PubMed

Ji, Xiao-Jun; Zhang, Ai-Hui; Nie, Zhi-Kui; Wu, Wen-Jia; Ren, Lu-Jing; Huang, He

2014-10-01

Arachidonic acid (ARA)-rich oil production by Mortierella alpina is a long fermentation period needed process due to the low growth rate of the filamentous fungus used. This causes the low productivity of ARA-rich oil and hinders its industrial mass scale production. In the present study, different fed-batch strategies were conducted to shorten the fermentation period. The result showed that compared with the batch culture, the fermentation period was shortened from 7days to 5days with the productivity of ARA-rich oil increased from 0.9g/(L·d) to 1.3g/(L·d) by using the fed-batch fermentation strategy. Furthermore, repeated fed-batch fermentation strategy was adopted to achieve the purpose of continuous production. By using this strategy, the fermentation period was shortened from 40days to 26days in a four cycle repeated fed-batch fermentation. This strategy proved to be convenient and economical for ARA-rich oil commercial production process. Copyright © 2014 Elsevier Ltd. All rights reserved.

Assuring the Quality of Next-Generation Sequencing in Clinical Microbiology and Public Health Laboratories.

PubMed

Gargis, Amy S; Kalman, Lisa; Lubin, Ira M

2016-12-01

Clinical microbiology and public health laboratories are beginning to utilize next-generation sequencing (NGS) for a range of applications. This technology has the potential to transform the field by providing approaches that will complement, or even replace, many conventional laboratory tests. While the benefits of NGS are significant, the complexities of these assays require an evolving set of standards to ensure testing quality. Regulatory and accreditation requirements, professional guidelines, and best practices that help ensure the quality of NGS-based tests are emerging. This review highlights currently available standards and guidelines for the implementation of NGS in the clinical and public health laboratory setting, and it includes considerations for NGS test validation, quality control procedures, proficiency testing, and reference materials. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Medication Waste Reduction in Pediatric Pharmacy Batch Processes

PubMed Central

Veltri, Michael A.; Hamrock, Eric; Mollenkopf, Nicole L.; Holt, Kristen; Levin, Scott

2014-01-01

OBJECTIVES: To inform pediatric cart-fill batch scheduling for reductions in pharmaceutical waste using a case study and simulation analysis. METHODS: A pre and post intervention and simulation analysis was conducted during 3 months at a 205-bed children's center. An algorithm was developed to detect wasted medication based on time-stamped computerized provider order entry information. The algorithm was used to quantify pharmaceutical waste and associated costs for both preintervention (1 batch per day) and postintervention (3 batches per day) schedules. Further, simulation was used to systematically test 108 batch schedules outlining general characteristics that have an impact on the likelihood for waste. RESULTS: Switching from a 1-batch-per-day to a 3-batch-per-day schedule resulted in a 31.3% decrease in pharmaceutical waste (28.7% to 19.7%) and annual cost savings of $183,380. Simulation results demonstrate how increasing batch frequency facilitates a more just-in-time process that reduces waste. The most substantial gains are realized by shifting from a schedule of 1 batch per day to at least 2 batches per day. The simulation exhibits how waste reduction is also achievable by avoiding batch preparation during daily time periods where medication administration or medication discontinuations are frequent. Last, the simulation was used to show how reducing batch preparation time per batch provides some, albeit minimal, opportunity to decrease waste. CONCLUSIONS: The case study and simulation analysis demonstrate characteristics of batch scheduling that may support pediatric pharmacy managers in redesign toward minimizing pharmaceutical waste. PMID:25024671

Effect of sequence of insemination after simultaneous thawing of multiple semen straws on conception rate to timed AI in suckled multiparous Nelore cows.

PubMed

Oliveira, L Z; Arruda, R P; de Andrade, A F C; Santos, R M; Beletti, M E; Peres, R F G; Martins, J P N; de Lima, V F M Hossepian

2012-11-01

The objective was to determine the effect of sequence of insemination after simultaneous thawing of multiple 0.5 mL semen straws on conception rate in suckled multiparous Nelore cows. The effect of this thawing procedure on in vitro sperm characteristics was also evaluated. All cows (N = 944) received the same timed AI protocol. Ten straws (0.5 mL) of frozen semen from the same batch were simultaneously thawed at 36 °C, for a minimum of 30 sec. One straw per cow was used for timed AI. Frozen semen from three Angus bulls was used. Timed AI records included sequence of insemination (first to tenth) and time of semen removal from thawing bath. For laboratory analyses, the same semen batches used in the field experiment were evaluated. Ten frozen straws from the same batch were thawed simultaneously in a thawing unit identical to that used in the field experiment. The following sperm characteristics were analyzed: sperm motility parameters, sperm thermal resistance, plasma and acrosomal membrane integrity, lipid peroxidation, chromatin structure, and sperm morphometry. Based on logistic regression, there were no significant effects of breeding group, body condition score, AI technician, and sire on conception rate, but there was an interaction between sire and straw group (P = 0.002). Semen from only one bull had decreased (P < 0.05) field fertility for the group of straws associated with the longest interval from thawing to AI. However, the results of the laboratory experiment were unable to explain the findings of the field experiment. Sperm width:length ratio of morphometric analysis was the single sperm characteristic with a significant interaction between sire and straw group (P = 0.02). It was concluded that sequence of insemination after simultaneous thawing of 10 semen straws can differently affect conception rates at timed AI, depending on the sire used. Nevertheless, the effects of this thawing environment on in vitro sperm characteristics, remain to be

Batch-to-batch uniformity of bacterial community succession and flavor formation in the fermentation of Zhenjiang aromatic vinegar.

PubMed

Wang, Zong-Min; Lu, Zhen-Ming; Yu, Yong-Jian; Li, Guo-Quan; Shi, Jin-Song; Xu, Zheng-Hong

2015-09-01

Solid-state fermentation of traditional Chinese vinegar is a mixed-culture refreshment process that proceeds for many centuries without spoilage. Here, we investigated bacterial community succession and flavor formation in three batches of Zhenjiang aromatic vinegar using pyrosequencing and metabolomics approaches. Temporal patterns of bacterial succession in the Pei (solid-state vinegar culture) showed no significant difference (P > 0.05) among three batches of fermentation. In all the batches investigated, the average number of community operational taxonomic units (OTUs) decreased dramatically from 119 ± 11 on day 1 to 48 ± 16 on day 3, and then maintained in the range of 61 ± 9 from day 5 to the end of fermentation. We confirmed that, within a batch of fermentation process, the patterns of bacterial diversity between the starter (took from the last batch of vinegar culture on day 7) and the Pei on day 7 were similar (90%). The relative abundance dynamics of two dominant members, Lactobacillus and Acetobacter, showed high correlation (coefficient as 0.90 and 0.98 respectively) among different batches. Furthermore, statistical analysis revealed dynamics of 16 main flavor metabolites were stable among different batches. The findings validate the batch-to-batch uniformity of bacterial community succession and flavor formation accounts for the quality of Zhenjiang aromatic vinegar. Based on our understanding, this is the first study helps to explain the rationality of age-old artistry from a scientific perspective. Copyright © 2015 Elsevier Ltd. All rights reserved.

Laboratory-Scale Evidence for Lightning-Mediated Gene Transfer in Soil

PubMed Central

Demanèche, Sandrine; Bertolla, Franck; Buret, François; Nalin, Renaud; Sailland, Alain; Auriol, Philippe; Vogel, Timothy M.; Simonet, Pascal

2001-01-01

Electrical fields and current can permeabilize bacterial membranes, allowing for the penetration of naked DNA. Given that the environment is subjected to regular thunderstorms and lightning discharges that induce enormous electrical perturbations, the possibility of natural electrotransformation of bacteria was investigated. We demonstrated with soil microcosm experiments that the transformation of added bacteria could be increased locally via lightning-mediated current injection. The incorporation of three genes coding for antibiotic resistance (plasmid pBR328) into the Escherichia coli strain DH10B recipient previously added to soil was observed only after the soil had been subjected to laboratory-scale lightning. Laboratory-scale lightning had an electrical field gradient (700 versus 600 kV m−1) and current density (2.5 versus 12.6 kA m−2) similar to those of full-scale lightning. Controls handled identically except for not being subjected to lightning produced no detectable antibiotic-resistant clones. In addition, simulated storm cloud electrical fields (in the absence of current) did not produce detectable clones (transformation detection limit, 10−9). Natural electrotransformation might be a mechanism involved in bacterial evolution. PMID:11472916

27 CFR 19.598 - Dump/batch records.

Code of Federal Regulations, 2014 CFR

2014-04-01

... ingredients used; (j) Formula number; (k) Quantity of ingredients used in the batch that have been previously... product transferred; (q) Batch gain or loss; and (r) For each batch to be tax determined in accordance...

27 CFR 19.598 - Dump/batch records.

Code of Federal Regulations, 2013 CFR

2013-04-01

... ingredients used; (j) Formula number; (k) Quantity of ingredients used in the batch that have been previously... product transferred; (q) Batch gain or loss; and (r) For each batch to be tax determined in accordance...

27 CFR 19.598 - Dump/batch records.

Code of Federal Regulations, 2011 CFR

2011-04-01

... ingredients used; (j) Formula number; (k) Quantity of ingredients used in the batch that have been previously... product transferred; (q) Batch gain or loss; and (r) For each batch to be tax determined in accordance...

27 CFR 19.598 - Dump/batch records.

Code of Federal Regulations, 2012 CFR

2012-04-01

... ingredients used; (j) Formula number; (k) Quantity of ingredients used in the batch that have been previously... product transferred; (q) Batch gain or loss; and (r) For each batch to be tax determined in accordance...

Mantis: A Fast, Small, and Exact Large-Scale Sequence-Search Index.

PubMed

Pandey, Prashant; Almodaresi, Fatemeh; Bender, Michael A; Ferdman, Michael; Johnson, Rob; Patro, Rob

2018-06-18

Sequence-level searches on large collections of RNA sequencing experiments, such as the NCBI Sequence Read Archive (SRA), would enable one to ask many questions about the expression or variation of a given transcript in a population. Existing approaches, such as the sequence Bloom tree, suffer from fundamental limitations of the Bloom filter, resulting in slow build and query times, less-than-optimal space usage, and potentially large numbers of false-positives. This paper introduces Mantis, a space-efficient system that uses new data structures to index thousands of raw-read experiments and facilitates large-scale sequence searches. In our evaluation, index construction with Mantis is 6× faster and yields a 20% smaller index than the state-of-the-art split sequence Bloom tree (SSBT). For queries, Mantis is 6-108× faster than SSBT and has no false-positives or -negatives. For example, Mantis was able to search for all 200,400 known human transcripts in an index of 2,652 RNA sequencing experiments in 82 min; SSBT took close to 4 days. Copyright © 2018 Elsevier Inc. All rights reserved.

European external quality control study on the competence of laboratories to recognize rare sequence variants resulting in unusual genotyping results.

PubMed

Márki-Zay, János; Klein, Christoph L; Gancberg, David; Schimmel, Heinz G; Dux, László

2009-04-01

Depending on the method used, rare sequence variants adjacent to the single nucleotide polymorphism (SNP) of interest may cause unusual or erroneous genotyping results. Because such rare variants are known for many genes commonly tested in diagnostic laboratories, we organized a proficiency study to assess their influence on the accuracy of reported laboratory results. Four external quality control materials were processed and sent to 283 laboratories through 3 EQA organizers for analysis of the prothrombin 20210G>A mutation. Two of these quality control materials contained sequence variants introduced by site-directed mutagenesis. One hundred eighty-nine laboratories participated in the study. When samples gave a usual result with the method applied, the error rate was 5.1%. Detailed analysis showed that more than 70% of the failures were reported from only 9 laboratories. Allele-specific amplification-based PCR had a much higher error rate than other methods (18.3% vs 2.9%). The variants 20209C>T and [20175T>G; 20179_20180delAC] resulted in unusual genotyping results in 67 and 85 laboratories, respectively. Eighty-three (54.6%) of these unusual results were not recognized, 32 (21.1%) were attributed to technical issues, and only 37 (24.3%) were recognized as another sequence variant. Our findings revealed that some of the participating laboratories were not able to recognize and correctly interpret unusual genotyping results caused by rare SNPs. Our study indicates that the majority of the failures could be avoided by improved training and careful selection and validation of the methods applied.

The PerkinElmer Omics Laboratory (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

ScienceCinema

Smith, Todd

2017-12-22

Todd Smith of the PerkinElmer Omics Laboratory gives a talk about his lab and its work at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

The PerkinElmer Omics Laboratory (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smith, Todd

2012-06-01

Todd Smith of the PerkinElmer Omics Laboratory gives a talk about his lab and its work at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

Cloud-based bioinformatics workflow platform for large-scale next-generation sequencing analyses.

PubMed

Liu, Bo; Madduri, Ravi K; Sotomayor, Borja; Chard, Kyle; Lacinski, Lukasz; Dave, Utpal J; Li, Jianqiang; Liu, Chunchen; Foster, Ian T

2014-06-01

Due to the upcoming data deluge of genome data, the need for storing and processing large-scale genome data, easy access to biomedical analyses tools, efficient data sharing and retrieval has presented significant challenges. The variability in data volume results in variable computing and storage requirements, therefore biomedical researchers are pursuing more reliable, dynamic and convenient methods for conducting sequencing analyses. This paper proposes a Cloud-based bioinformatics workflow platform for large-scale next-generation sequencing analyses, which enables reliable and highly scalable execution of sequencing analyses workflows in a fully automated manner. Our platform extends the existing Galaxy workflow system by adding data management capabilities for transferring large quantities of data efficiently and reliably (via Globus Transfer), domain-specific analyses tools preconfigured for immediate use by researchers (via user-specific tools integration), automatic deployment on Cloud for on-demand resource allocation and pay-as-you-go pricing (via Globus Provision), a Cloud provisioning tool for auto-scaling (via HTCondor scheduler), and the support for validating the correctness of workflows (via semantic verification tools). Two bioinformatics workflow use cases as well as performance evaluation are presented to validate the feasibility of the proposed approach. Copyright © 2014 Elsevier Inc. All rights reserved.

Batch-batch stable microbial community in the traditional fermentation process of huyumei broad bean pastes.

PubMed

Zhu, Linjiang; Fan, Zihao; Kuai, Hui; Li, Qi

2017-09-01

During natural fermentation processes, a characteristic microbial community structure (MCS) is naturally formed, and it is interesting to know about its batch-batch stability. This issue was explored in a traditional semi-solid-state fermentation process of huyumei, a Chinese broad bean paste product. The results showed that this MCS mainly contained four aerobic Bacillus species (8 log CFU per g), including B. subtilis, B. amyloliquefaciens, B. methylotrophicus, and B. tequilensis, and the facultative anaerobe B. cereus with a low concentration (4 log CFU per g), besides a very small amount of the yeast Zygosaccharomyces rouxii (2 log CFU per g). The dynamic change of the MCS in the brine fermentation process showed that the abundance of dominant species varied within a small range, and in the beginning of process the growth of lactic acid bacteria was inhibited and Staphylococcus spp. lost its viability. Also, the MCS and its dynamic change were proved to be highly reproducible among seven batches of fermentation. Therefore, the MCS naturally and stably forms between different batches of the traditional semi-solid-state fermentation of huyumei. Revealing microbial community structure and its batch-batch stability is helpful for understanding the mechanisms of community formation and flavour production in a traditional fermentation. This issue in a traditional semi-solid-state fermentation of huyumei broad bean paste was firstly explored. This fermentation process was revealed to be dominated by a high concentration of four aerobic species of Bacillus, a low concentration of B. cereus and a small amount of Zygosaccharomyces rouxii. Lactic acid bacteria and Staphylococcus spp. lost its viability at the beginning of fermentation. Such the community structure was proved to be highly reproducible among seven batches. © 2017 The Society for Applied Microbiology.

Advances in DNA sequencing technologies for high resolution HLA typing.

PubMed

Cereb, Nezih; Kim, Hwa Ran; Ryu, Jaejun; Yang, Soo Young

2015-12-01

This communication describes our experience in large-scale G group-level high resolution HLA typing using three different DNA sequencing platforms - ABI 3730 xl, Illumina MiSeq and PacBio RS II. Recent advances in DNA sequencing technologies, so-called next generation sequencing (NGS), have brought breakthroughs in deciphering the genetic information in all living species at a large scale and at an affordable level. The NGS DNA indexing system allows sequencing multiple genes for large number of individuals in a single run. Our laboratory has adopted and used these technologies for HLA molecular testing services. We found that each sequencing technology has its own strengths and weaknesses, and their sequencing performances complement each other. HLA genes are highly complex and genotyping them is quite challenging. Using these three sequencing platforms, we were able to meet all requirements for G group-level high resolution and high volume HLA typing. Copyright © 2015 American Society for Histocompatibility and Immunogenetics. Published by Elsevier Inc. All rights reserved.

An integer batch scheduling model considering learning, forgetting, and deterioration effects for a single machine to minimize total inventory holding cost

NASA Astrophysics Data System (ADS)

Yusriski, R.; Sukoyo; Samadhi, T. M. A. A.; Halim, A. H.

2018-03-01

This research deals with a single machine batch scheduling model considering the influenced of learning, forgetting, and machine deterioration effects. The objective of the model is to minimize total inventory holding cost, and the decision variables are the number of batches (N), batch sizes (Q[i], i = 1, 2, .., N) and the sequence of processing the resulting batches. The parts to be processed are received at the right time and the right quantities, and all completed parts must be delivered at a common due date. We propose a heuristic procedure based on the Lagrange method to solve the problem. The effectiveness of the procedure is evaluated by comparing the resulting solution to the optimal solution obtained from the enumeration procedure using the integer composition technique and shows that the average effectiveness is 94%.

Collaborative study for the calibration of the Ph. Eur. prekallikrein activator in albumin BRP batches 4, 5 and 6.

PubMed

Lackner, F; Daas, A; Terao, E

2015-01-01

An international collaborative study was organised by the European Directorate for the Quality of Medicines & HealthCare (EDQM, Council of Europe) to calibrate replacement batches for the current European Pharmacopoeia (Ph. Eur.) prekallikrein activator (PKA) in albumin biological reference preparation (BRP), whose stocks were dwindling. The study was run in the framework of the Biological Standardisation Programme (BSP) of the Council of Europe and the European Union (EU) Commission. Twenty three laboratories from official medicines control authorities and manufacturers in Europe and outside Europe took part in the study. Three candidate replacement batches were produced from the same material as the one used for the World Health Organization (WHO) 2(nd) International Standard (IS) for PKA in albumin (02/168) and the Ph. Eur. PKA in albumin BRP batches 1, 2 and 3. Participants were requested to evaluate the candidate batches against the current WHO IS using their routine assay method. The Ph. Eur. PKA in albumin BRP batch 3 (BRP3) was also included in the test panel to ensure the continuity of the consecutive BRP batches. The study confirmed the stability of the PKA content of the current BRP3. The candidate batches were found to be comparable. Previous data on the starting material support its high stability. Thermal stress study on the candidate batches confirmed the stability of their PKA activity. The Commission of the Ph. Eur. officially adopted in November 2013 the 3 candidate batches as Ph. Eur. PKA in albumin BRP batches 4, 5 and 6 with an assigned content of 38 IU/vial. The activity of the 3 new batches of Ph. Eur. PKA in albumin BRP will be regularly monitored.

Conjugated Polymers Via Direct Arylation Polymerization in Continuous Flow: Minimizing the Cost and Batch-to-Batch Variations for High-Throughput Energy Conversion.

PubMed

Gobalasingham, Nemal S; Carlé, Jon E; Krebs, Frederik C; Thompson, Barry C; Bundgaard, Eva; Helgesen, Martin

2017-11-01

Continuous flow methods are utilized in conjunction with direct arylation polymerization (DArP) for the scaled synthesis of the roll-to-roll compatible polymer, poly[(2,5-bis(2-hexyldecyloxy)phenylene)-alt-(4,7-di(thiophen-2-yl)-benzo[c][1,2,5]thiadiazole)] (PPDTBT). PPDTBT is based on simple, inexpensive, and scalable monomers using thienyl-flanked benzothiadiazole as the acceptor, which is the first β-unprotected substrate to be used in continuous flow via DArP, enabling critical evaluation of the suitability of this emerging synthetic method for minimizing defects and for the scaled synthesis of high-performance materials. To demonstrate the usefulness of the method, DArP-prepared PPDTBT via continuous flow synthesis is employed for the preparation of indium tin oxide (ITO)-free and flexible roll-coated solar cells to achieve a power conversion efficiency of 3.5% for 1 cm 2 devices, which is comparable to the performance of PPDTBT polymerized through Stille cross coupling. These efforts demonstrate the distinct advantages of the continuous flow protocol with DArP avoiding use of toxic tin chemicals, reducing the associated costs of polymer upscaling, and minimizing batch-to-batch variations for high-quality material. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A direct comparison of U.S. Environmental Protection Agency's method 304B and batch tests for determining activated-sludge biodegradation rate constants for volatile organic compounds

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cano, M.L.; Wilcox, M.E.; Compernolle, R. van

Biodegradation rate constants for volatile organic compounds (VOCs) in activated-sludge systems are needed to quantify emissions. One current US environmental Protection Agency method for determining a biodegradation rate constant is Method 304B. In this approach, a specific activated-sludge unit is simulated by a continuous biological treatment system with a sealed headspace. Batch experiments, however, can be alternatives to Method 304B. Two of these batch methods are the batch test that uses oxygen addition (BOX) and the serum bottle test (SBT). In this study, Method 304B was directly compared to BOX and SBT experiments. A pilot-scale laboratory reactor was constructed tomore » serve as the Method 304B unit. Biomass from the unit was also used to conduct BOX and modified SBT experiments (modification involved use of a sealed draft-tube reactor with a headspace recirculation pump instead of a serum bottle) for 1,2-dichloroethane, diisopropyl ether, methyl tertiary butyl ether, and toluene. Three experimental runs--each consisting of one Method 304B experiment, one BOX experiment, and one modified SBT experiment--were completed. The BOX and SBT data for each run were analyzed using a Monod model, and best-fit biodegradation kinetic parameters were determined for each experiment, including a first-order biodegradation rate constant (K{sub 1}). Experimental results suggest that for readily biodegradable VOCs the two batch techniques can provide improved means of determining biodegradation rate constants compared with Method 304B. In particular, these batch techniques avoid the Method 304B problem associated with steady-state effluent concentrations below analytical detection limits. However, experimental results also suggest that the two batch techniques should not be used to determine biodegradation rate constants for slowly degraded VOCs (i.e., K{sub 1} {lt} 0.1 L/g VSS-h).« less

Ilchulbong tuff cone, Jeju Island, Korea, revisited: A compound monogenetic volcano involving multiple magma batches, shifting vents, and discrete eruptive phases

NASA Astrophysics Data System (ADS)

Sohn, Y.; Brenna, M.; Smith, I. E.; Nemeth, K.; White, J. D.; Murtagh, R.; Jeon, Y.; Kwon, C.; Cronin, S. J.

2010-12-01

Ilchulbong (Sunrise Peak) tuff cone is a UNESCO World Heritage site that owes its scientific importance to the outstanding coastal exposures that surround it. It is also one of the classic sites that provided the sedimentary evidence for the primary pyroclastic processes that occur during phreatomagmatic basaltic eruptions. It has been long considered, based on the cone morphology, that this classic cone was produced via eruption from a single vent site. Reanalysis of the detailed sedimentary sequence has now revealed that two subtle paraconformities occur in this deposition sequence, one representing a significant time break of perhaps days to weeks or months, during which erosion and compaction of the lower cone occurred, the conduit cooled and solidified and a subsequent resumption of eruption took place in a new vent location. Detailed geochemical study of the juvenile clasts through this cone reveals that three separate alkali basaltic magma batches were erupted, the first and third erupted may be genetically related, with the latter showing evidence for longer periods of shallow-level fractionation. The second magma batch erupted was generated in a different mantle source area. Reconstructing the eruption sequence, the lower Ilchulbong cone was formed by eruption of magma 1. Cessation of eruption was accompanied by erosion to generate a volcano-wide unconformity, associated with reworked deposits in the lower cone flanks. The eruption resumed with magma 2 that, due to the cooled earlier conduit, was forced to erupt in a new site to the west of the initial vent. This formed the middle cone sequence over the initially formed structure. The third magma batch erupted with little or no interval after magma 2 from the same vent location, associated with cone instability and slumping, and making up the deposits of the upper cone. These results demonstrate how critical the examination for sedimentary evidence for time breaks in such eruption sequences is for

Actual Waste Demonstration of the Nitric-Glycolic Flowsheet for Sludge Batch 9 Qualification

DOE Office of Scientific and Technical Information (OSTI.GOV)

J. D. Newell; Pareizs, J. M.; Martino, C. J.

For each sludge batch that is processed in the Defense Waste Processing Facility (DWPF), the Savannah River National Laboratory (SRNL) performs qualification testing to demonstrate that the sludge batch is processable. Testing performed by the Savannah River National Laboratory has shown glycolic acid to be effective in replacing the function of formic acid in the DWPF chemical process. The nitric-glycolic flowsheet reduces mercury, significantly lowers the catalytic generation of hydrogen and ammonia which could allow purge reduction in the Sludge Receipt and Adjustment Tank (SRAT), stabilizes the pH and chemistry in the SRAT and the Slurry Mix Evaporator (SME), allowsmore » for effective rheology adjustment, and is favorable with respect to melter flammability. In order to implement the new flowsheet, SRAT and SME cycles, designated SC-18, were performed using a Sludge Batch (SB) 9 slurry blended from SB8 Tank 40H and Tank 51H samples. The SRAT cycle involved adding nitric and glycolic acids to the sludge, refluxing to steam strip mercury, and dewatering to a targeted solids concentration. Data collected during the SRAT cycle included offgas analyses, process temperatures, heat transfer, and pH measurements. The SME cycle demonstrated the addition of glass frit and the replication of six canister decontamination additions. The demonstration concluded with dewatering to a targeted solids concentration. Data collected during the SME cycle included offgas analyses, process temperatures, heat transfer, and pH measurements. Slurry and condensate samples were collected for subsequent analysis« less

Scale-Up of GRCop: From Laboratory to Rocket Engines

NASA Technical Reports Server (NTRS)

Ellis, David L.

2016-01-01

GRCop is a high temperature, high thermal conductivity copper-based series of alloys designed primarily for use in regeneratively cooled rocket engine liners. It began with laboratory-level production of a few grams of ribbon produced by chill block melt spinning and has grown to commercial-scale production of large-scale rocket engine liners. Along the way, a variety of methods of consolidating and working the alloy were examined, a database of properties was developed and a variety of commercial and government applications were considered. This talk will briefly address the basic material properties used for selection of compositions to scale up, the methods used to go from simple ribbon to rocket engines, the need to develop a suitable database, and the issues related to getting the alloy into a rocket engine or other application.

GIDEP Batching Tool

NASA Technical Reports Server (NTRS)

Fong, Danny; Odell,Dorice; Barry, Peter; Abrahamian, Tomik

2008-01-01

This software provides internal, automated search mechanics of GIDEP (Government- Industry Data Exchange Program) Alert data imported from the GIDEP government Web site. The batching tool allows the import of a single parts list in tab-delimited text format into the local JPL GIDEP database. Delimiters from every part number are removed. The original part numbers with delimiters are compared, as well as the newly generated list without the delimiters. The two lists run against the GIDEP imports, and output any matches. This feature only works with Netscape 2.0 or greater, or Internet Explorer 4.0 or greater. The user selects the browser button to choose a text file to import. When the submit button is pressed, this script will import alerts from the text file into the local JPL GIDEP database. This batch tool provides complete in-house control over exported material and data for automated batch match abilities. The batching tool has the ability to match capabilities of the parts list to tables, and yields results that aid further research and analysis. This provides more control over GIDEP information for metrics and reports information not provided by the government site. This software yields results quickly and gives more control over external data from the government site in order to generate other reports not available from the external source. There is enough space to store years of data. The program relates to risk identification and management with regard to projects and GIDEP alert information encompassing flight parts for space exploration.

Design of two-column batch-to-batch recirculation to enhance performance in ion-exchange chromatography.

PubMed

Persson, Oliver; Andersson, Niklas; Nilsson, Bernt

2018-01-05

Preparative liquid chromatography is a separation technique widely used in the manufacturing of fine chemicals and pharmaceuticals. A major drawback of traditional single-column batch chromatography step is the trade-off between product purity and process performance. Recirculation of impure product can be utilized to make the trade-off more favorable. The aim of the present study was to investigate the usage of a two-column batch-to-batch recirculation process step to increase the performance compared to single-column batch chromatography at a high purity requirement. The separation of a ternary protein mixture on ion-exchange chromatography columns was used to evaluate the proposed process. The investigation used modelling and simulation of the process step, experimental validation and optimization of the simulated process. In the presented case the yield increases from 45.4% to 93.6% and the productivity increases 3.4 times compared to the performance of a batch run for a nominal case. A rapid concentration build-up product can be seen during the first cycles, before the process reaches a cyclic steady-state with reoccurring concentration profiles. The optimization of the simulation model predicts that the recirculated salt can be used as a flying start of the elution, which would enhance the process performance. The proposed process is more complex than a batch process, but may improve the separation performance, especially while operating at cyclic steady-state. The recirculation of impure fractions reduces the product losses and ensures separation of product to a high degree of purity. Copyright © 2017 Elsevier B.V. All rights reserved.

Large-Scale Concatenation cDNA Sequencing

PubMed Central

Yu, Wei; Andersson, Björn; Worley, Kim C.; Muzny, Donna M.; Ding, Yan; Liu, Wen; Ricafrente, Jennifer Y.; Wentland, Meredith A.; Lennon, Greg; Gibbs, Richard A.

1997-01-01

A total of 100 kb of DNA derived from 69 individual human brain cDNA clones of 0.7–2.0 kb were sequenced by concatenated cDNA sequencing (CCS), whereby multiple individual DNA fragments are sequenced simultaneously in a single shotgun library. The method yielded accurate sequences and a similar efficiency compared with other shotgun libraries constructed from single DNA fragments (>20 kb). Computer analyses were carried out on 65 cDNA clone sequences and their corresponding end sequences to examine both nucleic acid and amino acid sequence similarities in the databases. Thirty-seven clones revealed no DNA database matches, 12 clones generated exact matches (≥98% identity), and 16 clones generated nonexact matches (57%–97% identity) to either known human or other species genes. Of those 28 matched clones, 8 had corresponding end sequences that failed to identify similarities. In a protein similarity search, 27 clone sequences displayed significant matches, whereas only 20 of the end sequences had matches to known protein sequences. Our data indicate that full-length cDNA insert sequences provide significantly more nucleic acid and protein sequence similarity matches than expressed sequence tags (ESTs) for database searching. [All 65 cDNA clone sequences described in this paper have been submitted to the GenBank data library under accession nos. U79240–U79304.] PMID:9110174

Enhanced treatment efficiency of an anaerobic sequencing batch reactor (ASBR) for cassava stillage with high solids content.

PubMed

Luo, Gang; Xie, Li; Zhou, Qi

2009-06-01

Cassava stillage is a high strength organic wastewater with high suspended solids (SS) content. The efficiency of cassava stillage treatment using an anaerobic sequencing batch reactor (ASBR) was significantly enhanced by discharging settled sludge to maintain a lower sludge concentration (about 30 g/L) in the reactor. Three hydraulic retention times (HRTs), namely 10 d, 7.5 d, 5 d, were evaluated at this condition. The study demonstrated that at an HRT of 5 d and an organic loading rate (OLR) of 11.3 kg COD/(m(3) d), the total chemical oxygen demand (TCOD) and soluble COD (SCOD) removal efficiency can still be maintained at above 80%. The settleability of digested cassava stillage was improved significantly, and thus only a small amount of settled sludge needed to be discharged to maintain the sludge concentration in the reactor. Furthermore, the performance of ASBR operated at low and high sludge concentration (about 79.5 g/L without sludge discharged) was evaluated at an HRT of 5 d. The TCOD removal efficiency and SS in the effluent were 61% and 21.9 g/L respectively at high sludge concentration, while the values were 85.1% and 2.4 g/L at low sludge concentration. Therefore, low sludge concentration is recommended for ASBR treating cassava stillage at an HRT 5 d due to lower TCOD and SS in the effluent, which could facilitate post-treatment.

Validation of laboratory-scale recycling test method of paper PSA label products

Treesearch

Carl Houtman; Karen Scallon; Richard Oldack

2008-01-01

Starting with test methods and a specification developed by the U.S. Postal Service (USPS) Environmentally Benign Pressure Sensitive Adhesive Postage Stamp Program, a laboratory-scale test method and a specification were developed and validated for pressure-sensitive adhesive labels, By comparing results from this new test method and pilot-scale tests, which have been...

7 CFR 58.728 - Cooking the batch.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 3 2010-01-01 2010-01-01 false Cooking the batch. 58.728 Section 58.728 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (Standards... Procedures § 58.728 Cooking the batch. Each batch of cheese within the cooker, including the optional...

Complete and simultaneous removal of ammonium and m-cresol in a nitrifying sequencing batch reactor.

PubMed

Zepeda, Alejandro; Ben-Youssef, Chérif; Rincón, Susana; Cuervo-López, Flor; Gómez, Jorge

2013-06-01

The kinetic behavior, oxidizing ability and tolerance to m-cresol of a nitrifying sludge exposed to different initial concentrations of m-cresol (0-150 mg C L(-1)) were evaluated in a sequencing batch reactor fed with 50 mg NH4 (+)-N L(-1) and operated during 4 months. Complete removal of ammonium and m-cresol was achieved independently of the initial concentration of aromatic compound in all the assays. Up to 25 mg m-cresol-C L(-1) (C/N ratio of 0.5), the nitrifying yield (Y-NO3 (-)) was 0.86 ± 0.05, indicating that the nitrate was the main product of the process; no biomass growth was detected. From 50 to 150 mg m-cresol-C L(-1) (1.0 ≤ C/N ≤ 3.0), simultaneous microbial growth and partial ammonium-to-nitrate conversion were obtained, reaching a maximum microbial total protein concentration of 0.763 g L(-1) (247 % of its initial value) and the lowest Y-NO3 (-) 0.53 ± 0.01 at 150 mg m-cresol-C L(-1). m-Cresol induced a significant decrease in the values of both specific rates of ammonium and nitrite oxidation, being the ammonium oxidation pathway the mainly inhibited. The nitrifying sludge was able to completely oxidize up to 150 mg m-cresol-C L(-1) by SBR cycle, reaching a maximum specific removal rate of 6.45 g m-cresol g(-1) microbial protein-N h(-1). The number of SBR cycles allowed a metabolic adaptation of the nitrifying consortium since nitrification inhibition decreased and faster oxidation of m-cresol took place throughout the cycles.

Estimation of spatial distribution of quorum sensing signaling in sequencing batch biofilm reactor (SBBR) biofilms.

PubMed

Wang, Jinfeng; Ding, Lili; Li, Kan; Huang, Hui; Hu, Haidong; Geng, Jinju; Xu, Ke; Ren, Hongqiang

2018-01-15

Quorum sensing (QS) signaling, plays a significant role in regulating formation of biofilms in the nature; however, little information about the occurrence and distribution of quorum sensing molecular in the biofilm of carriers has been reported. In this study, distribution of QS signaling molecules (the acylated homoserine lactones-AHLs, and AI-2), extracellular polymeric substances (EPS) and the mechanical properties in sequencing batch biofilm reactor (SBBR) biofilms have been investigated. Using increased centrifugal force, the biofilms were detached into different fractions. The AHLs ranged from 5.2ng/g to 98.3ng/g in different fractions of biofilms, and N-decanoyl-dl-homoserine lactone (C10-HSL) and N-dodecanoyl-dl-homoserine lactone (C12-HSL) in the biofilms obtained at various centrifugal forces displayed significant differences (p<0.01). Interspecies communication signal autoinducer-2(AI-2) in the biofilms ranged from 79.2ng/g to 98.3ng/g. Soluble EPS and loosely bound EPS content in the different fractions of biofilms displayed significant positive relationship with the distribution of C12-HSL (r=0.86, p<0.05). Furthermore, 49.62% of bacteria in the biofilms were positively related with AHLs with 22.76% was significantly positively (p<0.05) related with AHLs. Biofilm adhesion and compliance was the strongest in the tightly-bound biofilm, the weakest in the supernatant/surface biofilm, which was in accordance with the distribution of C12 HSL(r=0.77, p<0.05) and C10-HSL(r=0.75, p<0.05), respectively. This study addressed on better understanding of possible methods for the improvement of wastewater bio-treatment through biofilm application. Copyright © 2017 Elsevier B.V. All rights reserved.

PIMS sequencing extension: a laboratory information management system for DNA sequencing facilities

PubMed Central

2011-01-01

Background Facilities that provide a service for DNA sequencing typically support large numbers of users and experiment types. The cost of services is often reduced by the use of liquid handling robots but the efficiency of such facilities is hampered because the software for such robots does not usually integrate well with the systems that run the sequencing machines. Accordingly, there is a need for software systems capable of integrating different robotic systems and managing sample information for DNA sequencing services. In this paper, we describe an extension to the Protein Information Management System (PIMS) that is designed for DNA sequencing facilities. The new version of PIMS has a user-friendly web interface and integrates all aspects of the sequencing process, including sample submission, handling and tracking, together with capture and management of the data. Results The PIMS sequencing extension has been in production since July 2009 at the University of Leeds DNA Sequencing Facility. It has completely replaced manual data handling and simplified the tasks of data management and user communication. Samples from 45 groups have been processed with an average throughput of 10000 samples per month. The current version of the PIMS sequencing extension works with Applied Biosystems 3130XL 96-well plate sequencer and MWG 4204 or Aviso Theonyx liquid handling robots, but is readily adaptable for use with other combinations of robots. Conclusions PIMS has been extended to provide a user-friendly and integrated data management solution for DNA sequencing facilities that is accessed through a normal web browser and allows simultaneous access by multiple users as well as facility managers. The system integrates sequencing and liquid handling robots, manages the data flow, and provides remote access to the sequencing results. The software is freely available, for academic users, from http://www.pims-lims.org/. PMID:21385349

PIMS sequencing extension: a laboratory information management system for DNA sequencing facilities.

PubMed

Troshin, Peter V; Postis, Vincent Lg; Ashworth, Denise; Baldwin, Stephen A; McPherson, Michael J; Barton, Geoffrey J

2011-03-07

Facilities that provide a service for DNA sequencing typically support large numbers of users and experiment types. The cost of services is often reduced by the use of liquid handling robots but the efficiency of such facilities is hampered because the software for such robots does not usually integrate well with the systems that run the sequencing machines. Accordingly, there is a need for software systems capable of integrating different robotic systems and managing sample information for DNA sequencing services. In this paper, we describe an extension to the Protein Information Management System (PIMS) that is designed for DNA sequencing facilities. The new version of PIMS has a user-friendly web interface and integrates all aspects of the sequencing process, including sample submission, handling and tracking, together with capture and management of the data. The PIMS sequencing extension has been in production since July 2009 at the University of Leeds DNA Sequencing Facility. It has completely replaced manual data handling and simplified the tasks of data management and user communication. Samples from 45 groups have been processed with an average throughput of 10000 samples per month. The current version of the PIMS sequencing extension works with Applied Biosystems 3130XL 96-well plate sequencer and MWG 4204 or Aviso Theonyx liquid handling robots, but is readily adaptable for use with other combinations of robots. PIMS has been extended to provide a user-friendly and integrated data management solution for DNA sequencing facilities that is accessed through a normal web browser and allows simultaneous access by multiple users as well as facility managers. The system integrates sequencing and liquid handling robots, manages the data flow, and provides remote access to the sequencing results. The software is freely available, for academic users, from http://www.pims-lims.org/.

Large-Scale Sequencing: The Future of Genomic Sciences Colloquium

DOE Office of Scientific and Technical Information (OSTI.GOV)

Margaret Riley; Merry Buckley

2009-01-01

Genetic sequencing and the various molecular techniques it has enabled have revolutionized the field of microbiology. Examining and comparing the genetic sequences borne by microbes - including bacteria, archaea, viruses, and microbial eukaryotes - provides researchers insights into the processes microbes carry out, their pathogenic traits, and new ways to use microorganisms in medicine and manufacturing. Until recently, sequencing entire microbial genomes has been laborious and expensive, and the decision to sequence the genome of an organism was made on a case-by-case basis by individual researchers and funding agencies. Now, thanks to new technologies, the cost and effort of sequencingmore » is within reach for even the smallest facilities, and the ability to sequence the genomes of a significant fraction of microbial life may be possible. The availability of numerous microbial genomes will enable unprecedented insights into microbial evolution, function, and physiology. However, the current ad hoc approach to gathering sequence data has resulted in an unbalanced and highly biased sampling of microbial diversity. A well-coordinated, large-scale effort to target the breadth and depth of microbial diversity would result in the greatest impact. The American Academy of Microbiology convened a colloquium to discuss the scientific benefits of engaging in a large-scale, taxonomically-based sequencing project. A group of individuals with expertise in microbiology, genomics, informatics, ecology, and evolution deliberated on the issues inherent in such an effort and generated a set of specific recommendations for how best to proceed. The vast majority of microbes are presently uncultured and, thus, pose significant challenges to such a taxonomically-based approach to sampling genome diversity. However, we have yet to even scratch the surface of the genomic diversity among cultured microbes. A coordinated sequencing effort of cultured organisms is an appropriate place

The bacterial biota of laboratory-reared edible mealworms (Tenebrio molitor L.): From feed to frass.

PubMed

Osimani, Andrea; Milanović, Vesna; Cardinali, Federica; Garofalo, Cristiana; Clementi, Francesca; Pasquini, Marina; Riolo, Paola; Ruschioni, Sara; Isidoro, Nunzio; Loreto, Nino; Franciosi, Elena; Tuohy, Kieran; Petruzzelli, Annalisa; Foglini, Martina; Gabucci, Claudia; Tonucci, Franco; Aquilanti, Lucia

2018-05-02

Tenebrio molitor represents one of the most popular species used for the large-scale conversion of plant biomass into protein and is characterized by high nutritional value. In the present laboratory study, the bacterial biota characterizing a pilot production chain of fresh T. molitor larvae was investigated. To this end, different batches of fresh mealworm larvae, their feeding substrate (wheatmeal) and frass were analyzed by viable microbial counts, PCR-DGGE and Illumina sequencing. Moreover, the occurrence of Coxiella burnetii, Pseudomonas aeruginosa and Shiga toxin-producing E. coli (STEC) was assessed through qualitative real-time PCR assays. Microbial viable counts highlighted low microbial contamination of the wheatmeal, whereas larvae and frass were characterized by high loads of Enterobacteriaceae, lactic acid bacteria, and several species of mesophilic aerobes. Spore-forming bacteria were detected to a lesser extent in all the samples. The combined molecular approach used to profile the microbiota confirmed the low microbial contamination of wheatmeal and allowed the detection of Enterobacter spp., Erwinia spp., Enterococcus spp. and Lactococcus spp. as dominant genera in both larvae and frass. Moreover, Klebsiella spp., Pantoea spp., and Xenorhabdus spp. were found to be in the minority. Entomoplasmatales (including Spiroplasma spp.) constituted a major fraction of the microbiota of one batch of larvae. From the real-time PCR assays, no sample was positive for either C. burnetii or STEC, whereas P. aeruginosa was detected in one sample of frass. Based on the overall results, two sources of microbial contamination were hypothesized, namely feeding with wheatmeal and vertical transmission of microorganisms from mother to offspring. Since mealworms are expected to be eaten as a whole, the overall outcomes collected in this laboratory study discourage the consumption of fresh mealworm larvae. Moreover, microbial loads and the absence of potential pathogens

Predicting the performance uncertainty of a 1-MW pilot-scale carbon capture system after hierarchical laboratory-scale calibration and validation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, Zhijie; Lai, Canhai; Marcy, Peter William

2017-05-01

A challenging problem in designing pilot-scale carbon capture systems is to predict, with uncertainty, the adsorber performance and capture efficiency under various operating conditions where no direct experimental data exist. Motivated by this challenge, we previously proposed a hierarchical framework in which relevant parameters of physical models were sequentially calibrated from different laboratory-scale carbon capture unit (C2U) experiments. Specifically, three models of increasing complexity were identified based on the fundamental physical and chemical processes of the sorbent-based carbon capture technology. Results from the corresponding laboratory experiments were used to statistically calibrate the physical model parameters while quantifying some of theirmore » inherent uncertainty. The parameter distributions obtained from laboratory-scale C2U calibration runs are used in this study to facilitate prediction at a larger scale where no corresponding experimental results are available. In this paper, we first describe the multiphase reactive flow model for a sorbent-based 1-MW carbon capture system then analyze results from an ensemble of simulations with the upscaled model. The simulation results are used to quantify uncertainty regarding the design’s predicted efficiency in carbon capture. In particular, we determine the minimum gas flow rate necessary to achieve 90% capture efficiency with 95% confidence.« less

Effect of residual H2O2 from advanced oxidation processes on subsequent biological water treatment: A laboratory batch study.

PubMed

Wang, Feifei; van Halem, Doris; Liu, Gang; Lekkerkerker-Teunissen, Karin; van der Hoek, Jan Peter

2017-10-01

H 2 O 2 residuals from advanced oxidation processes (AOPs) may have critical impacts on the microbial ecology and performance of subsequent biological treatment processes, but little is known. The objective of this study was to evaluate how H 2 O 2 residuals influence sand systems with an emphasis on dissolved organic carbon (DOC) removal, microbial activity change and bacterial community evolution. The results from laboratory batch studies showed that 0.25 mg/L H 2 O 2 lowered DOC removal by 10% while higher H 2 O 2 concentrations at 3 and 5 mg/L promoted DOC removal by 8% and 28%. A H 2 O 2 dosage of 0.25 mg/L did not impact microbial activity (as measured by ATP) while high H 2 O 2 dosages, 1, 3 and 5 mg/L, resulted in reduced microbial activity of 23%, 37% and 37% respectively. Therefore, DOC removal was promoted by the increase of H 2 O 2 dosage while microbial activity was reduced. The pyrosequencing results illustrated that bacterial communities were dominated by Proteobacteria. The presence of H 2 O 2 showed clear influence on the diversity and composition of bacterial communities, which became more diverse under 0.25 mg/L H 2 O 2 but conversely less diverse when the dosage increased to 5 mg/L H 2 O 2 . Anaerobic bacteria were found to be most sensitive to H 2 O 2 as their growth in batch reactors was limited by both 0.25 and 5 mg/L H 2 O 2 (17-88% reduction). In conclusion, special attention should be given to effects of AOPs residuals on microbial ecology before introducing AOPs as a pre-treatment to biological (sand) processes. Additionally, the guideline on the maximum allowable H 2 O 2 concentration should be properly evaluated. Copyright © 2017 The Author(s). Published by Elsevier Ltd.. All rights reserved.

A novel model-based control strategy for aerobic filamentous fungal fed-batch fermentation processes.

PubMed

Mears, Lisa; Stocks, Stuart M; Albaek, Mads O; Cassells, Benny; Sin, Gürkan; Gernaey, Krist V

2017-07-01

A novel model-based control strategy has been developed for filamentous fungal fed-batch fermentation processes. The system of interest is a pilot scale (550 L) filamentous fungus process operating at Novozymes A/S. In such processes, it is desirable to maximize the total product achieved in a batch in a defined process time. In order to achieve this goal, it is important to maximize both the product concentration, and also the total final mass in the fed-batch system. To this end, we describe the development of a control strategy which aims to achieve maximum tank fill, while avoiding oxygen limited conditions. This requires a two stage approach: (i) calculation of the tank start fill; and (ii) on-line control in order to maximize fill subject to oxygen transfer limitations. First, a mechanistic model was applied off-line in order to determine the appropriate start fill for processes with four different sets of process operating conditions for the stirrer speed, headspace pressure, and aeration rate. The start fills were tested with eight pilot scale experiments using a reference process operation. An on-line control strategy was then developed, utilizing the mechanistic model which is recursively updated using on-line measurements. The model was applied in order to predict the current system states, including the biomass concentration, and to simulate the expected future trajectory of the system until a specified end time. In this way, the desired feed rate is updated along the progress of the batch taking into account the oxygen mass transfer conditions and the expected future trajectory of the mass. The final results show that the target fill was achieved to within 5% under the maximum fill when tested using eight pilot scale batches, and over filling was avoided. The results were reproducible, unlike the reference experiments which show over 10% variation in the final tank fill, and this also includes over filling. The variance of the final tank fill is

HalX: an open-source LIMS (Laboratory Information Management System) for small- to large-scale laboratories.

PubMed

Prilusky, Jaime; Oueillet, Eric; Ulryck, Nathalie; Pajon, Anne; Bernauer, Julie; Krimm, Isabelle; Quevillon-Cheruel, Sophie; Leulliot, Nicolas; Graille, Marc; Liger, Dominique; Trésaugues, Lionel; Sussman, Joel L; Janin, Joël; van Tilbeurgh, Herman; Poupon, Anne

2005-06-01

Structural genomics aims at the establishment of a universal protein-fold dictionary through systematic structure determination either by NMR or X-ray crystallography. In order to catch up with the explosive amount of protein sequence data, the structural biology laboratories are spurred to increase the speed of the structure-determination process. To achieve this goal, high-throughput robotic approaches are increasingly used in all the steps leading from cloning to data collection and even structure interpretation is becoming more and more automatic. The progress made in these areas has begun to have a significant impact on the more 'classical' structural biology laboratories, dramatically increasing the number of individual experiments. This automation creates the need for efficient data management. Here, a new piece of software, HalX, designed as an 'electronic lab book' that aims at (i) storage and (ii) easy access and use of all experimental data is presented. This should lead to much improved management and tracking of structural genomics experimental data.

Results of initial analyses of the salt (macro) batch 9 tank 21H qualification samples

DOE Office of Scientific and Technical Information (OSTI.GOV)

Peters, T. B.

2015-10-01

Savannah River National Laboratory (SRNL) analyzed samples from Tank 21H in support of qualification of Interim Salt Disposition Project (ISDP) Salt (Macro) Batch 9 for processing through the Actinide Removal Process (ARP) and the Modular Caustic-Side Solvent Extraction Unit (MCU). This document reports the initial results of the analyses of samples of Tank 21H. Analysis of the Tank 21H Salt (Macro) Batch 9 composite sample indicates that the material does not display any unusual characteristics or observations, such as floating solids, the presence of large amount of solids, or unusual colors. Further results on the chemistry and other tests willmore » be issued in the future.« less

Recovery of phosphorus and volatile fatty acids from wastewater and food waste with an iron-flocculation sequencing batch reactor and acidogenic co-fermentation.

PubMed

Li, Ruo-Hong; Li, Xiao-Yan

2017-12-01

A sequencing batch reactor-based system was developed for enhanced phosphorus (P) removal and recovery from municipal wastewater. The system consists of an iron-dosing SBR for P precipitation and a side-stream anaerobic reactor for sludge co-fermentation with food waste. During co-fermentation, sludge and food waste undergo acidogenesis, releasing phosphates under acidic conditions and producing volatile fatty acids (VFAs) into the supernatant. A few types of typical food waste were investigated for their effectiveness in acidogenesis and related enzymatic activities. The results show that approximately 96.4% of total P in wastewater was retained in activated sludge. Food waste with a high starch content favoured acidogenic fermentation. Around 55.7% of P from wastewater was recovered as vivianite, and around 66% of food waste loading was converted into VFAs. The new integration formed an effective system for wastewater treatment, food waste processing and simultaneous recovery of P and VFAs. Copyright © 2017 Elsevier Ltd. All rights reserved.

Effects of region, demography, and protection from fishing on batch fecundity of common coral trout ( Plectropomus leopardus)

NASA Astrophysics Data System (ADS)

Carter, Alex B.; Davies, Campbell R.; Mapstone, Bruce D.; Russ, Garry R.; Tobin, Andrew J.; Williams, Ashley J.

2014-09-01

Batch fecundity of female Plectropomus leopardus, a coral reef fish targeted by commercial and recreational fishing, was compared between reefs open to fishing and reefs within no-take marine reserves within three regions of the Great Barrier Reef (GBR), Australia. Length, weight, and age had positive effects on batch fecundity of spawners from northern and central reefs but negligible effects on spawners from southern reefs. Females were least fecund for a given length, weight, and age in the southern GBR. Batch fecundity of a 500-mm fork length female was 430 % greater on central reefs and 207 % greater on northern reefs than on southern reefs. The effects of length and age on batch fecundity did not differ significantly between reserve and fished reefs in any region, but weight-specific fecundity was 100 % greater for large 2.0 kg females on reserve reefs compared with fished reefs in the central GBR. We hypothesize that regional variation in batch fecundity is likely driven by water temperature and prey availability. Significant regional variation in batch fecundity highlights the need for understanding spatial variation in reproductive output where single conservation or fishery management strategies cover large, potentially diverse, spatial scales.

NDA BATCH 2002-02

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lawrence Livermore National Laboratory

2009-12-09

QC sample results (daily background checks, 20-gram and 100-gram SGS drum checks) were within acceptable criteria established by WIPP's Quality Assurance Objectives for TRU Waste Characterization. Replicate runs were performed on 5 drums with IDs LL85101099TRU, LL85801147TRU, LL85801109TRU, LL85300999TRU and LL85500979TRU. All replicate measurement results are identical at the 95% confidence level as established by WIPP criteria. Note that the batch covered 5 weeks of SGS measurements from 23-Jan-2002 through 22-Feb-2002. Data packet for SGS Batch 2002-02 generated using gamma spectroscopy with the Pu Facility SGS unit is technically reasonable. All QC samples are in compliance with established control limits.more » The batch data packet has been reviewed for correctness, completeness, consistency and compliance with WIPP's Quality Assurance Objectives and determined to be acceptable. An Expert Review was performed on the data packet between 28-Feb-02 and 09-Jul-02 to check for potential U-235, Np-237 and Am-241 interferences and address drum cases where specific scan segments showed Se gamma ray transmissions for the 136-keV gamma to be below 0.1 %. Two drums in the batch showed Pu-238 at a relative mass ratio more than 2% of all the Pu isotopes.« less

Enhanced biological phosphorus removal in a sequencing batch reactor using propionate as the sole carbon source.

PubMed

Pijuan, M; Saunders, A M; Guisasola, A; Baeza, J A; Casas, C; Blackall, L L

2004-01-05

An enhanced biological phosphorus removal (EBPR) system was developed in a sequencing batch reactor (SBR) using propionate as the sole carbon source. The microbial community was followed using fluorescence in situ hybridization (FISH) techniques and Candidatus 'Accumulibacter phosphatis' were quantified from the start up of the reactor until steady state. A series of SBR cycle studies was performed when 55% of the SBR biomass was Accumulibacter, a confirmed polyphosphate accumulating organism (PAO) and when Candidatus 'Competibacter phosphatis', a confirmed glycogen-accumulating organism (GAO), was essentially undetectable. These experiments evaluated two different carbon sources (propionate and acetate), and in every case, two different P-release rates were detected. The highest rate took place while there was volatile fatty acid (VFA) in the mixed liquor, and after the VFA was depleted a second P-release rate was observed. This second rate was very similar to the one detected in experiments performed without added VFA.A kinetic and stoichiometric model developed as a modification of Activated Sludge Model 2 (ASM2) including glycogen economy, was fitted to the experimental profiles. The validation and calibration of this model was carried out with the cycle study experiments performed using both VFAs. The effect of pH from 6.5 to 8.0 on anaerobic P-release and VFA-uptake and aerobic P-uptake was also studied using propionate. The optimal overall working pH was around 7.5. This is the first study of the microbial community involved in EBPR developed with propionate as a sole carbon source along with detailed process performance investigations of the propionate-utilizing PAOs. Copyright 2003 Wiley Periodicals, Inc.

Potential for improved radiation thermometry measurement uncertainty through implementing a primary scale in an industrial laboratory

NASA Astrophysics Data System (ADS)

Willmott, Jon R.; Lowe, David; Broughton, Mick; White, Ben S.; Machin, Graham

2016-09-01

A primary temperature scale requires realising a unit in terms of its definition. For high temperature radiation thermometry in terms of the International Temperature Scale of 1990 this means extrapolating from the signal measured at the freezing temperature of gold, silver or copper using Planck’s radiation law. The difficulty in doing this means that primary scales above 1000 °C require specialist equipment and careful characterisation in order to achieve the extrapolation with sufficient accuracy. As such, maintenance of the scale at high temperatures is usually only practicable for National Metrology Institutes, and calibration laboratories have to rely on a scale calibrated against transfer standards. At lower temperatures it is practicable for an industrial calibration laboratory to have its own primary temperature scale, which reduces the number of steps between the primary scale and end user. Proposed changes to the SI that will introduce internationally accepted high temperature reference standards might make it practicable to have a primary high temperature scale in a calibration laboratory. In this study such a scale was established by calibrating radiation thermometers directly to high temperature reference standards. The possible reduction in uncertainty to an end user as a result of the reduced calibration chain was evaluated.

Batch Model for Batched Timestamps Data Analysis with Application to the SSA Disability Program

PubMed Central

Yue, Qingqi; Yuan, Ao; Che, Xuan; Huynh, Minh; Zhou, Chunxiao

2016-01-01

The Office of Disability Adjudication and Review (ODAR) is responsible for holding hearings, issuing decisions, and reviewing appeals as part of the Social Security Administration’s disability determining process. In order to control and process cases, the ODAR has established a Case Processing and Management System (CPMS) to record management information since December 2003. The CPMS provides a detailed case status history for each case. Due to the large number of appeal requests and limited resources, the number of pending claims at ODAR was over one million cases by March 31, 2015. Our National Institutes of Health (NIH) team collaborated with SSA and developed a Case Status Change Model (CSCM) project to meet the ODAR’s urgent need of reducing backlogs and improve hearings and appeals process. One of the key issues in our CSCM project is to estimate the expected service time and its variation for each case status code. The challenge is that the systems recorded job departure times may not be the true job finished times. As the CPMS timestamps data of case status codes showed apparent batch patterns, we proposed a batch model and applied the constrained least squares method to estimate the mean service times and the variances. We also proposed a batch search algorithm to determine the optimal batch partition, as no batch partition was given in the real data. Simulation studies were conducted to evaluate the performance of the proposed methods. Finally, we applied the method to analyze a real CPMS data from ODAR/SSA. PMID:27747132

Fault healing and earthquake spectra from stick slip sequences in the laboratory and on active faults

NASA Astrophysics Data System (ADS)

McLaskey, G. C.; Glaser, S. D.; Thomas, A.; Burgmann, R.

2011-12-01

Repeating earthquake sequences (RES) are thought to occur on isolated patches of a fault that fail in repeated stick-slip fashion. RES enable researchers to study the effect of variations in earthquake recurrence time and the relationship between fault healing and earthquake generation. Fault healing is thought to be the physical process responsible for the 'state' variable in widely used rate- and state-dependent friction equations. We analyze RES created in laboratory stick slip experiments on a direct shear apparatus instrumented with an array of very high frequency (1KHz - 1MHz) displacement sensors. Tests are conducted on the model material polymethylmethacrylate (PMMA). While frictional properties of this glassy polymer can be characterized with the rate- and state- dependent friction laws, the rate of healing in PMMA is higher than room temperature rock. Our experiments show that in addition to a modest increase in fault strength and stress drop with increasing healing time, there are distinct spectral changes in the recorded laboratory earthquakes. Using the impact of a tiny sphere on the surface of the test specimen as a known source calibration function, we are able to remove the instrument and apparatus response from recorded signals so that the source spectrum of the laboratory earthquakes can be accurately estimated. The rupture of a fault that was allowed to heal produces a laboratory earthquake with increased high frequency content compared to one produced by a fault which has had less time to heal. These laboratory results are supported by observations of RES on the Calaveras and San Andreas faults, which show similar spectral changes when recurrence time is perturbed by a nearby large earthquake. Healing is typically attributed to a creep-like relaxation of the material which causes the true area of contact of interacting asperity populations to increase with time in a quasi-logarithmic way. The increase in high frequency seismicity shown here

SEQassembly: A Practical Tools Program for Coding Sequences Splicing

NASA Astrophysics Data System (ADS)

Lee, Hongbin; Yang, Hang; Fu, Lei; Qin, Long; Li, Huili; He, Feng; Wang, Bo; Wu, Xiaoming

CDS (Coding Sequences) is a portion of mRNA sequences, which are composed by a number of exon sequence segments. The construction of CDS sequence is important for profound genetic analysis such as genotyping. A program in MATLAB environment is presented, which can process batch of samples sequences into code segments under the guide of reference exon models, and splice these code segments of same sample source into CDS according to the exon order in queue file. This program is useful in transcriptional polymorphism detection and gene function study.

Nitrogen removal via nitrite in a partial nitrification sequencing batch biofilm reactor treating high strength ammonia wastewater and its greenhouse gas emission.

PubMed

Wei, Dong; Zhang, Keyi; Ngo, Huu Hao; Guo, Wenshan; Wang, Siyu; Li, Jibin; Han, Fei; Du, Bin; Wei, Qin

2017-04-01

In present study, the feasibility of partial nitrification (PN) process achievement and its greenhouse gas emission were evaluated in a sequencing batch biofilm reactor (SBBR). After 90days' operation, the average effluent NH 4 + -N removal efficiency and nitrite accumulation rate of PN-SBBR were high of 98.2% and 87.6%, respectively. Both polysaccharide and protein contents were reduced in loosely bound extracellular polymeric substances (LB-EPS) and tightly bound EPS (TB-EPS) during the achievement of PN-biofilm. Excitation-emission matrix spectra implied that aromatic protein-like, tryptophan protein-like and humic acid-like substances were the main compositions of both kinds of EPS in seed sludge and PN-biofilm. According to typical cycle, the emission rate of CO 2 had a much higher value than that of N 2 O, and their total amounts per cycle were 67.7 and 16.5mg, respectively. Free ammonia (FA) played a significant role on the inhibition activity of nitrite-oxidizing bacteria and the occurrence of nitrite accumulation. Copyright © 2017 Elsevier Ltd. All rights reserved.

Monitoring Uranium Transformations Determined by the Evolution of Biogeochemical Processes: Design of Mixed Batch Reactor and Column Studies at Oak Ridge National Laboratory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Criddle, Craig S.; Wu, Weimin

2013-04-17

With funds provided by the US DOE, Argonne National Laboratory subcontracted the design of batch and column studies to a Stanford University team with field experience at the ORNL IFRC, Oak Ridge, TN. The contribution of the Stanford group ended in 2011 due to budget reduction in ANL. Over the funded research period, the Stanford research team characterized ORNL IFRC groundwater and sediments and set up microcosm reactors and columns at ANL to ensure that experiments were relevant to field conditions at Oak Ridge. The results of microcosm testing demonstrated that U(VI) in sediments was reduced to U(IV) with themore » addition of ethanol. The reduced products were not uraninite but were instead U(IV) complexes associated with Fe. Fe(III) in solid phase was only partially reduced. The Stanford team communicated with the ANL team members through email and conference calls and face to face at the annual ERSP PI meeting and national meetings.« less

Stepwise heating in Stille polycondensation toward no batch-to-batch variations in polymer solar cell performance.

PubMed

Lee, Sang Myeon; Park, Kwang Hyun; Jung, Seungon; Park, Hyesung; Yang, Changduk

2018-05-14

For a given π-conjugated polymer, the batch-to-batch variations in molecular weight (M w ) and polydispersity index (Ð) can lead to inconsistent process-dependent material properties and consequent performance variations in the device application. Using a stepwise-heating protocol in the Stille polycondensation in conjunction with optimized processing, we obtained an ultrahigh-quality PTB7 polymer having high M w and very narrow Ð. The resulting ultrahigh-quality polymer-based solar cells demonstrate up to 9.97% power conversion efficiencies (PCEs), which is over 24% enhancement from the control devices fabricated with commercially available PTB7. Moreover, we observe almost negligible batch-to-batch variations in the overall PCE values from ultrahigh-quality polymer-based devices. The proposed stepwise polymerization demonstrates a facile and effective strategy for synthesizing high-quality semiconducting polymers that can significantly improve device yield in polymer-based solar cells, an important factor for the commercialization of organic solar cells, by mitigating device-to-device variations.

Collaborative study for the calibration of replacement batches for the heparin low-molecular-mass for assay biological reference preparation.

PubMed

Terao, E; Daas, A

2016-01-01

The European Pharmacopoeia (Ph. Eur.) prescribes the control of the activity of low molecular mass heparins by assays for anti-Xa and anti-IIa activities (monograph 0828), using a reference standard calibrated in International Units (IU). An international collaborative study coded BSP133 was launched in the framework of the Biological Standardisation Programme (BSP) run under the aegis of the Council of Europe and the European Commission to calibrate replacement batches for the dwindling stocks of the Heparin low-molecular-mass for assay Biological Reference Preparation (BRP) batch 8. Thirteen official medicines control and manufacturers laboratories from European and non-European countries took part in this study to calibrate two freeze-dried candidate batches against the 3rd International Standard (IS) for heparin, low molecular weight (11/176; 3rd IS). The Heparin low-molecular-mass for assay BRP (batch 8) was also included in the test panel to check the continuity between subsequent BRP batches. Taking into account the stability data, the results of this collaborative study and on the basis of the central statistical analysis performed at the European Directorate for the Quality of Medicines & HealthCare (EDQM), the 2 candidate batches were officially adopted by the Commission of the European Pharmacopoeia as Heparin low-molecular-mass for assay BRP batches 9 and 10 with assigned anti-Xa activities of 102 and 100 IU/vial and anti-IIa activities of 34 and 33 IU/vial respectively.

EMISSIONS REDUCTION OF COMMERCIAL GLASSMAKING USING SELECTIVE BATCHING

EPA Science Inventory

The vertical bubble populations of selectively batched melts were compared to the vertical bubble populations of conventionally batched melts. “Conventional” refers to the use of a powdered batch. Bubble position and diameter measurements were taken on 24 crucibles...

Characteristics of aerobic granules grown on glucose a sequential batch shaking reactor.

PubMed

Cai, Chun-guang; Zhu, Nan-wen; Liu, Jun-shen; Wang, Zhen-peng; Cai, Wei-min

2004-01-01

Aerobic heterotrophic granular sludge was cultivated in a sequencing batch shaking reactor (SBSR) in which a synthetic wastewater containing glucose as carbon source was fed. The characteristics of the aerobic granules were investigated. Compared with the conventional activated sludge flocs, the aerobic granules exhibit excellent physical characteristics in terms of settleability, size, shape, biomass density, and physical strength. Scanning electron micrographs revealed that in mature granules little filamentous bacteria could be found, rod-shaped and coccoid bacteria were the dominant microorganisms.

Integration of the Uncertainties of Anion and TOC Measurements into the Flammability Control Strategy for Sludge Batch 8 at the DWPF

DOE Office of Scientific and Technical Information (OSTI.GOV)

Edwards, T. B.

2013-03-14

The Savannah River National Laboratory (SRNL) has been working with the Savannah River Remediation (SRR) Defense Waste Processing Facility (DWPF) in the development and implementation of a flammability control strategy for DWPF’s melter operation during the processing of Sludge Batch 8 (SB8). SRNL’s support has been in response to technical task requests that have been made by SRR’s Waste Solidification Engineering (WSE) organization. The flammability control strategy relies on measurements that are performed on Slurry Mix Evaporator (SME) samples by the DWPF Laboratory. Measurements of nitrate, oxalate, formate, and total organic carbon (TOC) standards generated by the DWPF Laboratory aremore » presented in this report, and an evaluation of the uncertainties of these measurements is provided. The impact of the uncertainties of these measurements on DWPF’s strategy for controlling melter flammability also is evaluated. The strategy includes monitoring each SME batch for its nitrate content and its TOC content relative to the nitrate content and relative to the antifoam additions made during the preparation of the SME batch. A linearized approach for monitoring the relationship between TOC and nitrate is developed, equations are provided that integrate the measurement uncertainties into the flammability control strategy, and sample calculations for these equations are shown to illustrate the impact of the uncertainties on the flammability control strategy.« less

Collaborative study for the establishment of replacement batches of heparin low- molecular-mass for assay biological reference preparations.

PubMed

Terao, E; Daas, A; Rautmann, G; Buchheit, K-H

2010-10-01

A collaborative study was run by the European Directorate for the Quality of Medicines & HealthCare (EDQM) in the context of the Biological Standardisation Programme (BSP), under the aegis of the Council of Europe and the European Commission, to establish replacement batches for the dwindling stocks of the Heparin low-molecular-mass for assay European Pharmacopoeia Biological Reference Preparation (BRP). The replacement batches of BRP are intended to be used in the assays for anti-Xa and anti-IIa activities, as described in the European Pharmacopoeia (Ph. Eur.) monograph Heparins, low-molecular-mass (0828). Three freeze-dried candidate batches were calibrated against the current International Standard (IS) for Heparin, lowmolecular- weight (2nd IS, 01/608). For the purpose of the continuity check between subsequent BRP batches, the current Heparin low-molecular-mass for assay BRP (batch 5) was also included in the test panel. Thirteen official medicines control and manufacturers laboratories from European and non-European countries contributed data. A central statistical analysis of the datasets was performed at the EDQM. On the basis of the results, the 3 candidate materials were assigned a potency of 104 IU/vial for the anti-Xa activity and 31 IU/vial for the anti-IIa activity. Taken into account the preliminary stability data and the results of this collaborative study, the 3 batches of candidate BRP were adopted in June 2010 by the Commission of the Ph. Eur. as Heparin low-molecular-mass for assay BRP batches 6, 7 and 8.

Passing in Command Line Arguments and Parallel Cluster/Multicore Batching in R with batch.

PubMed

Hoffmann, Thomas J

2011-03-01

It is often useful to rerun a command line R script with some slight change in the parameters used to run it - a new set of parameters for a simulation, a different dataset to process, etc. The R package batch provides a means to pass in multiple command line options, including vectors of values in the usual R format, easily into R. The same script can be setup to run things in parallel via different command line arguments. The R package batch also provides a means to simplify this parallel batching by allowing one to use R and an R-like syntax for arguments to spread a script across a cluster or local multicore/multiprocessor computer, with automated syntax for several popular cluster types. Finally it provides a means to aggregate the results together of multiple processes run on a cluster.

Sludge granulation and performance of a low superficial gas velocity sequencing batch reactor (SBR) in the treatment of prepared sanitary wastewater.

PubMed

Ji, Guodong; Zhai, Fengmin; Wang, Rongjing; Ni, Jinren

2010-12-01

A sequencing batch reactor (SBR) employing a low superficial gas velocity was used to produce aerobic granular sludge for wastewater treatment. At a gas velocity of 0.0056 m s(-1) sludge containing a mixture of light yellow and black granules with similar functional groups was quickly formed. The black granules contained crystals of CaCO(3), FeS, and Fe(2)O(3) as well as filamentous bacteria that strengthened the particles and reduced the mass transfer resistance. No inorganic crystals were detected in the yellow sludge granules, and their structure was maintained through cohesion mediated by extracellular polymeric substances (EPS). The light yellow granules were denser and offered better settling performance than the black granules, enhancing the settling properties of the mixed sludge. During a 12-h cycle, the maximum reductions in chemical oxygen demand (COD), NH(3)-N, and total nitrogen (TN) occurred at 240, 480, and 360 min with removal efficiencies of 90%, 90%, and 54%. When the cycle time was limited to 480 min, self-dissolution of the granules was avoided while sill maintaining removal efficiencies for COD, NH(3)-N, and TN of 88%, 90%, and 53%. 2010 Elsevier Ltd. All rights reserved.

Results of initial analyses of the salt (macro) batch 10 tank 21H qualification samples

DOE Office of Scientific and Technical Information (OSTI.GOV)

Peters, T. B.

2017-01-01

Savannah River National Laboratory (SRNL) analyzed samples from Tank 21H in support of qualification of Interim Salt Disposition Project (ISDP) Salt (Macro) Batch 10 for processing through the Actinide Removal Process (ARP) and the Modular Caustic-Side Solvent Extraction Unit (MCU). This document reports the initial results of the analyses of samples of Tank 21H. Analysis of the Tank 21H Salt (Macro) Batch 10 composite sample indicates that the material does not display any unusual characteristics or observations, such as floating solids, the presence of large amount of solids, or unusual colors. Further sample results will be reported in a futuremore » document. This memo satisfies part of Deliverable 3 of the Technical Task Request (TTR).« less

Results of initial analyses of the salt (macro) batch 11 Tank 21H qualification samples

DOE Office of Scientific and Technical Information (OSTI.GOV)

Peters, T. B.

Savannah River National Laboratory (SRNL) analyzed samples from Tank 21H in support of qualification of Interim Salt Disposition Project (ISDP) Salt (Macro) Batch 11 for processing through the Actinide Removal Process (ARP) and the Modular Caustic-Side Solvent Extraction Unit (MCU). This document reports the initial results of the analyses of samples of Tank 21H. Analysis of the Tank 21H Salt (Macro) Batch 11 composite sample indicates that the material does not display any unusual characteristics or observations, such as floating solids, the presence of large amounts of solids, or unusual colors. Further sample results will be reported in a futuremore » document. This memo satisfies part of Deliverable 3 of the Technical Task Request (TTR).« less

Evaluation of Municipal Wastewater Treatment Plant Activated Sludge for Biodegradation of Propylene Glycol as an Aircraft Deicing Fluid

DTIC Science & Technology

2012-03-01

Propylene Glycol Deicer Biodegredation Kinetics: Complete-Mix Stirred Tank Reactors , Filter, and Fluidized Bed . Journal of Environmental...scale sequencing batch reactor containing municipal waste water treatment facility activated sludge (AS) performing simultaneous organic carbon...Sequencing Batch Reactor Operation ..................................................................... 13 PG extraction from AS

Molecular microbial and chemical investigation of the bioremediation of two-phase olive mill waste using laboratory-scale bioreactors.

PubMed

Morillo, J A; Aguilera, M; Antízar-Ladislao, B; Fuentes, S; Ramos-Cormenzana, A; Russell, N J; Monteoliva-Sánchez, M

2008-05-01

Two-phase olive mill waste (TPOMW) is a semisolid effluent that is rich in contaminating polyphenols and is produced in large amounts by the industry of olive oil production. Laboratory-scale bioreactors were used to investigate the biodegradation of TPOMW by its indigenous microbiota. The effect of nutrient addition (inorganic N and P) and aeration of the bioreactors was studied. Microbial changes were investigated by PCR-temperature time gradient electrophoresis (TTGE) and following the dynamics of polar lipid fatty acids (PLFA). The greatest decrease in the polyphenolic and organic matter contents of bioreactors was concomitant with an increase in the PLFA fungal/bacterial ratio. Amplicon sequences of nuclear ribosomal internal transcribed spacer region (ITS) and 16S rDNA allowed identification of fungal and bacterial types, respectively, by comparative DNA sequence analyses. Predominant fungi identified included members of the genera Penicillium, Candida, Geotrichum, Pichia, Cladosporium, and Aschochyta. A total of 14 bacterial genera were detected, with a dominance of organisms that have previously been associated with plant material. Overall, this work highlights that indigenous microbiota within the bioreactors through stimulation of the fungal fraction, is able to degrade the polyphenolic content without the inoculation of specific microorganisms.

An Undergraduate Laboratory Exercise for Studying Kinetics of Batch Crystallization

ERIC Educational Resources Information Center

Louhi­-Kultanen, Marjatta; Han, Bing; Nurkka, Annikka; Hatakka, Henry

2015-01-01

The present work describes an undergraduate laboratory exercise for improving understanding of fundamental phenomena in cooling crystallization. The exercise of nucleation and crystal growth kinetics supports learning of theories and models presented in lectures and calculation exercises. The teaching methodology incorporates precepts the…

Aerobic granules formation and nutrients removal characteristics in sequencing batch airlift reactor (SBAR) at low temperature.

PubMed

Bao, Ruiling; Yu, Shuili; Shi, Wenxin; Zhang, Xuedong; Wang, Yulan

2009-09-15

To understand the effect of low temperature on the formation of aerobic granules and their nutrient removal characteristics, an aerobic granular sequencing batch airlift reactor (SBAR) has been operated at 10 degrees C using a mixed carbon source of glucose and sodium acetate. The results showed that aerobic granules were obtained and that the reactor performed in stable manner under the applied conditions. The granules had a compact structure and a clear out-surface. The average parameters of the granules were: diameter 3.4mm, wet density 1.036 g mL(-1), sludge volume index 37 mL g(-1), and settling velocity 18.6-65.1 cm min(-1). Nitrite accumulation was observed, with a nitrite accumulation rate (NO(2)(-)-N/NO(x)(-)-N) between 35% and 43% at the beginning of the start-up stage. During the stable stage, NO(x) was present at a level below the detection limit. However, when the influent COD concentration was halved (resulting in COD/N a reduction of the COD/N from 20:1 to 10:1) nitrite accumulation was observed once more with an effluent nitrite accumulation rate of 94.8%. Phosphorus release was observed in the static feeding phase and also during the initial 20-30 min of the aerobic phase. Neither the low temperature nor adjustment of the COD/P ratio from 100:1 to 25:1 had any influence on the phosphorus removal efficiency under the operating conditions. In the granular reactor with the influent load rates for COD, NH(4)(+)-N, and PO(4)(3-)-P of 1.2-2.4, 0.112 and 0.012-0.024 kg m(-3)d(-1), the respective removal efficiencies at low temperature were 90.6-95.4%, 72.8-82.1% and 95.8-97.9%.

The fate of crop nutrients during digestion of swine manure in psychrophilic anaerobic sequencing batch reactors.

PubMed

Massé, D I; Croteau, F; Masse, L

2007-11-01

The objectives of the study were to measure the levels of manure nutrients retained in psychrophilic anaerobic sequencing batch reactors (PASBRs) digesting swine manure, and to determine the distribution of nutrients in the sludge and supernatant zones of settled bioreactor effluent. Anaerobic digestion reduced the total solids (TS) concentration and the soluble chemical oxygen demand (SCOD) of manure by 71.4% and 79.9%, respectively. The nitrogen, potassium, and sodium fed with the manure to the PASBRs were recovered in the effluent. The bioreactors retained on average 25.5% of the P, 8.7% of the Ca, 41.5% of the Cu, 18.4% of the Zn, and 67.7% of the S fed to the PASBRs. The natural settling of bioreactor effluent allowed further nutrient separation. The supernatant fraction, which represented 71.4% of effluent volume, contained 61.8% of the total N, 67.1% of the NH4-N, and 73.3% of the Na. The settled sludge fraction, which represented 28.6% of the volume, contained 57.6% of the solids, 62.3% of the P, 71.6% of the Ca, 89.6% of the Mg, 76.1% of the Al, 90.0% of the Cu, 74.2% of the Zn, and 52.2% of the S. The N/P ratio was increased from 3.9 in the raw manure to 5.2 in the bioreactor effluent and 9.2 in the supernatant fraction of the settled effluent. The PASBR technology will then substantially decrease the manure management costs of swine operations producing excess phosphorus, by reducing the volume of manure to export outside the farm. The separation of nutrients will also allow land spreading strategies that increase the agronomic value of manure by matching more closely the crop nutrient requirements.

Transferring Exome Sequencing Data from Clinical Laboratories to Healthcare Providers: Lessons Learned at a Pediatric Hospital

PubMed Central

Swaminathan, Rajeswari; Huang, Yungui; Miller, Katherine; Pastore, Matthew; Hashimoto, Sayaka; Jacobson, Theodora; Mouhlas, Danielle; Lin, Simon

2018-01-01

The adoption rate of genome sequencing for clinical diagnostics has been steadily increasing leading to the possibility of improvement in diagnostic yields. Although laboratories generate a summary clinical report, sharing raw genomic data with healthcare providers is equally important, both for secondary research studies as well as for a deeper analysis of the data itself, as seen by the efforts from organizations such as American College of Medical Genetics and Genomics and Global Alliance for Genomics and Health. Here, we aim to describe the existing protocol of genomic data sharing between a certified clinical laboratory and a healthcare provider and highlight some of the lessons learned. This study tracked and subsequently evaluated the data transfer workflow for 19 patients, all of whom consented to be part of this research study and visited the genetics clinic at a tertiary pediatric hospital between April 2016 to December 2016. Two of the most noticeable elements observed through this study are the manual validation steps and the discrepancies in patient identifiers used by a clinical lab vs. healthcare provider. Both of these add complexity to the transfer process as well as make it more susceptible to errors. The results from this study highlight some of the critical changes that need to be made in order to improve genomic data sharing workflows between healthcare providers and clinical sequencing laboratories. PMID:29515625

Spatial Variation of Pressure in the Lyophilization Product Chamber Part 2: Experimental Measurements and Implications for Scale-up and Batch Uniformity.

PubMed

Sane, Pooja; Varma, Nikhil; Ganguly, Arnab; Pikal, Michael; Alexeenko, Alina; Bogner, Robin H

2017-02-01

Product temperature during the primary drying step of freeze-drying is controlled by a set point chamber pressure and shelf temperature. However, recent computational modeling suggests a possible variation in local chamber pressure. The current work presents an experimental verification of the local chamber pressure gradients in a lab-scale freeze-dryer. Pressure differences between the center and the edges of a lab-scale freeze-dryer shelf were measured as a function of sublimation flux and clearance between the sublimation front and the shelf above. A modest 3-mTorr difference in pressure was observed as the sublimation flux was doubled from 0.5 to 1.0 kg·h -1 ·m -2 at a clearance of 2.6 cm. Further, at a constant sublimation flux of 1.0 kg·h -1 ·m -2 , an 8-fold increase in the pressure drop was observed across the shelf as the clearance was decreased from 4 to 1.6 cm. Scale-up of the pressure variation from lab- to a manufacturing-scale freeze-dryer predicted an increased uniformity in drying rates across the batch for two frequently used pharmaceutical excipients (mannitol and sucrose at 5% w/w). However, at an atypical condition of shelf temperature of +10°C and chamber pressure of 50 mTorr, the product temperature in the center vials was calculated to be a degree higher than the edge vial for a low resistance product, thus reversing the typical edge and center vial behavior. Thus, the effect of local pressure variation is more significant at the manufacturing-scale than at a lab-scale and accounting for the contribution of variations in the local chamber pressures can improve success in scale-up.

Development of self-compressing BLSOM for comprehensive analysis of big sequence data.

PubMed

Kikuchi, Akihito; Ikemura, Toshimichi; Abe, Takashi

2015-01-01

With the remarkable increase in genomic sequence data from various organisms, novel tools are needed for comprehensive analyses of available big sequence data. We previously developed a Batch-Learning Self-Organizing Map (BLSOM), which can cluster genomic fragment sequences according to phylotype solely dependent on oligonucleotide composition and applied to genome and metagenomic studies. BLSOM is suitable for high-performance parallel-computing and can analyze big data simultaneously, but a large-scale BLSOM needs a large computational resource. We have developed Self-Compressing BLSOM (SC-BLSOM) for reduction of computation time, which allows us to carry out comprehensive analysis of big sequence data without the use of high-performance supercomputers. The strategy of SC-BLSOM is to hierarchically construct BLSOMs according to data class, such as phylotype. The first-layer BLSOM was constructed with each of the divided input data pieces that represents the data subclass, such as phylotype division, resulting in compression of the number of data pieces. The second BLSOM was constructed with a total of weight vectors obtained in the first-layer BLSOMs. We compared SC-BLSOM with the conventional BLSOM by analyzing bacterial genome sequences. SC-BLSOM could be constructed faster than BLSOM and cluster the sequences according to phylotype with high accuracy, showing the method's suitability for efficient knowledge discovery from big sequence data.

A scalable architecture for online anomaly detection of WLCG batch jobs

NASA Astrophysics Data System (ADS)

Kuehn, E.; Fischer, M.; Giffels, M.; Jung, C.; Petzold, A.

2016-10-01

For data centres it is increasingly important to monitor the network usage, and learn from network usage patterns. Especially configuration issues or misbehaving batch jobs preventing a smooth operation need to be detected as early as possible. At the GridKa data and computing centre we therefore operate a tool BPNetMon for monitoring traffic data and characteristics of WLCG batch jobs and pilots locally on different worker nodes. On the one hand local information itself are not sufficient to detect anomalies for several reasons, e.g. the underlying job distribution on a single worker node might change or there might be a local misconfiguration. On the other hand a centralised anomaly detection approach does not scale regarding network communication as well as computational costs. We therefore propose a scalable architecture based on concepts of a super-peer network.

Laboratory formation of a scaled protostellar jet by coaligned poloidal magnetic field.

PubMed

Albertazzi, B; Ciardi, A; Nakatsutsumi, M; Vinci, T; Béard, J; Bonito, R; Billette, J; Borghesi, M; Burkley, Z; Chen, S N; Cowan, T E; Herrmannsdörfer, T; Higginson, D P; Kroll, F; Pikuz, S A; Naughton, K; Romagnani, L; Riconda, C; Revet, G; Riquier, R; Schlenvoigt, H-P; Skobelev, I Yu; Faenov, A Ya; Soloviev, A; Huarte-Espinosa, M; Frank, A; Portugall, O; Pépin, H; Fuchs, J

2014-10-17

Although bipolar jets are seen emerging from a wide variety of astrophysical systems, the issue of their formation and morphology beyond their launching is still under study. Our scaled laboratory experiments, representative of young stellar object outflows, reveal that stable and narrow collimation of the entire flow can result from the presence of a poloidal magnetic field whose strength is consistent with observations. The laboratory plasma becomes focused with an interior cavity. This gives rise to a standing conical shock from which the jet emerges. Following simulations of the process at the full astrophysical scale, we conclude that it can also explain recently discovered x-ray emission features observed in low-density regions at the base of protostellar jets, such as the well-studied jet HH 154. Copyright © 2014, American Association for the Advancement of Science.

Removing Batch Effects from Longitudinal Gene Expression - Quantile Normalization Plus ComBat as Best Approach for Microarray Transcriptome Data

PubMed Central

Müller, Christian; Schillert, Arne; Röthemeier, Caroline; Trégouët, David-Alexandre; Proust, Carole; Binder, Harald; Pfeiffer, Norbert; Beutel, Manfred; Lackner, Karl J.; Schnabel, Renate B.; Tiret, Laurence; Wild, Philipp S.; Blankenberg, Stefan

2016-01-01

Technical variation plays an important role in microarray-based gene expression studies, and batch effects explain a large proportion of this noise. It is therefore mandatory to eliminate technical variation while maintaining biological variability. Several strategies have been proposed for the removal of batch effects, although they have not been evaluated in large-scale longitudinal gene expression data. In this study, we aimed at identifying a suitable method for batch effect removal in a large study of microarray-based longitudinal gene expression. Monocytic gene expression was measured in 1092 participants of the Gutenberg Health Study at baseline and 5-year follow up. Replicates of selected samples were measured at both time points to identify technical variability. Deming regression, Passing-Bablok regression, linear mixed models, non-linear models as well as ReplicateRUV and ComBat were applied to eliminate batch effects between replicates. In a second step, quantile normalization prior to batch effect correction was performed for each method. Technical variation between batches was evaluated by principal component analysis. Associations between body mass index and transcriptomes were calculated before and after batch removal. Results from association analyses were compared to evaluate maintenance of biological variability. Quantile normalization, separately performed in each batch, combined with ComBat successfully reduced batch effects and maintained biological variability. ReplicateRUV performed perfectly in the replicate data subset of the study, but failed when applied to all samples. All other methods did not substantially reduce batch effects in the replicate data subset. Quantile normalization plus ComBat appears to be a valuable approach for batch correction in longitudinal gene expression data. PMID:27272489

The genome sequence of E. coli W (ATCC 9637): comparative genome analysis and an improved genome-scale reconstruction of E. coli

PubMed Central

2011-01-01

Background Escherichia coli is a model prokaryote, an important pathogen, and a key organism for industrial biotechnology. E. coli W (ATCC 9637), one of four strains designated as safe for laboratory purposes, has not been sequenced. E. coli W is a fast-growing strain and is the only safe strain that can utilize sucrose as a carbon source. Lifecycle analysis has demonstrated that sucrose from sugarcane is a preferred carbon source for industrial bioprocesses. Results We have sequenced and annotated the genome of E. coli W. The chromosome is 4,900,968 bp and encodes 4,764 ORFs. Two plasmids, pRK1 (102,536 bp) and pRK2 (5,360 bp), are also present. W has unique features relative to other sequenced laboratory strains (K-12, B and Crooks): it has a larger genome and belongs to phylogroup B1 rather than A. W also grows on a much broader range of carbon sources than does K-12. A genome-scale reconstruction was developed and validated in order to interrogate metabolic properties. Conclusions The genome of W is more similar to commensal and pathogenic B1 strains than phylogroup A strains, and therefore has greater utility for comparative analyses with these strains. W should therefore be the strain of choice, or 'type strain' for group B1 comparative analyses. The genome annotation and tools created here are expected to allow further utilization and development of E. coli W as an industrial organism for sucrose-based bioprocesses. Refinements in our E. coli metabolic reconstruction allow it to more accurately define E. coli metabolism relative to previous models. PMID:21208457

40 CFR 63.1321 - Batch process vents provisions.

Code of Federal Regulations, 2010 CFR

2010-07-01

... Standards for Hazardous Air Pollutant Emissions: Group IV Polymers and Resins § 63.1321 Batch process vents..., owners and operators of new and existing affected sources with batch process vents shall comply with the... applicable reporting requirements in § 63.1327. (b) New SAN batch affected sources. Owners and operators of...

European Pharmacopoeia biological reference preparation for poliomyelitis vaccine (inactivated): collaborative study for the establishment of batch No. 3.

PubMed

Martin, J; Daas, A; Milne, C

2016-01-01

Inactivated poliomyelitis vaccines are an important part of the World Health Organization (WHO) control strategy to eradicate poliomyelitis. Requirements for the quality control of poliomyelitis vaccines (inactivated) include the use of an in vitro D antigen quantification assay for potency determination on the final lot as outlined in the European Pharmacopoeia (Ph. Eur.) monograph 0214. Performance of this assay requires a reference preparation calibrated in International Units (IU). A Ph. Eur. biological reference preparation (BRP) for poliomyelitis vaccine (inactivated) calibrated in IU has been established for this purpose. Due to the dwindling stocks of batch 2 of the BRP a collaborative study was run as part of the European Directorate for the Quality of Medicines & HealthCare (EDQM) Biological Standardisation Programme to establish BRP batch 3 (BRP3). Twelve laboratories including Official Medicines Control Laboratories (OMCLs) and manufacturers participated. The candidate BRP3 (cBRP3) was from the same source and had the same characteristics as BRP batch 2 (BRP2). During the study the candidate was calibrated against the 3 rd International Standard for inactivated poliomyelitis vaccine using in-house D antigen ELISA assays in line with the Ph. Eur. monograph 0214. The candidate was also compared to BRP2 to evaluate the continuity. Based on the results of the study, values of 320 DU/mL, 78 DU/mL and 288 DU/mL (D antigen units/mL) (IU) for poliovirus type 1, 2 and 3 respectively were assigned to the candidate. In June 2016, the Ph. Eur. Commission adopted the material as Ph. Eur. BRP for poliomyelitis vaccine (inactivated) batch 3.

Batching System for Superior Service

NASA Technical Reports Server (NTRS)

2001-01-01

Veridian's Portable Batch System (PBS) was the recipient of the 1997 NASA Space Act Award for outstanding software. A batch system is a set of processes for managing queues and jobs. Without a batch system, it is difficult to manage the workload of a computer system. By bundling the enterprise's computing resources, the PBS technology offers users a single coherent interface, resulting in efficient management of the batch services. Users choose which information to package into "containers" for system-wide use. PBS also provides detailed system usage data, a procedure not easily executed without this software. PBS operates on networked, multi-platform UNIX environments. Veridian's new version, PBS Pro,TM has additional features and enhancements, including support for additional operating systems. Veridian distributes the original version of PBS as Open Source software via the PBS website. Customers can register and download the software at no cost. PBS Pro is also available via the web and offers additional features such as increased stability, reliability, and fault tolerance.A company using PBS can expect a significant increase in the effective management of its computing resources. Tangible benefits include increased utilization of costly resources and enhanced understanding of computational requirements and user needs.

Beware batch culture: Seasonality and niche construction predicted to favor bacterial adaptive diversification

PubMed Central

Knibbe, Carole; Schneider, Dominique; Beslon, Guillaume

2017-01-01

Metabolic cross-feeding interactions between microbial strains are common in nature, and emerge during evolution experiments in the laboratory, even in homogeneous environments providing a single carbon source. In sympatry, when the environment is well-mixed, the reasons why emerging cross-feeding interactions may sometimes become stable and lead to monophyletic genotypic clusters occupying specific niches, named ecotypes, remain unclear. As an alternative to evolution experiments in the laboratory, we developed Evo2Sim, a multi-scale model of in silico experimental evolution, equipped with the whole tool case of experimental setups, competition assays, phylogenetic analysis, and, most importantly, allowing for evolvable ecological interactions. Digital organisms with an evolvable genome structure encoding an evolvable metabolic network evolved for tens of thousands of generations in environments mimicking the dynamics of real controlled environments, including chemostat or batch culture providing a single limiting resource. We show here that the evolution of stable cross-feeding interactions requires seasonal batch conditions. In this case, adaptive diversification events result in two stably co-existing ecotypes, with one feeding on the primary resource and the other on by-products. We show that the regularity of serial transfers is essential for the maintenance of the polymorphism, as it allows for at least two stable seasons and thus two temporal niches. A first season is externally generated by the transfer into fresh medium, while a second one is internally generated by niche construction as the provided nutrient is replaced by secreted by-products derived from bacterial growth. In chemostat conditions, even if cross-feeding interactions emerge, they are not stable on the long-term because fitter mutants eventually invade the whole population. We also show that the long-term evolution of the two stable ecotypes leads to character displacement, at the level of

Biogas Production from Protein-Rich Biomass: Fed-Batch Anaerobic Fermentation of Casein and of Pig Blood and Associated Changes in Microbial Community Composition

PubMed Central

Kovács, Etelka; Wirth, Roland; Maróti, Gergely; Bagi, Zoltán; Rákhely, Gábor; Kovács, Kornél L.

2013-01-01

It is generally accepted as a fact in the biogas technology that protein-rich biomass substrates should be avoided due to inevitable process inhibition. Substrate compositions with a low C/N ratio are considered difficult to handle and may lead to process failure, though protein-rich industrial waste products have outstanding biogas generation potential. This common belief has been challenged by using protein-rich substrates, i.e. casein and precipitated pig blood protein in laboratory scale continuously stirred mesophilic fed-batch biogas fermenters. Both substrates proved suitable for sustained biogas production (0.447 L CH4/g protein oDM, i.e. organic total solids) in high yield without any additives, following a period of adaptation of the microbial community. The apparent key limiting factors in the anaerobic degradation of these proteinaceous materials were the accumulation of ammonia and hydrogen sulfide. Changes in time in the composition of the microbiological community were determined by next-generation sequencing-based metagenomic analyses. Characteristic rearrangements of the biogas-producing community upon protein feeding and specific differences due to the individual protein substrates were recognized. The results clearly demonstrate that sustained biogas production is readily achievable, provided the system is well-characterized, understood and controlled. Biogas yields (0.45 L CH4/g oDM) significantly exceeding those of the commonly used agricultural substrates (0.25-0.28 L CH4/g oDM) were routinely obtained. The results amply reveal that these high-energy-content waste products can be converted to biogas, a renewable energy carrier with flexible uses that can replace fossil natural gas in its applications. Process control, with appropriate acclimation of the microbial community to the unusual substrate, is necessary. Metagenomic analysis of the microbial community by next-generation sequencing allows a precise determination of the alterations in

Optimization of the moving-bed biofilm sequencing batch reactor (MBSBR) to control aeration time by kinetic computational modeling: Simulated sugar-industry wastewater treatment.

PubMed

Faridnasr, Maryam; Ghanbari, Bastam; Sassani, Ardavan

2016-05-01

A novel approach was applied for optimization of a moving-bed biofilm sequencing batch reactor (MBSBR) to treat sugar-industry wastewater (BOD5=500-2500 and COD=750-3750 mg/L) at 2-4 h of cycle time (CT). Although the experimental data showed that MBSBR reached high BOD5 and COD removal performances, it failed to achieve the standard limits at the mentioned CTs. Thus, optimization of the reactor was rendered by kinetic computational modeling and using statistical error indicator normalized root mean square error (NRMSE). The results of NRMSE revealed that Stover-Kincannon (error=6.40%) and Grau (error=6.15%) models provide better fits to the experimental data and may be used for CT optimization in the reactor. The models predicted required CTs of 4.5, 6.5, 7 and 7.5 h for effluent standardization of 500, 1000, 1500 and 2500 mg/L influent BOD5 concentrations, respectively. Similar pattern of the experimental data also confirmed these findings. Copyright © 2016 Elsevier Ltd. All rights reserved.

Batch compositions for cordierite ceramics

DOEpatents

Hickman, David L.

1994-07-26

Ceramic products consisting principally of cordierite and a method for making them are provided, the method employing batches comprising a mineral component and a chemical component, the mineral component comprising clay and talc and the chemical component consisting essentially of a combination of the powdered oxides, hydroxides, or hydrous oxides of magnesium, aluminum and silicon. Ceramics made by extrusion and firing of the batches can exhibit low porosity, high strength and low thermal expansion coefficients.

A Framework for Batched and GPU-Resident Factorization Algorithms Applied to Block Householder Transformations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dong, Tingzing Tim; Tomov, Stanimire Z; Luszczek, Piotr R

As modern hardware keeps evolving, an increasingly effective approach to developing energy efficient and high-performance solvers is to design them to work on many small size and independent problems. Many applications already need this functionality, especially for GPUs, which are currently known to be about four to five times more energy efficient than multicore CPUs. We describe the development of one-sided factorizations that work for a set of small dense matrices in parallel, and we illustrate our techniques on the QR factorization based on Householder transformations. We refer to this mode of operation as a batched factorization. Our approach ismore » based on representing the algorithms as a sequence of batched BLAS routines for GPU-only execution. This is in contrast to the hybrid CPU-GPU algorithms that rely heavily on using the multicore CPU for specific parts of the workload. But for a system to benefit fully from the GPU's significantly higher energy efficiency, avoiding the use of the multicore CPU must be a primary design goal, so the system can rely more heavily on the more efficient GPU. Additionally, this will result in the removal of the costly CPU-to-GPU communication. Furthermore, we do not use a single symmetric multiprocessor(on the GPU) to factorize a single problem at a time. We illustrate how our performance analysis, and the use of profiling and tracing tools, guided the development and optimization of our batched factorization to achieve up to a 2-fold speedup and a 3-fold energy efficiency improvement compared to our highly optimized batched CPU implementations based on the MKL library(when using two sockets of Intel Sandy Bridge CPUs). Compared to a batched QR factorization featured in the CUBLAS library for GPUs, we achieved up to 5x speedup on the K40 GPU.« less

Integration of ozonation and an anaerobic sequencing batch reactor (AnSBR) for the treatment of cherry stillage.

PubMed

Alvarez, Pedro M; Beltrán, Fernando J; Rodríguez, Eva M

2005-01-01

Cherry stillage is a high strength organic wastewater arising from the manufacture of alcoholic products by distillation of fermented cherries. It is made up of biorefractory polyphenols in addition to readily biodegradable organic matter. An anaerobic sequencing batch reactor (AnSBR) was used to treat cherry stillage at influent COD ranging from 5 to 50 g/L. Different cycle times were selected to test biomass organic loading rates (OLR(B)), from 0.3 to 1.2 g COD/g VSS.d. COD and TOC efficiency removals higher than 80% were achieved at influent COD up to 28.5 g/L but minimum OLR(B) tested. However, as a result of the temporary inhibition of acetogens and methanogens, volatile fatty acids (VFA) noticeably accumulated and methane production came to a transient standstill when operating at influent COD higher than 10 g/L. At these conditions, the AnSBR showed signs of instability and could not operate efficiently at OLR(B) higher than 0.3 g COD/g VSS.d. A feasible explanation for this inhibition is the presence of toxic polyphenols in cherry stillage. Thus, an ozonation step prior to the AnSBR was observed to be useful, since more than 75% of polyphenols could be removed by ozone. The integrated process was shown to be a suitable treatment technology as the following advantages compared to the single AnSBR treatment were observed: greater polyphenols and color removals, higher COD and TOC removal rates thus enabling the process to effectively operate at higher OLR, higher degree of biomethanation, and good stability with less risk of acidification.

DETAIL VIEW OF BATCH CAR, BUILT BY ATLAS CAR & ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

DETAIL VIEW OF BATCH CAR, BUILT BY ATLAS CAR & MANUFACTURING COMPANY. BATCH STORAGE SILOS IN BACKGROUND - Chambers Window Glass Company, Batch Plant, North of Drey (Nineteenth) Street, West of Constitution Boulevard, Arnold, Westmoreland County, PA

Pilot scale system for the production of palm-based Monoester-OH

NASA Astrophysics Data System (ADS)

Ngah, Muhammad Syukri; Badri, Khairiah Haji

2016-11-01

A mechanically agitate reactor vessel in a moderate scale size of 500 L has been developed. This vessel was constructed to produce palm-based polyurethane polyol with a capacity of maximum 400 L. This is to accomodate the demand required for marketing trial run as part of the commercialization intention. The chemistry background of the process design was thoroughly studied. The esterification and condensation in batch process was maintained from the laboratory scale. Only RBD palm kernel oil was used in this study. This paper will describe the engineering design for the reactor vessel development beginning at the stoichiometric equations for the production process to the detail engineering including the equipment selection and fabrication in order to meet the design and objective specifications.

Note: Measurement system for the radiative forcing of greenhouse gases in a laboratory scale.

PubMed

Kawamura, Yoshiyuki

2016-01-01

The radiative forcing of the greenhouse gases has been studied being based on computational simulations or the observation of the real atmosphere meteorologically. In order to know the greenhouse effect more deeply and to study it from various viewpoints, the study on it in a laboratory scale is important. We have developed a direct measurement system for the infrared back radiation from the carbon dioxide (CO2) gas. The system configuration is similar with that of the practical earth-atmosphere-space system. Using this system, the back radiation from the CO2 gas was directly measured in a laboratory scale, which roughly coincides with meteorologically predicted value.

Testing of the Defense Waste Processing Facility Cold Chemical Dissolution Method in Sludge Batch 9 Qualification

DOE Office of Scientific and Technical Information (OSTI.GOV)

Edwards, T.; Pareizs, J.; Coleman, C.

For each sludge batch that is processed in the Defense Waste Processing Facility (DWPF), the Savannah River National Laboratory (SRNL) tests the applicability of the digestion methods used by the DWPF Laboratory for elemental analysis of Sludge Receipt and Adjustment Tank (SRAT) Receipt samples and SRAT Product process control samples. DWPF SRAT samples are typically dissolved using a method referred to as the DWPF Cold Chemical or Cold Chem Method (CC), (see DWPF Procedure SW4- 15.201). Testing indicates that the CC method produced mixed results. The CC method did not result in complete dissolution of either the SRAT Receipt ormore » SRAT Product with some fine, dark solids remaining. However, elemental analyses did not reveal extreme biases for the major elements in the sludge when compared with analyses obtained following dissolution by hot aqua regia (AR) or sodium peroxide fusion (PF) methods. The CC elemental analyses agreed with the AR and PF methods well enough that it should be adequate for routine process control analyses in the DWPF after much more extensive side-by-side tests of the CC method and the PF method are performed on the first 10 SRAT cycles of the Sludge Batch 9 (SB9) campaign. The DWPF Laboratory should continue with their plans for further tests of the CC method during these 10 SRAT cycles.« less

Decontamination of Pangasius fish (Pangasius hypophthalmus) with chlorine or peracetic acid in the laboratory and in a Vietnamese processing company.

PubMed

Tong Thi, Anh Ngoc; Sampers, Imca; Van Haute, Sam; Samapundo, Simbarashe; Ly Nguyen, Binh; Heyndrickx, Marc; Devlieghere, Frank

2015-09-02

This study evaluated the decontamination of Pangasius fillets in chlorine or peracetic acid treated wash water. First, the decontamination efficacy of the washing step with chlorinated water applied by a Vietnamese processing company during trimming of Pangasius fillets was evaluated and used as the basis for the experiments performed on a laboratory scale. As chlorine was only added at the beginning of the batch and used continuously without renewal for 239min; a rapid increase of the bacterial counts and a fast decrease of chlorine in the wash water were found. This could be explained by the rapid accumulation of organic matter (ca. 400mg O2/L of COD after only 24min). Secondly, for the experiments performed on a laboratory scale, a single batch approach (one batch of wash water for treating a fillet) was used. Chlorine and PAA were evaluated at 10, 20, 50 and 150ppm at contact times of 10, 20 and 240s. Washing with chlorine and PAA wash water resulted in a reduction of Escherichia coli on Pangasius fish which ranged from 0-1.0 and 0.4-1.4logCFU/g, respectively while less to no reduction of total psychrotrophic counts, lactic acid bacteria and coliforms on Pangasius fish was observed. However, in comparison to PAA, chlorine was lost rapidly. As an example, 53-83% of chlorine and 15-17% of PAA were lost after washing for 40s (COD=238.2±66.3mg O2/L). Peracetic acid can therefore be an alternative sanitizer. However, its higher cost will have to be taken into consideration. Where (cheaper) chlorine is used, the processors have to pay close attention to the residual chlorine level, pH and COD level during treatment for optimal efficacy. Copyright © 2015. Published by Elsevier B.V.

Batch manufacturing: Six strategic needs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ash, R.H.; Chappell, D.A.

1995-08-01

Since the advent of industrial digital control systems in the mid-1970s, industry has had the promise of integrated, configurable digital batch control systems to replace the morass of electromechanical devices like relays and stepping switches, recorders, and indicators which comprised the components of previous generations of batch control systems - the {open_quotes}monolithic monsters{close_quotes} of the 1960s and earlier. To help fulfill that promise, there have been many wide-ranging proprietary automation solutions for batch control since 1975, many of them technically excellent. However, even the best examples suffered from the lack of a common language and unifying concept permitting separate systemsmore » to be interconnected and work together. Today, some 20 years after the digital revolution began, industry has microprocessors, memory chips, data highways, and other marvelous technology to help automate the control of discontinuous processes. They also are on the way to having an accepted standard for batch automation, ISA S88. Batching systems are at once conceptually simple but executionally complex. The notion of adding ingredients one at a time to a vat, mixing, and then processing into final form is as old as the stone age. Every homemaker on earth, male or female, is familiar with how to follow a recipe to create some sumptuous item of culinary delight. Food recipes, so familiar and ubiquitous, are really just microcosms of the S88 recipe standard. They contain the same components: (1) Header (name and description of item being prepared, sometimes serving size); (2) Formula (list and amount of ingredients); (3) Equipment requirements (pans, mixing and cooking equipment); (4) Procedure (description of order of ingredient addition, mixing and other processing steps, baking/cooling time, and other processing steps); and (5) Other information (safety, cautions, and other miscellaneous instructions).« less

Perfusion cell culture decreases process and product heterogeneity in a head-to-head comparison with fed-batch.

PubMed

Walther, Jason; Lu, Jiuyi; Hollenbach, Myles; Yu, Marcella; Hwang, Chris; McLarty, Jean; Brower, Kevin

2018-05-30

In this study, we compared the impacts of fed-batch and perfusion platforms on process and product attributes for IgG1- and IgG4-producing cell lines. A "plug-and-play" approach was applied to both platforms at bench scale, using commercially available basal and feed media, a standard feed strategy for fed-batch, and ATF filtration for perfusion. Product concentration in fed-batch was 2.5 times greater than perfusion, while average productivity in perfusion was 7.5 times greater than fed-batch. PCA revealed more variability in the cell environment and metabolism during the fed-batch run. LDH measurements showed that exposure of product to cell lysate was 7-10 times greater in fed-batch. Product analysis shows larger abundances of neutral species in perfusion, likely due to decreased bioreactor residence times and extracellular exposure. The IgG1 perfusion product also had higher purity and lower half-antibody. Glycosylation was similar across both culture modes. The first perfusion harvest slice for both product types showed different glycosylation than subsequent harvests, suggesting that product quality lags behind metabolism. In conclusion, process and product data indicate that intra-lot heterogeneity is decreased in perfusion cultures. Additional data and discussion is required to understand the developmental, clinical and commercial implications, and in what situations increased uniformity would be beneficial. This article is protected by copyright. All rights reserved.

Improving laboratory efficiencies to scale-up HIV viral load testing.

PubMed

Alemnji, George; Onyebujoh, Philip; Nkengasong, John N

2017-03-01

Viral load measurement is a key indicator that determines patients' response to treatment and risk for disease progression. Efforts are ongoing in different countries to scale-up access to viral load testing to meet the Joint United Nations Programme on HIV and AIDS target of achieving 90% viral suppression among HIV-infected patients receiving antiretroviral therapy. However, the impact of these initiatives may be challenged by increased inefficiencies along the viral load testing spectrum. This will translate to increased costs and ineffectiveness of scale-up approaches. This review describes different parameters that could be addressed across the viral load testing spectrum aimed at improving efficiencies and utilizing test results for patient management. Though progress is being made in some countries to scale-up viral load, many others still face numerous challenges that may affect scale-up efficiencies: weak demand creation, ineffective supply chain management systems; poor specimen referral systems; inadequate data and quality management systems; and weak laboratory-clinical interface leading to diminished uptake of test results. In scaling up access to viral load testing, there should be a renewed focus to address efficiencies across the entire spectrum, including factors related to access, uptake, and impact of test results.

Regionalization of laboratory care: a viable option for the 21st century.

PubMed

Steiner, J W; Root, J M

1990-06-01

The conversion of the hospital laboratory to a cost center under pressure of prospective payment and fixed reimbursement is increasingly forcing hospitals to consider alternative modes for delivery of laboratory care. Changes in the health care environment, amended statutes and regulations, and, particularly, dramatic developments in laboratory equipment, methodologies, and data processing technology make it advisable and feasible to contemplate the creation of regional laboratory consortia. A fundamental step in this direction is the "commercialization" of the hospital laboratory through a change in focus from being an in-house support program to becoming a regional resource. By the same token, the hospital laboratory can become an effective competitor of independent laboratories and be reconverted to a profit center. Creation of hospital laboratory consortia in a splintered, competitive environment requires a committed entrepreneurial effort and convincing evidence of potential benefits. The sequence of steps needed to achieve regional laboratory integration include concerting the goals and objectives of the interested parties, creating an appropriate committee structure, conducting a feasibility assessment, identifying alternative organizational and operational options, selecting a favorite option viewed by all parties as a win/win proposition, developing a business plan, and determining an implementation action plan. The major disadvantages of regionalization of laboratories are employee displacement, potential leveling of quality standards, and reduced hospital control. The major advantages include elimination of duplicate capital, personnel, and service costs, improved efficiency through test batching, reduced unit costs, increased technical capability through staff, instrument, and systems sharing, disengagement from hospital-imposed limitations, strengthened ability to penetrate the marketplace, freeing of hospital space for more direct patient care

The mechanism of enhanced wastewater nitrogen removal by photo-sequencing batch reactors based on comprehensive analysis of system dynamics within a cycle.

PubMed

Ye, Jianfeng; Liang, Junyu; Wang, Liang; Markou, Giorgos

2018-07-01

To understand the mechanism of enhanced nitrogen removal by photo-sequencing batch reactors (photo-SBRs), which incorporated microalgal photosynthetic oxygenation into the aerobic phases of a conventional cycle, this study performed comprehensive analysis of one-cycle dynamics. Under a low aeration intensity (about 0.02 vvm), a photo-SBR, illuminated with light at 92.27 μ·mol·m -2 ·s -1 , could remove 99.45% COD, 99.93% NH 4 + -N, 90.39% TN, and 95.17% TP, while the control SBR could only remove 98.36% COD, 83.51% NH 4 + -N, 78.96% TN, and 97.75% TP, for a synthetic domestic sewage. The specific oxygen production rate (SOPR) of microalgae in the photo-SBR could reach 6.63 fmol O 2 ·cell -1 ·h -1 . One-cycle dynamics shows that the enhanced nitrogen removal by photo-SBRs is related to photosynthetic oxygenation, resulting in strengthened nitrification, instead of direct nutrient uptake by microalgae. A too high light or aeration intensity could deteriorate anoxic conditions and thus adversely affect the removal of TN and TP in photo-SBRs. Copyright © 2018 Elsevier Ltd. All rights reserved.

Upscaling of U (VI) desorption and transport from decimeter‐scale heterogeneity to plume‐scale modeling

USGS Publications Warehouse

Curtis, Gary P.; Kohler, Matthias; Kannappan, Ramakrishnan; Briggs, Martin A.; Day-Lewis, Frederick D.

2015-01-01

Scientifically defensible predictions of field scale U(VI) transport in groundwater requires an understanding of key processes at multiple scales. These scales range from smaller than the sediment grain scale (less than 10 μm) to as large as the field scale which can extend over several kilometers. The key processes that need to be considered include both geochemical reactions in solution and at sediment surfaces as well as physical transport processes including advection, dispersion, and pore-scale diffusion. The research summarized in this report includes both experimental and modeling results in batch, column and tracer tests. The objectives of this research were to: (1) quantify the rates of U(VI) desorption from sediments acquired from a uranium contaminated aquifer in batch experiments;(2) quantify rates of U(VI) desorption in column experiments with variable chemical conditions, and(3) quantify nonreactive tracer and U(VI) transport in field tests.

Batch Proving and Proof Scripting in PVS

NASA Technical Reports Server (NTRS)

Munoz, Cesar A.

2007-01-01

The batch execution modes of PVS are powerful, but highly technical, features of the system that are mostly accessible to expert users. This paper presents a PVS tool, called ProofLite, that extends the theorem prover interface with a batch proving utility and a proof scripting notation. ProofLite enables a semi-literate proving style where specification and proof scripts reside in the same file. The goal of ProofLite is to provide batch proving and proof scripting capabilities to regular, non-expert, users of PVS.

GenBank.

PubMed

Benson, Dennis A; Karsch-Mizrachi, Ilene; Lipman, David J; Ostell, James; Sayers, Eric W

2009-01-01

GenBank is a comprehensive database that contains publicly available nucleotide sequences for more than 300,000 organisms named at the genus level or lower, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and accession numbers are assigned by GenBank(R) staff upon receipt. Daily data exchange with the European Molecular Biology Laboratory Nucleotide Sequence Database in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through the National Center for Biotechnology Information (NCBI) Entrez retrieval system, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI Homepage: www.ncbi.nlm.nih.gov.

GenBank.

PubMed

Benson, Dennis A; Karsch-Mizrachi, Ilene; Lipman, David J; Ostell, James; Wheeler, David L

2008-01-01

GenBank (R) is a comprehensive database that contains publicly available nucleotide sequences for more than 260 000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the web-based BankIt or standalone Sequin programs and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the European Molecular Biology Laboratory Nucleotide Sequence Database in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through NCBI's retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI Homepage: www.ncbi.nlm.nih.gov.

GenBank

PubMed Central

Benson, Dennis A.; Karsch-Mizrachi, Ilene; Lipman, David J.; Ostell, James; Wheeler, David L.

2008-01-01

GenBank (R) is a comprehensive database that contains publicly available nucleotide sequences for more than 260 000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the web-based BankIt or standalone Sequin programs and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the European Molecular Biology Laboratory Nucleotide Sequence Database in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through NCBI's retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI Homepage: www.ncbi.nlm.nih.gov PMID:18073190

Limestone and Zeolite as Alternative Media in Horizontal Subsurface Flow Constructed Wetlands: Laboratory-Scale Studies

NASA Astrophysics Data System (ADS)

Lizama, K.; Jaque, I.; Ayala, J.

2016-12-01

Arsenic is well known for its chronic toxicity. Millions of people around the world are currently at risk, drinking water with As concentrations above 10 ppb, the WHO drinking water guideline. Although different treatment options exist, they are often limited by elevated costs and maintenance requirements. Constructed wetlands are a natural water treatment system, capable to remove metals and metalloids -including As- via different physical, chemical and biological processes. The use of alternative supporting media to enhance As removal in subsurface flow wetlands has been recommended, but not sufficiently studied. Limestone and zeolite have been identified as effective supporting media in subsurface flow wetlands aiming As removal. However, there are still key aspects to be addressed, such as the implications of using these media, the speciation in the solid phase, the role of vegetation, etc. This study investigated the performance of limestone and zeolite in three types of experiments: batch, column and as main supporting media in a bench scale horizontal subsurface flow wetland system. Synthetic water resembling a contaminated river in Chile (As concentration=3 mg/L, Fe concentration= 100 mg/L, pH=2) was used in all experiments. In the batch experiments, the As concentration, the mass of media and the contact time were varied. The column system consisted of three limestone columns and three zeolite columns, operated under a hydraulic loading of 20 mm/d. The wetland system consisted of twelve PVC cells: six filled with zeolite and six with limestone. Phragmites australis were planted in three cells of each media type, as control cells. From the batch experiments, maximum As sorption capacities as indicated by Langmuir model were 1.3 mg/g for limestone and 0.17 mg/g for zeolite, at 18 h contact time and 6.3 g/L medium concentration. EDS and XPS analyses revealed that As and Fe were retained in zeolite at the end of the batch experiments. Zeolite and limestone

Physicochemical Characteristics of Transferon™ Batches.

PubMed

Medina-Rivero, Emilio; Vallejo-Castillo, Luis; Vázquez-Leyva, Said; Pérez-Sánchez, Gilberto; Favari, Liliana; Velasco-Velázquez, Marco; Estrada-Parra, Sergio; Pavón, Lenin; Pérez-Tapia, Sonia Mayra

2016-01-01

Transferon, a biotherapeutic agent that has been used for the past 2 decades for diseases with an inflammatory component, has been approved by regulatory authorities in Mexico (COFEPRIS) for the treatment of patients with herpes infection. The active pharmaceutical ingredient (API) of Transferon is based on polydispersion of peptides that have been extracted from lysed human leukocytes by a dialysis process and a subsequent ultrafiltration step to select molecules below 10 kDa. To physicochemically characterize the drug product, we developed chromatographic methods and an SDS-PAGE approach to analyze the composition and the overall variability of Transferon. Reversed-phase chromatographic profiles of peptide populations demonstrated batch-to-batch consistency from 10 representative batches that harbored 4 primary peaks with a relative standard deviation (RSD) of less than 7%. Aminogram profiles exhibited 17 proteinogenic amino acids and showed that glycine was the most abundant amino acid, with a relative content of approximately 18%. Further, based on their electrophoretic migration, the peptide populations exhibited a molecular mass of about 10 kDa. Finally, we determined the Transferon fingerprint using a mass spectrometry tool. Because each batch was produced from independent pooled buffy coat samples from healthy donors, supplied by a local blood bank, our results support the consistency of the production of Transferon and reveal its peptide identity with regard to its physicochemical attributes.

Physicochemical Characteristics of Transferon™ Batches

PubMed Central

Pérez-Sánchez, Gilberto; Favari, Liliana; Estrada-Parra, Sergio

2016-01-01

Transferon, a biotherapeutic agent that has been used for the past 2 decades for diseases with an inflammatory component, has been approved by regulatory authorities in Mexico (COFEPRIS) for the treatment of patients with herpes infection. The active pharmaceutical ingredient (API) of Transferon is based on polydispersion of peptides that have been extracted from lysed human leukocytes by a dialysis process and a subsequent ultrafiltration step to select molecules below 10 kDa. To physicochemically characterize the drug product, we developed chromatographic methods and an SDS-PAGE approach to analyze the composition and the overall variability of Transferon. Reversed-phase chromatographic profiles of peptide populations demonstrated batch-to-batch consistency from 10 representative batches that harbored 4 primary peaks with a relative standard deviation (RSD) of less than 7%. Aminogram profiles exhibited 17 proteinogenic amino acids and showed that glycine was the most abundant amino acid, with a relative content of approximately 18%. Further, based on their electrophoretic migration, the peptide populations exhibited a molecular mass of about 10 kDa. Finally, we determined the Transferon fingerprint using a mass spectrometry tool. Because each batch was produced from independent pooled buffy coat samples from healthy donors, supplied by a local blood bank, our results support the consistency of the production of Transferon and reveal its peptide identity with regard to its physicochemical attributes. PMID:27525277

Preconception Carrier Screening by Genome Sequencing: Results from the Clinical Laboratory.

PubMed

Punj, Sumit; Akkari, Yassmine; Huang, Jennifer; Yang, Fei; Creason, Allison; Pak, Christine; Potter, Amiee; Dorschner, Michael O; Nickerson, Deborah A; Robertson, Peggy D; Jarvik, Gail P; Amendola, Laura M; Schleit, Jennifer; Simpson, Dana Kostiner; Rope, Alan F; Reiss, Jacob; Kauffman, Tia; Gilmore, Marian J; Himes, Patricia; Wilfond, Benjamin; Goddard, Katrina A B; Richards, C Sue

2018-06-07

Advances in sequencing technologies permit the analysis of a larger selection of genes for preconception carrier screening. The study was designed as a sequential carrier screen using genome sequencing to analyze 728 gene-disorder pairs for carrier and medically actionable conditions in 131 women and their partners (n = 71) who were planning a pregnancy. We report here on the clinical laboratory results from this expanded carrier screening program. Variants were filtered and classified using the latest American College of Medical Genetics and Genomics (ACMG) guideline; only pathogenic and likely pathogenic variants were confirmed by orthologous methods before being reported. Novel missense variants were classified as variants of uncertain significance. We reported 304 variants in 202 participants. Twelve carrier couples (12/71 couples tested) were identified for common conditions; eight were carriers for hereditary hemochromatosis. Although both known and novel variants were reported, 48% of all reported variants were missense. For novel splice-site variants, RNA-splicing assays were performed to aid in classification. We reported ten copy-number variants and five variants in non-coding regions. One novel variant was reported in F8, associated with hemophilia A; prenatal testing showed that the male fetus harbored this variant and the neonate suffered a life-threatening hemorrhage which was anticipated and appropriately managed. Moreover, 3% of participants had variants that were medically actionable. Compared with targeted mutation screening, genome sequencing improves the sensitivity of detecting clinically significant variants. While certain novel variant interpretation remains challenging, the ACMG guidelines are useful to classify variants in a healthy population. Copyright © 2018 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

Sludge Washing and Demonstration of the DWPF Nitric/Formic Flowsheet in the SRNL Shielded Cells for Sludge Batch 9 Qualification

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pareizs, J.; Newell, D.; Martino, C.

Savannah River National Laboratory (SRNL) was requested by Savannah River Remediation (SRR) to qualify the next batch of sludge – Sludge Batch 9 (SB9). Current practice is to prepare sludge batches in Tank 51 by transferring sludge to Tank 51 from other tanks. The sludge is washed and transferred to Tank 40, the current Defense Waste Process Facility (DWPF) feed tank. Prior to sludge transfer from Tank 51 to Tank 40, the Tank 51 sludge must be qualified. SRNL qualifies the sludge in multiple steps. First, a Tank 51 sample is received, then characterized, washed, and again characterized. SRNL thenmore » demonstrates the DWPF Chemical Process Cell (CPC) flowsheet with the sludge. The final step of qualification involves chemical durability measurements of glass fabricated in the DWPF CPC demonstrations. In past sludge batches, SRNL had completed the DWPF demonstration with Tank 51 sludge. For SB9, SRNL has been requested to process a blend of Tank 51 and Tank 40 at a targeted ratio of 44% Tank 51 and 56% Tank 40 on an insoluble solids basis.« less

Citric acid production from hydrolysate of pretreated straw cellulose by Yarrowia lipolytica SWJ-1b using batch and fed-batch cultivation.

PubMed

Liu, Xiaoyan; Lv, Jinshun; Zhang, Tong; Deng, Yuanfang

2015-01-01

In this study, crude cellulase produced by Trichoderma reesei Rut-30 was used to hydrolyze pretreated straw. After the compositions of the hydrolysate of pretreated straw were optimized, the study showed that natural components of pretreated straw without addition of any other components such as (NH4)2SO4, KH2PO4, or Mg(2+) were suitable for citric acid production by Yarrowia lipolytica SWJ-1b, and the optimal ventilatory capacity was 10.0 L/min/L medium. Batch and fed-batch production of citric acid from the hydrolysate of pretreated straw by Yarrowia lipolytica SWJ-1b has been investigated. In the batch cultivation, 25.4 g/L and 26.7 g/L citric acid were yields from glucose and hydrolysate of straw cellulose, respectively, while the cultivation time was 120 hr. In the three-cycle fed-batch cultivation, citric acid (CA) production was increased to 42.4 g/L and the cultivation time was extended to 240 hr. However, iso-citric acid (ICA) yield in fed-batch cultivation (4.0 g/L) was similar to that during the batch cultivation (3.9 g/L), and only 1.6 g/L of reducing sugar was left in the medium at the end of fed-batch cultivation, suggesting that most of the added carbon was used in the cultivation.

A Batch Feeder for Inhomogeneous Bulk Materials

NASA Astrophysics Data System (ADS)

Vislov, I. S.; Kladiev, S. N.; Slobodyan, S. M.; Bogdan, A. M.

2016-04-01

The work includes the mechanical analysis of mechanical feeders and batchers that find application in various technological processes and industrial fields. Feeders are usually classified according to their design features into two groups: conveyor-type feeders and non-conveyor feeders. Batchers are used to batch solid bulk materials. Less frequently, they are used for liquids. In terms of a batching method, they are divided into volumetric and weighting batchers. Weighting batchers do not provide for sufficient batching accuracy. Automatic weighting batchers include a mass controlling sensor and systems for automatic material feed and automatic mass discharge control. In terms of operating principle, batchers are divided into gravitational batchers and batchers with forced feed of material using conveyors and pumps. Improved consumption of raw materials, decreased loss of materials, ease of use in automatic control systems of industrial facilities allows increasing the quality of technological processes and improve labor conditions. The batch feeder suggested by the authors is a volumetric batcher that has no comparable counterparts among conveyor-type feeders and allows solving the problem of targeted feeding of bulk material batches increasing reliability and hermeticity of the device.

The effect of impeller type on silica sol formation in laboratory scale agitated tank

NASA Astrophysics Data System (ADS)

Nurtono, Tantular; Suprana, Yayang Ade; Latif, Abdul; Dewa, Restu Mulya; Machmudah, Siti; Widiyastuti, Winardi, Sugeng

2016-02-01

The multiphase polymerization reaction of the silica sol formation produced from silicic acid and potassium hydroxide solutions in laboratory scale agitated tank was studied. The reactor is equipped with four segmental baffle and top entering impeller. The inside diameter of reactor is 9 cm, the baffle width is 0.9 cm, and the impeller position is 3 cm from tank bottom. The diameter of standard six blades Rushton and three blades marine propeller impellers are 5 cm. The silicic acid solution was made from 0.2 volume fraction of water glass (sodium silicate) solution in which the sodium ion was exchanged by hydrogen ion from cation resin. The reactor initially filled with 286 ml silicic acid solution was operated in semi batch mode and the temperature was kept constant in 60 °C. The 3 ml/minute of 1 M potassium hydroxide solution was added into stirred tank and the solution was stirred. The impeller rotational speed was varied from 100 until 700 rpm. This titration was stopped if the solution in stirred tank had reached the pH of 10-The morphology of the silica particles in the silica sol product was analyzed by Scanning Electron Microscope (SEM). The size of silica particles in silica sol was measured based on the SEM image. The silica particle obtained in this research was amorphous particle and the shape was roughly cylinder. The flow field generated by different impeller gave significant effect on particle size and shape. The smallest geometric mean of length and diameter of particle (4.92 µm and 2.42 µm, respectively) was generated in reactor with marine propeller at 600 rpm. The reactor with Rushton impeller produced particle which the geometric mean of length and diameter of particle was 4.85 µm and 2.36 µm, respectively, at 150 rpm.

Batch and multi-step fed-batch enzymatic saccharification of Formiline-pretreated sugarcane bagasse at high solid loadings for high sugar and ethanol titers.

PubMed

Zhao, Xuebing; Dong, Lei; Chen, Liang; Liu, Dehua

2013-05-01

Formiline pretreatment pertains to a biomass fractionation process. In the present work, Formiline-pretreated sugarcane bagasse was hydrolyzed with cellulases by batch and multi-step fed-batch processes at 20% solid loading. For wet pulp, after 144 h incubation with cellulase loading of 10 FPU/g dry solid, fed-batch process obtained ~150 g/L glucose and ~80% glucan conversion, while batch process obtained ~130 g/L glucose with corresponding ~70% glucan conversion. Solid loading could be further increased to 30% for the acetone-dried pulp. By fed-batch hydrolysis of the dried pulp in pH 4.8 buffer solution, glucose concentration could be 247.3±1.6 g/L with corresponding 86.1±0.6% glucan conversion. The enzymatic hydrolyzates could be well converted to ethanol by a subsequent fermentation using Saccharomices cerevisiae with ethanol titer of 60-70 g/L. Batch and fed-batch SSF indicated that Formiline-pretreated substrate showed excellent fermentability. The final ethanol concentration was 80 g/L with corresponding 82.7% of theoretical yield. Copyright © 2012 Elsevier Ltd. All rights reserved.

Reduction of excess sludge in a sequencing batch reactor by lysis-cryptic growth using quick lime for disintegration under low temperature.

PubMed

Lv, Xiao-Mei; Song, Ju-Sheng; Li, Ji; Zhai, Kun

2017-08-01

In the present study, quick-lime-based thermal-alkaline sludge disintegration (SD) under low temperature was combined with cryptic growth to investigate the excess sludge reduction efficiency in the sequencing batch reactor (SBR). The optimized condition of SD was as follows: T = 80℃, pH = 11, t = 180 min, and the SD rate was about 42.1%. With 65.6% of excess sludge disintegrated and returned to the SBR, the system achieved sludge reduction rate of about 40.1%. The lysis-cryptic growth still obtained satisfactory sludge reduction efficiency despite the comparative low SD rate, which suggested that disintegration rate might not be the decisive factor for cryptic-growth-based sludge reduction. Lysis-cryptic growth did not impact the effluent quality, yet the phosphorus removal performance was enhanced, with effluent total phosphorus concentration decreased by 0.3 mg/L (33%). Crystal compounds of calcium phosphate precipitate were detected in the system by Fourier transform infrared spectroscopy and X-ray diffraction, which indicated the phosphorus removal potential of SD using lime. Moreover, endogenous dehydrogenase activity of activated sludge in the lysis-cryptic system was enhanced, which was beneficial for sludge reduction. SD and cryptic growth in the present study demonstrates an economical and effective approach for sludge reduction.

Performance comparison of biofilm and suspended sludge from a sequencing batch biofilm reactor treating mariculture wastewater under oxytetracycline stress.

PubMed

Zheng, Dong; Gao, Mengchun; Wang, Zhe; She, Zonglian; Jin, Chunji; Chang, Qingbo

2016-09-01

The performance, extracellular polymeric substances (EPS) and microbial community of a sequencing batch biofilm reactor (SBBR) were investigated in treating mariculture wastewater under oxytetracycline stress. The chemical oxygen demand and [Formula: see text]-N removal efficiencies of the SBBR decreased with the increase of oxytetracycline concentration, and no obvious [Formula: see text]-N and [Formula: see text]-N accumulation in the effluent appeared at less than 10 mg L(-1) oxytetracycline. The specific oxygen utilization rate of the suspended sludge was more than that of the biofilm at different oxytetracycline concentrations. The specific ammonium oxidation rate (SAOR) of the biofilm was more easily affected by oxytetracycline than that of the suspended sludge, whereas the effect of oxytetracycline on the specific nitrite oxidation rate (SNOR) of the biofilm was less than that of the suspended sludge. The specific nitrate reduction rate of both the biofilm and suspended sludge was higher than the sum of the SAOR and SNOR at different oxytetracycline concentrations. The protein and polysaccharide contents in the EPS of the biofilm and suspended sludge increased with the increase of oxytetracycline concentration. The appearance of oxytetracycline in the influent could affect the chemical composition of the loosely bound EPS and tightly bound EPS. The amino, carboxyl and hydroxyl groups might be involved with interaction between EPS and oxytetracycline. The denaturing gradient gel electrophoresis profiles indicated that the variation of oxytetracycline concentration in the influent could affect the microbial communities of both the biofilm and suspended sludge.

Formulation and development of tablets based on Ludipress and scale-up from laboratory to production scale.

PubMed

Heinz, R; Wolf, H; Schuchmann, H; End, L; Kolter, K

2000-05-01

In spite of the wealth of experience available in the pharmaceutical industry, tablet formulations are still largely developed on an empirical basis, and the scale-up from laboratory to production is a time-consuming and costly process. Using Ludipress greatly simplifies formulation development and the manufacturing process because only the active ingredient Ludipress and a lubricant need to be mixed briefly before being compressed into tablets. The studies described here were designed to investigate the scale-up of Ludipress-based formulations from laboratory to production scale, and to predict changes in tablet properties due to changes in format, compaction pressure, and the use of different tablet presses. It was found that the tensile strength of tablets made of Ludipress increased linearly with compaction pressures up to 300 MPa. It was also independent of the geometry of the tablets (diameter, thickness, shape). It is therefore possible to give an equation with which the compaction pressure required to achieve a given hardness can be calculated for a given tablet form. The equation has to be modified slightly to convert from a single-punch press to a rotary tableting machine. Tablets produced in the rotary machine at the same pressure have a slightly higher tensile strength. The rate of increase in pressure, and therefore the throughput, has no effect on the tensile strength of Ludipress tablets. It is thought that a certain minimum dwell time is responsible for this difference. The production of tablets based on Ludipress can be scaled up from one rotary press to another without problem if the powder mixtures are prepared with the same mixing energy. The tensile strength curve determined for tablets made with Ludipress alone can also be applied to tablets with a small quantity (< 10%) of an active ingredient.

Effect of different salt adaptation strategies on the microbial diversity, activity, and settling of nitrifying sludge in sequencing batch reactors.

PubMed

Bassin, João Paulo; Kleerebezem, Robbert; Muyzer, Gerard; Rosado, Alexandre Soares; van Loosdrecht, Mark C M; Dezotti, Marcia

2012-02-01

The effect of salinity on the activity of nitrifying bacteria, floc characteristics, and microbial community structure accessed by fluorescent in situ hybridization and polymerase chain reaction-denaturing gradient gel electrophoresis techniques was investigated. Two sequencing batch reactors (SRB₁ and SBR₂) treating synthetic wastewater were subjected to increasing salt concentrations. In SBR₁, four salt concentrations (5, 10, 15, and 20 g NaCl/L) were tested, while in SBR₂, only two salt concentrations (10 and 20 g NaCl/L) were applied in a more shock-wise manner. The two different salt adaptation strategies caused different changes in microbial community structure, but did not change the nitrification performance, suggesting that regardless of the different nitrifying bacterial community present in the reactor, the nitrification process can be maintained stable within the salt range tested. Specific ammonium oxidation rates were more affected when salt increase was performed more rapidly and dropped 50% and 60% at 20 g NaCl/L for SBR₁ and SBR₂, respectively. A gradual increase in NaCl concentration had a positive effect on the settling properties (i.e., reduction of sludge volume index), although it caused a higher amount of suspended solids in the effluent. Higher organisms (e.g., protozoa, nematodes, and rotifers) as well as filamentous bacteria could not withstand the high salt concentrations.

A novel fed-batch based strategy for enhancing cell-density and recombinant cyprosin B production in bioreactors.

PubMed

Sampaio, P N; Pais, M S; Fonseca, L P

2014-12-01

Nowadays, the dairy industry is continuously looking for new and more efficient clotting enzymes to create innovative products. Cyprosin B is a plant aspartic protease characterized by clotting activity that was previously cloned in Saccharomyces cerevisiae BJ1991 strain. The production of recombinant cyprosin B by a batch and fed-batch culture was compared using glucose and galactose as carbon sources. The strategy for fed-batch cultivation involved two steps: in the first batch phase, the culture medium presented glucose 1 % (w/v) and galactose 0.5 % (w/v), while in the feed step the culture medium was constituted by 5 % (w/v) galactose with the aim to minimize the GAL7 promoter repression. Based on fed-batch, in comparison to batch growth, an increase in biomass (6.6-fold), protein concentration (59 %) and cyprosin B activity (91 %) was achieved. The recombinant cyprosin B was purified by a single hydrophobic chromatography, presenting a specific activity of 6 × 10(4) U·mg(-1), corresponding to a purification degree of 12.5-fold and a recovery yield of 16.4 %. The SDS-PAGE analysis showed that recovery procedure is suitable for achieving the purified recombinant cyprosin B. The results show that the recombinant cyprosin B production can be improved based on two distinct steps during the fed-batch, presenting that this strategy, associated with a simplified purification procedure, could be applied to large-scale production, constituting a new and efficient alternative for animal and fungal enzymes widely used in cheese making.

Full-scale and laboratory-scale anaerobic treatment of citric acid production wastewater.

PubMed

Colleran, E; Pender, S; Philpott, U; O'Flaherty, V; Leahy, B

1998-01-01

This paper reviews the operation of a full-scale, fixed-bed digester treating a citric acid production wastewater with a COD:sulphate ratio of 3-4:1. Support matrix pieces were removed from the digester at intervals during the first 5 years of operation in order to quantify the vertical distribution of biomass within the digester. Detailed analysis of the digester biomass after 5 years of operation indicated that H2 and propionate-utilising SRB had outcompeted hydrogenophilic methanogens and propionate syntrophs. Acetoclastic methanogens were shown to play the dominant role in acetate conversion. Butyrate and ethanol-degrading syntrophs also remained active in the digester after 5 years of operation. Laboratory-scale hybrid reactor treatment at 55 degrees C of a diluted molasses influent, with and without sulphate supplementation, showed that the reactors could be operated with high stability at volumetric loading rates of 24 kgCOD.m-3.d-1 (12 h HRT). In the presence of sulphate (2 g/l-1; COD/sulphate ratio of 6:1), acetate conversion was severely inhibited, resulting in effluent acetate concentrations of up to 4000 mg.l-1.

Fluid dynamics structures in a fire environment observed in laboratory-scale experiments

Treesearch

J. Lozano; W. Tachajapong; D.R. Weise; S. Mahalingam; M. Princevac

2010-01-01

Particle Image Velocimetry (PIV) measurements were performed in laboratory-scale experimental fires spreading across horizontal fuel beds composed of aspen (Populus tremuloides Michx) excelsior. The continuous flame, intermittent flame, and thermal plume regions of a fire were investigated. Utilizing a PIV system, instantaneous velocity fields for...

Nano iron particles transport in fractured rocks: laboratory and field scale

NASA Astrophysics Data System (ADS)

Cohen, Meirav; Weisbrod, Noam

2017-04-01

Our study deals with the transport potential of nano iron particles (NIPs) in fractured media. Two different systemswere used to investigate transport on two scales: (1 )a laboratory flow system of a naturally discrete fractured chalk core, 0.43 and 0.18 m in length and diamater, respectively; and (2) a field system of hydraulically connected boreholes located 47 m apart which penetrate a fractured chalk aquifer. We started by testing the transport potential of various NIPs under different conditions. Particle stability experiments were conducted using various NIPs and different stabilizersat two ionic strengths. Overall, four different NIPs and three stabilizers were tested. Particles and solution properties (stability, aggregate/particle size, viscosity and density) were tested in batch experiments, and transport experiments (breakthrough curves (BTCs) and recovery) were conduted in the fractured chalk core. We have learned that the key parameters controlling particle transport are the particle/aggregate size and stability, which govern NIP settling rates and ultimately their migration distance. The governing mechanism controlling NIP transport was found to be sedimentation, and to a much lesser extent, processes such as diffusion, straining or interception. On the basis of these experiments, Carbo-Iron® particles ( 800 nm activated carbon particles doped with nano zero valent iron particles) and Carboxymethyl cellulose (CMC) stabilizer were selected for the field test injection. In the field, Carbo-Iron particles were initially injected into the fractured aquifer using an excess of stabilizer in order to ensure maximum recovery. This resulted in high particle recovery and fast arrival time, similar to the ideal tracer (iodide). The high recovery of the stable particle solution emphasized the importance of particle stability for transport in fractures. To test mobility manipulation potential of the particles and simulate more realistic scenarios, a second field

40 CFR 63.1326 - Batch process vents-recordkeeping provisions.

Code of Federal Regulations, 2013 CFR

2013-07-01

... (CONTINUED) National Emission Standards for Hazardous Air Pollutant Emissions: Group IV Polymers and Resins § 63.1326 Batch process vents—recordkeeping provisions. (a) Group determination records for batch... this section for each batch process vent subject to the group determination procedures of § 63.1323...

On the dominant noise components of tactical aircraft: Laboratory to full scale

NASA Astrophysics Data System (ADS)

Tam, Christopher K. W.; Aubert, Allan C.; Spyropoulos, John T.; Powers, Russell W.

2018-05-01

This paper investigates the dominant noise components of a full-scale high performance tactical aircraft. The present study uses acoustic measurements of the exhaust jet from a single General Electric F414-400 turbofan engine installed in a Boeing F/A-18E Super Hornet aircraft operating from flight idle to maximum afterburner. The full-scale measurements are to the ANSI S12.75-2012 standard employing about 200 microphones. By comparing measured noise spectra with those from hot supersonic jets observed in the laboratory, the dominant noise components specific to the F/A-18E aircraft at different operating power levels are identified. At intermediate power, it is found that the dominant noise components of an F/A-18E aircraft are essentially the same as those of high temperature supersonic laboratory jets. However, at military and afterburner powers, there are new dominant noise components. Their characteristics are then documented and analyzed. This is followed by an investigation of their origin and noise generation mechanisms.

Effect of nacelle on wake meandering in a laboratory scale wind turbine using LES

NASA Astrophysics Data System (ADS)

Foti, Daniel; Yang, Xiaolei; Guala, Michele; Sotiropoulos, Fotis

2015-11-01

Wake meandering, large scale motion in the wind turbine wakes, has considerable effects on the velocity deficit and turbulence intensity in the turbine wake from the laboratory scale to utility scale wind turbines. In the dynamic wake meandering model, the wake meandering is assumed to be caused by large-scale atmospheric turbulence. On the other hand, Kang et al. (J. Fluid Mech., 2014) demonstrated that the nacelle geometry has a significant effect on the wake meandering of a hydrokinetic turbine, through the interaction of the inner wake of the nacelle vortex with the outer wake of the tip vortices. In this work, the significance of the nacelle on the wake meandering of a miniature wind turbine previously used in experiments (Howard et al., Phys. Fluid, 2015) is demonstrated with large eddy simulations (LES) using immersed boundary method with fine enough grids to resolve the turbine geometric characteristics. The three dimensionality of the wake meandering is analyzed in detail through turbulent spectra and meander reconstruction. The computed flow fields exhibit wake dynamics similar to those observed in the wind tunnel experiments and are analyzed to shed new light into the role of the energetic nacelle vortex on wake meandering. This work was supported by Department of Energy DOE (DE-EE0002980, DE-EE0005482 and DE-AC04-94AL85000), and Sandia National Laboratories. Computational resources were provided by Sandia National Laboratories and the University of Minnesota Supercomputing.

Sequence analysis of chromosome 1 revealed different selection patterns between Chinese wild mice and laboratory strains.

PubMed

Xu, Fuyi; Hu, Shixian; Chao, Tianzhu; Wang, Maochun; Li, Kai; Zhou, Yuxun; Xu, Hongyan; Xiao, Junhua

2017-10-01

Both natural and artificial selection play a critical role in animals' adaptation to the environment. Detection of the signature of selection in genomic regions can provide insights for understanding the function of specific phenotypes. It is generally assumed that laboratory mice may experience intense artificial selection while wild mice more natural selection. However, the differences of selection signature in the mouse genome and underlying genes between wild and laboratory mice remain unclear. In this study, we used two mouse populations: chromosome 1 (Chr 1) substitution lines (C1SLs) derived from Chinese wild mice and mouse genome project (MGP) sequenced inbred strains and two selection detection statistics: Fst and Tajima's D to identify the signature of selection footprint on Chr 1. For the differentiation between the C1SLs and MGP, 110 candidate selection regions containing 47 protein coding genes were detected. A total of 149 selection regions which encompass 7.215 Mb were identified in the C1SLs by Tajima's D approach. While for the MGP, we identified nearly twice selection regions (243) compared with the C1SLs which accounted for 13.27 Mb Chr 1 sequence. Through functional annotation, we identified several biological processes with significant enrichment including seven genes in the olfactory transduction pathway. In addition, we searched the phenotypes associated with the 47 candidate selection genes identified by Fst. These genes were involved in behavior, growth or body weight, mortality or aging, and immune systems which align well with the phenotypic differences between wild and laboratory mice. Therefore, the findings would be helpful for our understanding of the phenotypic differences between wild and laboratory mice and applications for using this new mouse resource (C1SLs) for further genetics studies.

Potential Uses and Inherent Challenges of Using Genome-Scale Sequencing to Augment Current Newborn Screening.

PubMed

Berg, Jonathan S; Powell, Cynthia M

2015-10-05

Since newborn screening (NBS) began in the 1960s, technological advances have enabled its expansion to include an increasing number of disorders. Recent developments now make it possible to sequence an infant's genome relatively quickly and economically. Clinical application of whole-exome and whole-genome sequencing is expanding at a rapid pace but presents many challenges. Its utility in NBS has yet to be demonstrated and its application in the pediatric population requires examination, not only for potential clinical benefits, but also for the unique ethical challenges it presents. Copyright © 2015 Cold Spring Harbor Laboratory Press; all rights reserved.

A Simple Laboratory Scale Model of Iceberg Dynamics and its Role in Undergraduate Education

NASA Astrophysics Data System (ADS)

Burton, J. C.; MacAyeal, D. R.; Nakamura, N.

2011-12-01

Lab-scale models of geophysical phenomena have a long history in research and education. For example, at the University of Chicago, Dave Fultz developed laboratory-scale models of atmospheric flows. The results from his laboratory were so stimulating that similar laboratories were subsequently established at a number of other institutions. Today, the Dave Fultz Memorial Laboratory for Hydrodynamics (http://geosci.uchicago.edu/~nnn/LAB/) teaches general circulation of the atmosphere and oceans to hundreds of students each year. Following this tradition, we have constructed a lab model of iceberg-capsize dynamics for use in the Fultz Laboratory, which focuses on the interface between glaciology and physical oceanography. The experiment consists of a 2.5 meter long wave tank containing water and plastic "icebergs". The motion of the icebergs is tracked using digital video. Movies can be found at: http://geosci.uchicago.edu/research/glaciology_files/tsunamigenesis_research.shtml. We have had 3 successful undergraduate interns with backgrounds in mathematics, engineering, and geosciences perform experiments, analyze data, and interpret results. In addition to iceberg dynamics, the wave-tank has served as a teaching tool in undergraduate classes studying dam-breaking and tsunami run-up. Motivated by the relatively inexpensive cost of our apparatus (~1K-2K dollars) and positive experiences of undergraduate students, we hope to serve as a model for undergraduate research and education that other universities may follow.

Upscaling of U(VI) Desorption and Transport from Decimeter-Scale Heterogeneity to Plume-Scale Modeling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Curtis, Gary P.; Kohler, Matthias; Kannappan, Ramakrishnan

2015-02-24

Scientifically defensible predictions of field scale U(VI) transport in groundwater requires an understanding of key processes at multiple scales. These scales range from smaller than the sediment grain scale (less than 10 μm) to as large as the field scale which can extend over several kilometers. The key processes that need to be considered include both geochemical reactions in solution and at sediment surfaces as well as physical transport processes including advection, dispersion, and pore-scale diffusion. The research summarized in this report includes both experimental and modeling results in batch, column and tracer tests. The objectives of this research weremore » to: (1) quantify the rates of U(VI) desorption from sediments acquired from a uranium contaminated aquifer in batch experiments;(2) quantify rates of U(VI) desorption in column experiments with variable chemical conditions, and(3) quantify nonreactive tracer and U(VI) transport in field tests.« less

Performance evaluation of a granular activated carbon-sequencing batch biofilm reactor pilot plant system used in treating real wastewater from recycled paper industry.

PubMed

Muhamad, Mohd Hafizuddin; Sheikh Abdullah, Siti Rozaimah; Mohamad, Abu Bakar; Rahman, Rakmi Abdul; Kadhum, Abdul Amir Hasan

2012-01-01

A pilot scale granular activated carbon-sequencing batch biofilm reactor with a capacity of 2.2 m3 was operated for over three months to evaluate its performance treating real recycled paper industry wastewater under different operational conditions. In this study, dissolved air floatation (DAF) and clarifier effluents were used as influent sources of the pilot plant. During the course of the study, the reactor was able to biodegrade the contaminants in the incoming recycled paper mill wastewater in terms of chemical oxygen demand (COD), adsorbable organic halides (AOX; specifically 2,4-dichlorophenol (2,4-DCP)) and ammoniacal nitrogen (NH3-N) removal efficiencies at varying hydraulic retention times (HRTs) of 1-3 days, aeration rates (ARs) of 2.1-3.4 m3/min and influent feed concentration of 40-950 mg COD/l. Percentages of COD, 2,4-DCP and NH3-N removals increased with increasing HRT, resulting in more than 90% COD, 2,4-DCP and NH3-N removals at HRT values above two days. Degradation of COD, 2,4-DCP and NH3-N were seriously affected by variation of ARs, which resulted in significant decrease of COD, 2,4-DCP and NH3-N removals by decreasing ARs from 3.4 m3/min to 2.1 m3/min, varying in the ranges of 24-80%, 6-96% and 5-42%, respectively. In comparison to the clarifier effluent, the treatment performance of DAF effluent, containing high COD concentration, resulted in a higher COD removal of 82%. The use of diluted DAF effluent did not improve significantly the COD removal. Higher NH3-N removal efficiency of almost 100% was observed during operation after maintenance shutdown compared to normal operation, even at the same HRT of one day due to the higher dissolved oxygen concentrations (1-7 mg/l), while no significant difference in COD removal efficiency was observed.

Microbial succession in response to pollutants in batch-enrichment culture

PubMed Central

Jiao, Shuo; Chen, Weimin; Wang, Entao; Wang, Junman; Liu, Zhenshan; Li, Yining; Wei, Gehong

2016-01-01

As a global problem, environmental pollution is an important factor to shape the microbial communities. The elucidation of the succession of microbial communities in response to pollutants is essential for developing bioremediation procedures. In the present study, ten batches of soil-enrichment subcultures were subjected to four treatments: phenanthrene, n-octadecane, phenanthrene + n-octadecane, or phenanthrene + n-octadecane + CdCl2. Forty pollutant-degrading consortia, corresponding to each batch of the four treatments were obtained. High-throughput sequencing of the 16S rRNA gene revealed that the diversity, richness and evenness of the consortia decreased throughout the subculturing procedure. The well-known hydrocarbon degraders Acinetobacter, Gordonia, Sphingobium, Sphingopyxis, and Castellaniella and several other genera, including Niabella and Naxibacter, were detected in the enriched consortia. The predominant microbes varied and the microbial community in the consortia gradually changed during the successive subculturing depending on the treatment, indicating that the pollutants influenced the microbial successions. Comparison of the networks in the treatments indicated that organic pollutants and CdCl2 affected the co-occurrence patterns in enriched consortia. In conclusion, single environmental factors, such as the addition of nutrients or selection pressure, can shape microbial communities and partially explain the extensive differences in microbial community structures among diverse environments. PMID:26905741

Manufacturing demonstration of microbially mediated zinc sulfide nanoparticles in pilot-plant scale reactors

DOE PAGES

Moon, Ji-Won; Phelps, Tommy J.; Fitzgerald Jr, Curtis L.; ...

2016-04-27

The thermophilic anaerobic metal-reducing bacterium Thermoanaerobacter sp. X513 efficiently produces zinc sulfide (ZnS) nanoparticles (NPs) in laboratory-scale ( ≤24-L) reactors. To determine whether this process can be up-scaled and adapted for pilot-plant production while maintaining NP yield and quality, a series of meso-scale experiments were performed using 100-l and 900-l reactors. Pasteurization and N 2-sparging replaced autoclaving and boiling for deoxygenating media in the transition from small-scale to pilot-plant reactors. Consecutive 100-L batches using new or recycled media produced ZnS NPs with highly reproducible ~2 nm average crystallite size (ACS) and yields of ~0.5g L -1, similar to small-scale batches.more » The 900-L pilot plant reactor produced ~ 320 g ZnS without process optimization or replacement of used medium; this quantity would be sufficient to form a ZnS thin film with ~120 nm thickness over 0.5 m width 13 km length. At all scales, the bacteria produced significant amounts of acetic, lactic and formic acids, which could be neutralized by the controlled addition of sodium hydroxide without the use of an organic pH buffer, eliminating 98% of the buffer chemical costs. In conclusion, the final NP products were characterized using XRD, ICP-OES, FTIR, DLS, and C/N analyses, which confirmed the growth medium without organic buffer enhanced the ZnS NP properties by reducing carbon and nitrogen surface coatings and supporting better dispersivity with similar ACS.« less

Manufacturing demonstration of microbially mediated zinc sulfide nanoparticles in pilot-plant scale reactors.

PubMed

Moon, Ji-Won; Phelps, Tommy J; Fitzgerald, Curtis L; Lind, Randall F; Elkins, James G; Jang, Gyoung Gug; Joshi, Pooran C; Kidder, Michelle; Armstrong, Beth L; Watkins, Thomas R; Ivanov, Ilia N; Graham, David E

2016-09-01

The thermophilic anaerobic metal-reducing bacterium Thermoanaerobacter sp. X513 efficiently produces zinc sulfide (ZnS) nanoparticles (NPs) in laboratory-scale (≤ 24-L) reactors. To determine whether this process can be up-scaled and adapted for pilot-plant production while maintaining NP yield and quality, a series of pilot-plant scale experiments were performed using 100-L and 900-L reactors. Pasteurization and N2-sparging replaced autoclaving and boiling for deoxygenating media in the transition from small-scale to pilot plant reactors. Consecutive 100-L batches using new or recycled media produced ZnS NPs with highly reproducible ~2-nm average crystallite size (ACS) and yields of ~0.5 g L(-1), similar to the small-scale batches. The 900-L pilot plant reactor produced ~320 g ZnS without process optimization or replacement of used medium; this quantity would be sufficient to form a ZnS thin film with ~120 nm thickness over 0.5 m width × 13 km length. At all scales, the bacteria produced significant amounts of acetic, lactic, and formic acids, which could be neutralized by the controlled addition of sodium hydroxide without the use of an organic pH buffer, eliminating 98 % of the buffer chemical costs. The final NP products were characterized using XRD, ICP-OES, TEM, FTIR, PL, DLS, HPLC, and C/N analyses, which confirmed that the growth medium without organic buffer enhanced the ZnS NP properties by reducing carbon and nitrogen surface coatings and supporting better dispersivity with similar ACS.

NDA Batch 2002-13

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hollister, R

QC sample results (daily background check drum and 100-gram SGS check drum) were within acceptance criteria established by WIPP's Quality Assurance Objectives for TRU Waste Characterization. Replicate runs were performed on drum LL85501243TRU. Replicate measurement results are identical at the 95% confidence level as established by WIPP criteria. HWM NCAR No. 02-1000168 issued on 17-Oct-2002 regarding a partially dislodged Cd sheet filter on the HPGe coaxial detector. This physical geometry occurred on 01-Oct-2002 and was not corrected until 10-Oct-2002, during which period is inclusive of the present batch run of drums. Per discussions among the Independent Technical Reviewer, Expert Reviewermore » and the Technical QA Supervisor, as well as in consultation with John Fleissner, Technical Point of Contact from Canberra, the analytical results are technically reliable. All QC standard runs during this period were in control. Data packet for SGS Batch 2002-13 generated using passive gamma-ray spectroscopy with the Pu Facility SGS unit is technically reasonable. All QC samples are in compliance with establiShed control limits. The batch data packet has been reviewed for correctness, completeness, consistency and compliance with WIPP's Quality Assurance Objectives and determined to be acceptable.« less

MODELING CST ION EXCHANGE FOR CESIUM REMOVAL FROM SCIX BATCHES 1 - 4

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smith, F.

2011-04-25

The objective of this work is, through modeling, to predict the performance of Crystalline Silicotitinate (CST) for the removal of cesium from Small Column Ion Exchange (SCIX) Batches 1-4 (as proposed in Revision 16 of the Liquid Waste System Plan). The scope of this task is specified in Technical Task Request (TTR) 'SCIX Feed Modeling', HLE-TTR-2011-003, which specified using the Zheng, Anthony, Miller (ZAM) code to predict CST isotherms for six given SCIX feed compositions and the VErsatile Reaction and SEparation simulator for Liquid Chromatography (VERSE-LC) code to predict ion-exchange column behavior. The six SCIX feed compositions provided in themore » TTR represent SCIX Batches 1-4 and Batches 1 and 2 without caustic addition. The study also investigated the sensitivity in column performance to: (1) Flow rates of 5, 10, and 20 gpm with 10 gpm as the nominal flow; and (2) Temperatures of 25, 35, and 45 C with 35 C as the nominal temperature. The isotherms and column predictions presented in this report reflect the expected performance of engineered CST IE-911. This form of CST was used in experiments conducted at the Savannah River National Laboratory (SRNL) that formed the basis for estimating model parameters (Hamm et al., 2002). As has been done previously, the engineered resin capacity is estimated to be 68% of the capacity of particulate CST without binder.« less

40 CFR 63.1406 - Reactor batch process vent provisions.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 11 2011-07-01 2011-07-01 false Reactor batch process vent provisions... § 63.1406 Reactor batch process vent provisions. (a) Emission standards. Owners or operators of reactor... reactor batch process vent located at a new affected source shall control organic HAP emissions by...

40 CFR 63.1406 - Reactor batch process vent provisions.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 11 2010-07-01 2010-07-01 true Reactor batch process vent provisions... § 63.1406 Reactor batch process vent provisions. (a) Emission standards. Owners or operators of reactor... reactor batch process vent located at a new affected source shall control organic HAP emissions by...

ReSeqTools: an integrated toolkit for large-scale next-generation sequencing based resequencing analysis.

PubMed

He, W; Zhao, S; Liu, X; Dong, S; Lv, J; Liu, D; Wang, J; Meng, Z

2013-12-04

Large-scale next-generation sequencing (NGS)-based resequencing detects sequence variations, constructs evolutionary histories, and identifies phenotype-related genotypes. However, NGS-based resequencing studies generate extraordinarily large amounts of data, making computations difficult. Effective use and analysis of these data for NGS-based resequencing studies remains a difficult task for individual researchers. Here, we introduce ReSeqTools, a full-featured toolkit for NGS (Illumina sequencing)-based resequencing analysis, which processes raw data, interprets mapping results, and identifies and annotates sequence variations. ReSeqTools provides abundant scalable functions for routine resequencing analysis in different modules to facilitate customization of the analysis pipeline. ReSeqTools is designed to use compressed data files as input or output to save storage space and facilitates faster and more computationally efficient large-scale resequencing studies in a user-friendly manner. It offers abundant practical functions and generates useful statistics during the analysis pipeline, which significantly simplifies resequencing analysis. Its integrated algorithms and abundant sub-functions provide a solid foundation for special demands in resequencing projects. Users can combine these functions to construct their own pipelines for other purposes.

The Mouse Genomes Project: a repository of inbred laboratory mouse strain genomes.

PubMed

Adams, David J; Doran, Anthony G; Lilue, Jingtao; Keane, Thomas M

2015-10-01

The Mouse Genomes Project was initiated in 2009 with the goal of using next-generation sequencing technologies to catalogue molecular variation in the common laboratory mouse strains, and a selected set of wild-derived inbred strains. The initial sequencing and survey of sequence variation in 17 inbred strains was completed in 2011 and included comprehensive catalogue of single nucleotide polymorphisms, short insertion/deletions, larger structural variants including their fine scale architecture and landscape of transposable element variation, and genomic sites subject to post-transcriptional alteration of RNA. From this beginning, the resource has expanded significantly to include 36 fully sequenced inbred laboratory mouse strains, a refined and updated data processing pipeline, and new variation querying and data visualisation tools which are available on the project's website ( http://www.sanger.ac.uk/resources/mouse/genomes/ ). The focus of the project is now the completion of de novo assembled chromosome sequences and strain-specific gene structures for the core strains. We discuss how the assembled chromosomes will power comparative analysis, data access tools and future directions of mouse genetics.

MBASIC batch processor architectural overview

NASA Technical Reports Server (NTRS)

Reynolds, S. M.

1978-01-01

The MBASIC (TM) batch processor, a language translator designed to operate in the MBASIC (TM) environment is described. Features include: (1) a CONVERT TO BATCH command, usable from the ready mode; and (2) translation of the users program in stages through several levels of intermediate language and optimization. The processor is to be designed and implemented in both machine-independent and machine-dependent sections. The architecture is planned so that optimization processes are transparent to the rest of the system and need not be included in the first design implementation cycle.

Complete Genome Sequence of a New Ruminococcaceae Bacterium Isolated from Anaerobic Biomass Hydrolysis.

PubMed

Hahnke, Sarah; Abendroth, Christian; Langer, Thomas; Codoñer, Francisco M; Ramm, Patrice; Porcar, Manuel; Luschnig, Olaf; Klocke, Michael

2018-04-05

A new Ruminococcaceae bacterium, strain HV4-5-B5C, participating in the anaerobic digestion of grass, was isolated from a mesophilic two-stage laboratory-scale leach bed biogas system. The draft annotated genome sequence presented in this study and 16S rRNA gene sequence analysis indicated the affiliation of HV4-5-B5C with the family Ruminococcaceae outside recently described genera. Copyright © 2018 Hahnke et al.

Using GenBank.

PubMed

Wheeler, David

2007-01-01

GenBank(R) is a comprehensive database of publicly available DNA sequences for more than 205,000 named organisms and for more than 60,000 within the embryophyta, obtained through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Daily data exchange with the European Molecular Biology Laboratory (EMBL) in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through the National Center for Biotechnology Information (NCBI) retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases with taxonomy, genome, mapping, protein structure, and domain information and the biomedical journal literature through PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available through FTP. GenBank usage scenarios ranging from local analyses of the data available through FTP to online analyses supported by the NCBI Web-based tools are discussed. To access GenBank and its related retrieval and analysis services, go to the NCBI Homepage at http://www.ncbi.nlm.nih.gov.

NG6: Integrated next generation sequencing storage and processing environment.

PubMed

Mariette, Jérôme; Escudié, Frédéric; Allias, Nicolas; Salin, Gérald; Noirot, Céline; Thomas, Sylvain; Klopp, Christophe

2012-09-09

Next generation sequencing platforms are now well implanted in sequencing centres and some laboratories. Upcoming smaller scale machines such as the 454 junior from Roche or the MiSeq from Illumina will increase the number of laboratories hosting a sequencer. In such a context, it is important to provide these teams with an easily manageable environment to store and process the produced reads. We describe a user-friendly information system able to manage large sets of sequencing data. It includes, on one hand, a workflow environment already containing pipelines adapted to different input formats (sff, fasta, fastq and qseq), different sequencers (Roche 454, Illumina HiSeq) and various analyses (quality control, assembly, alignment, diversity studies,…) and, on the other hand, a secured web site giving access to the results. The connected user will be able to download raw and processed data and browse through the analysis result statistics. The provided workflows can easily be modified or extended and new ones can be added. Ergatis is used as a workflow building, running and monitoring system. The analyses can be run locally or in a cluster environment using Sun Grid Engine. NG6 is a complete information system designed to answer the needs of a sequencing platform. It provides a user-friendly interface to process, store and download high-throughput sequencing data.

The effect of hydraulic retention time on the performance and fouling characteristics of membrane sequencing batch reactors used for the treatment of synthetic petroleum refinery wastewater.

PubMed

Shariati, Seyed Ramin Pajoum; Bonakdarpour, Babak; Zare, Nasim; Ashtiani, Farzin Zokaee

2011-09-01

The use of membrane sequencing batch reactors, operated at HRT of 8, 16 and 24h, was considered for the treatment of a synthetic petroleum wastewater. Increase in HRT resulted in statistically significant decrease in MLSS. Removal efficiencies higher than 97% were found for the three model hydrocarbon pollutants at all HRTs, with air stripping making a small contribution to overall removal. Particle size distribution (PSD) and microscopic analysis showed reduction in the protozoan populations in the activated sludge with decreasing HRT. PSD analysis also showed a higher proportion of larger and smaller sized particles at the lowest HRT. The rate of membrane fouling was found to increase with decreasing HRT; SMP, especially carbohydrate SMP, and mixed liquor apparent viscosity also showed a pronounced increase with decreasing HRT, whereas the concentration of EPS and its components decreased. FTIR analysis identified organic compounds as the main component of membrane pore fouling. Copyright © 2011 Elsevier Ltd. All rights reserved.

Attempt to model laboratory-scale diffusion and retardation data.

PubMed

Hölttä, P; Siitari-Kauppi, M; Hakanen, M; Tukiainen, V

2001-02-01

Different approaches for measuring the interaction between radionuclides and rock matrix are needed to test the compatibility of experimental retardation parameters and transport models used in assessing the safety of the underground repositories for the spent nuclear fuel. In this work, the retardation of sodium, calcium and strontium was studied on mica gneiss, unaltered, moderately altered and strongly altered tonalite using dynamic fracture column method. In-diffusion of calcium into rock cubes was determined to predict retardation in columns. In-diffusion of calcium into moderately and strongly altered tonalite was interpreted using a numerical code FTRANS. The code was able to interprete in-diffusion of weakly sorbing calcium into the saturated porous matrix. Elution curves of calcium for the moderately and strongly altered tonalite fracture columns were explained adequately using FTRANS code and parameters obtained from in-diffusion calculations. In this paper, mass distribution ratio values of sodium, calcium and strontium for intact rock are compared to values, previously obtained for crushed rock from batch and crushed rock column experiments. Kd values obtained from fracture column experiments were one order of magnitude lower than Kd values from batch experiments.

Effect of skill laboratory training on academic performance of medical students.

PubMed

Khan, Muhammad Alamgir; Shabbir, Faizania; Qamar, Khadija; Rajput, Tausif Ahmed

2017-05-01

To observe the effect of skill lab training on academic performance of final year medical students in terms of marks obtained in long case, short case, objective structured clinical examination and viva. The cross-sectional comparative study was conducted at Army Medical College, Rawalpindi from February to April 2015. Two batches of final year MBBS were recruited for the study. Batch 1 received conventional training, and Batch 2 received skill lab training. The performance of students was assessed by comparing the marks obtained in long case, short case, objective structured clinical examination and viva. Data was analysed using SPSS 23. Of the 335 subjects, 168(50.1%) were male and 167(49.9%) were female students with a mean age of 21.79±1.02 years. Batch 1 had 151(45%) students and Batch 2 had 184(55%). Batch 2 got significantly higher marks in long case, short case and objective structured clinical examination (p<0.05 each). Viva result was not found to be related to training (p>0.05). Acquisition of clinical skills significantly improved when medial students were trained in skill laboratories.

Whole-Genome Sequence of Coxiella burnetii Nine Mile RSA439 (Phase II, Clone 4), a Laboratory Workhorse Strain

PubMed Central

Beare, Paul A.; Moses, Abraham S.; Martens, Craig A.; Heinzen, Robert A.

2017-01-01

ABSTRACT Here, we report the whole-genome sequence of Coxiella burnetii Nine Mile RSA439 (phase II, clone 4), a laboratory strain used extensively to investigate the biology of this intracellular bacterial pathogen. The genome consists of a 1.97-Mb chromosome and a 37.32-kb plasmid. PMID:28596399

Scale-up of recombinant Opc protein production in Escherichia coli for a meningococcal vaccine.

PubMed

Pérez, Raúl Espinosa; Lasa, Alexis Musacchio; Rodríguez, Ricardo Silva; Menéndez, Evelin Caballero; Suárez, José García; Balaguer, Héctor Díaz

2006-12-15

Opc is an outer membrane protein from Neisseria meningitidis present in meningococcal vaccine preparations. The opc gene, codifying for this protein, was cloned in to Escherichia coli and the Opc protein was expressed under the control of a tryptophan promoter. The recombinant strain was grown in batch cultures. Opc was expressed as inclusion bodies at about 32% of the total cellular protein. We examined the scale-up culture conditions for the production of the recombinant Opc. The scale-up process was performed from 1.5 l to 50 l culture, using first, the constant power per unit of volume (P/V) as main scaling criteria, and then the oxygen mass transfer coefficient (K(L)a) scaling criteria to adjust the optimal aeration conditions. A final productivity of 52 mgl(-1)h(-1) was obtained at the 50l culture scale compared with the 49 mgl(-1)h(-1) productivity at 1.5l laboratory scale.

Laboratory- and full-scale studies on the removal of pharmaceuticals in an aerated constructed wetland: effects of aeration and hydraulic retention time on the removal efficiency and assessment of the aquatic risk.

PubMed

Auvinen, Hannele; Gebhardt, Wilhelm; Linnemann, Volker; Du Laing, Gijs; Rousseau, Diederik P L

2017-09-01

Pharmaceutical residues in wastewater pose a challenge to wastewater treatment technologies. Constructed wetlands (CWs) are common wastewater treatment systems in rural areas and they discharge often in small water courses in which the ecology can be adversely affected by the discharged pharmaceuticals. Hence, there is a need for studies aiming to improve the removal of pharmaceuticals in CWs. In this study, the performance of a full-scale aerated sub-surface flow hybrid CW treating wastewater from a healthcare facility was studied in terms of common water parameters and pharmaceutical removal. In addition, a preliminary aquatic risk assessment based on hazard quotients was performed to estimate the likelihood of adverse effects on aquatic organisms in the forest creek where this CW discharges. The (combined) effect of aeration and hydraulic retention time (HRT) was evaluated in a laboratory-scale batch experiment. Excellent removal of the targeted pharmaceuticals was obtained in the full-scale CW (>90%) and, as a result, the aquatic risk was estimated low. The removal efficiency of only a few of the targeted pharmaceuticals was found to be dependent on the applied aeration (namely gabapentin, metformin and sotalol). Longer and the HRT increased the removal of carbamazepine, diclofenac and tramadol.

The design of dapog rice seeder model for laboratory scale

NASA Astrophysics Data System (ADS)

Purba, UI; Rizaldi, T.; Sumono; Sigalingging, R.

2018-02-01

The dapog system is seeding rice seeds using a special nursery tray. Rice seedings with dapog systems can produce seedlings in the form of higher quality and uniform seed rolls. This study aims to reduce the cost of making large-scale apparatus by designing models for small-scale and can be used for learning in the laboratory. Parameters observed were soil uniformity, seeds and fertilizers, soil looses, seeds and fertilizers, effective capacity of apparatus, and power requirements. The results showed a high uniformity in soil, seed and fertilizer respectively 92.8%, 1-3 seeds / cm2 and 82%. The scattered materials for soil, seed and fertilizer were respectively 6.23%, 2.7% and 2.23%. The effective capacity of apparatus was 360 boxes / hour with 237.5 kWh of required power.

Errors introduced by dose scaling for relative dosimetry

PubMed Central

Watanabe, Yoichi; Hayashi, Naoki

2012-01-01

Some dosimeters require a relationship between detector signal and delivered dose. The relationship (characteristic curve or calibration equation) usually depends on the environment under which the dosimeters are manufactured or stored. To compensate for the difference in radiation response among different batches of dosimeters, the measured dose can be scaled by normalizing the measured dose to a specific dose. Such a procedure, often called “relative dosimetry”, allows us to skip the time‐consuming production of a calibration curve for each irradiation. In this study, the magnitudes of errors due to the dose scaling procedure were evaluated by using the characteristic curves of BANG3 polymer gel dosimeter, radiographic EDR2 films, and GAFCHROMIC EBT2 films. Several sets of calibration data were obtained for each type of dosimeters, and a calibration equation of one set of data was used to estimate doses of the other dosimeters from different batches. The scaled doses were then compared with expected doses, which were obtained by using the true calibration equation specific to each batch. In general, the magnitude of errors increased with increasing deviation of the dose scaling factor from unity. Also, the errors strongly depended on the difference in the shape of the true and reference calibration curves. For example, for the BANG3 polymer gel, of which the characteristic curve can be approximated with a linear equation, the error for a batch requiring a dose scaling factor of 0.87 was larger than the errors for other batches requiring smaller magnitudes of dose scaling, or scaling factors of 0.93 or 1.02. The characteristic curves of EDR2 and EBT2 films required nonlinear equations. With those dosimeters, errors larger than 5% were commonly observed in the dose ranges of below 50% and above 150% of the normalization dose. In conclusion, the dose scaling for relative dosimetry introduces large errors in the measured doses when a large dose scaling is

INTERIOR VIEW OF MIXER LOCATED ON SECOND FLOOR OF BATCH ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

INTERIOR VIEW OF MIXER LOCATED ON SECOND FLOOR OF BATCH PLANT. RECENTLY PURCHASED TO REPLACE OLD MIXER. USED TO MIX THE BATCH - Chambers-McKee Window Glass Company, Batch Plant, Clay Avenue Extension, Jeannette, Westmoreland County, PA

The role of the independent clinical laboratory in new assay development and commercialization.

PubMed

Ellis, David G

2003-01-01

Most would agree that these are exciting times in the field of laboratory medicine. As the body of scientific knowledge expands and research activities, such as those catalyzed by the sequencing of the human genome, bring us closer to the promise of personalized medicine, the clinical laboratory industry will have increasing opportunities to partner with owners of intellectual property to develop and commercialize new diagnostic tests. The large, independent clinical laboratories are particularly well positioned to commercialize important new tests, with their broad market penetration, infrastructure, and the scale to run esoteric tests cost-effectively.

Internal quality assurance in a clinical virology laboratory. II. Internal quality control.

PubMed Central

Gray, J J; Wreghitt, T G; McKee, T A; McIntyre, P; Roth, C E; Smith, D J; Sutehall, G; Higgins, G; Geraghty, R; Whetstone, R

1995-01-01

AIMS--In April 1991 additional quality control procedures were introduced into the virology section of the Clinical Microbiology and Public Health Laboratory, Cambridge. Internal quality control (IQC) samples were gradually included in the serological assays performed in the laboratory and supplemented kit controls and standard sera. METHODS--From April 1991 to December 1993, 2421 IQC procedures were carried out with reference sera. RESULTS--The IQC samples were evaluated according to the Westgard rules. Violations were recorded in 60 of 1808 (3.3%) controls and were highest in the IQC samples of complement fixation tests (25/312 (8%) of controls submitted for complement fixation tests). CONCLUSIONS--The inclusion of IQC samples in the serological assays performed in the laboratory has highlighted batch to batch variation in commercial assays. The setting of acceptable limits for the IQC samples has increased confidence in the validity of assay results. PMID:7730475

Comparative meta-analysis and experimental kinetic investigation of column and batch bottle microcosm treatability studies informing in situ groundwater remedial design.

PubMed

Driver, Erin M; Roberts, Jeff; Dollar, Peter; Charles, Maurissa; Hurst, Paul; Halden, Rolf U

2017-02-05

A systematic comparison was performed between batch bottle and continuous-flow column microcosms (BMs and CMs, respectively) commonly used for in situ groundwater remedial design. Review of recent literature (2000-2014) showed a preference for reporting batch kinetics, even when corresponding column data were available. Additionally, CMs produced higher observed rate constants, exceeding those of BMs by a factor of 6.1±1.1 standard error. In a subsequent laboratory investigation, 12 equivalent microcosm pairs were constructed from fractured bedrock and perchloroethylene (PCE) impacted groundwater. First-order PCE transformation kinetics of CMs were 8.0±4.8 times faster than BMs (rates: 1.23±0.87 vs. 0.16±0.05d -1 , respectively). Additionally, CMs transformed 16.1±8.0-times more mass than BMs owing to continuous-feed operation. CMs are concluded to yield more reliable kinetic estimates because of much higher data density stemming from long-term, steady-state conditions. Since information from BMs and CMs is valuable and complementary, treatability studies should report kinetic data from both when available. This first systematic investigation of BMs and CMs highlights the need for a more unified framework for data use and reporting in treatability studies informing decision-making for field-scale groundwater remediation. Copyright © 2016 Elsevier B.V. All rights reserved.

Recommendation of ruthenium source for sludge batch flowsheet studies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Woodham, W.

Included herein is a preliminary analysis of previously-generated data from sludge batches 7a, 7b, 8, and 9 sludge simulant and real-waste testing, performed to recommend a form of ruthenium for future sludge batch simulant testing under the nitric-formic flowsheet. Focus is given to reactions present in the Sludge Receipt and Adjustment Tank cycle, given that this cycle historically produces the most changes in chemical composition during Chemical Process Cell processing. Data is presented and analyzed for several runs performed under the nitric-formic flowsheet, with consideration given to effects on the production of hydrogen gas, nitrous oxide gas, consumption of formate,more » conversion of nitrite to nitrate, and the removal and recovery of mercury during processing. Additionally, a brief discussion is given to the effect of ruthenium source selection under the nitric-glycolic flowsheet. An analysis of data generated from scaled demonstration testing, sludge batch 9 qualification testing, and antifoam degradation testing under the nitric-glycolic flowsheet is presented. Experimental parameters of interest under the nitric-glycolic flowsheet include N2O production, glycolate destruction, conversion of glycolate to formate and oxalate, and the conversion of nitrite to nitrate. To date, the number of real-waste experiments that have been performed under the nitric-glycolic flowsheet is insufficient to provide a complete understanding of the effects of ruthenium source selection in simulant experiments with regard to fidelity to real-waste testing. Therefore, a determination of comparability between the two ruthenium sources as employed under the nitric-glycolic flowsheet is made based on available data in order to inform ruthenium source selection for future testing under the nitric-glycolic flowsheet.« less

Whole-Genome Sequence of Coxiella burnetii Nine Mile RSA439 (Phase II, Clone 4), a Laboratory Workhorse Strain.

PubMed

Millar, Jess A; Beare, Paul A; Moses, Abraham S; Martens, Craig A; Heinzen, Robert A; Raghavan, Rahul

2017-06-08

Here, we report the whole-genome sequence of Coxiella burnetii Nine Mile RSA439 (phase II, clone 4), a laboratory strain used extensively to investigate the biology of this intracellular bacterial pathogen. The genome consists of a 1.97-Mb chromosome and a 37.32-kb plasmid. Copyright © 2017 Millar et al.

A start-up of psychrophilic anaerobic sequence batch reactor digesting a 35 % total solids feed of dairy manure and wheat straw.

PubMed

Saady, Noori M Cata; Massé, Daniel I

2015-12-01

Zero liquid discharge is currently an objective in livestock manure management to minimize water pollution. This paper reports the start-up phase of a novel psychrophilic (20 °C) dry anaerobic digestion of dairy manure with bedding fed at 35 % total solids and an organic loading rate of 3.0 g total chemical oxygen demand kg(-1) inoculum day(-1) in anaerobic sequence batch reactors. The specific methane (CH4) yield ranged from 165.4 ± 9.8 to 213.9 ± 13.6 NL CH4 kg(-1) volatile solids (VS) with an overall average of 188 ± 17 NL CH4 kg(-1) VS during 11 successive start-up cycles (231 days) and a maximum CH4 production rate of 10.2 ± 0.6 NL CH4 kg(-1) VS day(-1). The inoculum-to-substrate (VS-based) ratio ranged from 4.06 to 4.47. Although methanogenesis proceeded fairly well the hydrolysis seemed to be the rate limiting step. It is possible start up psychrophilic dry anaerobic digestion of cow feces and wheat straw at feed TS of 35 % within 7-10 successive cycles (147-210 days).

Evaluation of a laboratory-scale bioreactive in situ sediment cap for the treatment of organic contaminants.

PubMed

Himmelheber, David W; Pennell, Kurt D; Hughes, Joseph B

2011-11-01

The development of bioreactive sediment caps, in which microorganisms capable of contaminant transformation are placed within an in situ cap, provides a potential remedial design that can sustainably treat sediment and groundwater contaminants. The goal of this study was to evaluate the ability and limitations of a mixed, anaerobic dechlorinating consortium to treat chlorinated ethenes within a sand-based cap. Results of batch experiments demonstrate that a tetrachloroethene (PCE)-to-ethene mixed consortium was able to completely dechlorinate dissolved-phase PCE to ethene when supplied only with sediment porewater obtained from a sediment column. To simulate a bioreactive cap, laboratory-scale sand columns inoculated with the mixed culture were placed in series with an upflow sediment column and directly supplied sediment effluent and dissolved-phase chlorinated ethenes. The mixed consortium was not able to sustain dechlorination activity at a retention time of 0.5 days without delivery of amendments to the sediment effluent, evidenced by the loss of cis-1,2-dichloroethene (cis-DCE) dechlorination to vinyl chloride. When soluble electron donor was supplied to the sediment effluent, complete dechlorination of cis-DCE to ethene was observed at retention times of 0.5 days, suggesting that sediment effluent lacked sufficient electron donor to maintain active dechlorination within the sediment cap. Introduction of elevated contaminant concentrations also limited biotransformation performance of the dechlorinating consortium within the cap. These findings indicate that in situ bioreactive capping can be a feasible remedial approach, provided that residence times are adequate and that appropriate levels of electron donor and contaminant exist within the cap. Copyright © 2011 Elsevier Ltd. All rights reserved.

Dry anaerobic digestion of high solids content dairy manure at high organic loading rates in psychrophilic sequence batch reactor.

PubMed

Massé, Daniel I; Saady, Noori M Cata

2015-05-01

Cow manure with bedding is renewable organic biomass available around the year on dairy farms. Developing efficient and cost-effective psychrophilic dry anaerobic digestion (PDAD) processes could contribute to solving farm-related environmental, energy, and manure management problems in cold-climate regions. This study was to increase the organic loading rate (OLR), fed to a novel psychrophilic (20 °C) dry anaerobic digestion of 27% total solid dairy manure (cow feces and wheat straw) in sequence batch reactor (PDAD-SBR), by 133 to 160%. The PDAD-SBR process operated at treatment cycle length of 21 days and OLR of 7.0 and 8.0 g total chemical oxygen demand (TCOD) kg(-1) inoculum day(-1) (5.2 ± 0.1 and 5.8 ± 0.0 g volatile solids (VS) kg(-1) inoculum day(-1)) for four successive cycles (84 days) produced average specific methane yields (SMYs) of 147.1 ± 17.2 and 143.2 ± 11.7 normalized liters (NL) CH4 kg(-1) VS fed, respectively. PDAD of cow feces and wheat straw is possible with VS-based inoculum-to-substrate ratio of 1.45 at OLR of 8.0 g TCOD kg(-1) inoculum day(-1). Hydrolysis was the limiting step reaction. The VS removal averaged around 57.4 ± 0.5 and 60.5 ± 5.7% at OLR 7.0 and 8.0 g TCOD kg(-1) inoculum day(-1), respectively.

Long-term exposure of bacterial and protozoan communities to TiO2 nanoparticles in an aerobic-sequencing batch reactor

NASA Astrophysics Data System (ADS)

Supha, Chitpisud; Boonto, Yuphada; Jindakaraked, Manee; Ananpattarachai, Jirapat; Kajitvichyanukul, Puangrat

2015-06-01

Titanium dioxide (TiO2) nanopowders at different concentrations (0-50 mg L-1) were injected into an aerobic-sequencing batch reactor (SBR) to investigate the effects of long-term exposure to nanoparticles on bacterial and protozoan communities. The detection of nanoparticles in the bioflocs was analyzed by scanning electron microscopy, transmission electron microscopy, and energy-dispersive x-ray spectroscopy. The SBR wastewater experiments were conducted under the influence of ultraviolet light with photocatalytic TiO2. The intrusion of TiO2 nanoparticles was found both on the surface and inside of the bioflocs. The change of microbial population in terms of mixed liquor-suspended solids and the sludge volume index was monitored. The TiO2 nanoparticles tentatively exerted an adverse effect on the microbial population, causing the reduction of microorganisms (both bacteria and protozoa) in the SBR. The respiration inhibition rate of the bacteria was increased, and the viability of the microbial population was reduced at the high concentration (50 mg L-1) of TiO2. The decreasing number of protozoa in the presence of TiO2 nanoparticles during 20 days of treatment with 0.5 and 1.0 mg L-1 TiO2 is clearly demonstrated. The measured chemical oxygen demand (COD) in the effluent tends to increase with a long-term operation. The increase of COD in the system suggests a decrease in the efficiency of the wastewater treatment plant. However, the SBR can effectively remove the TiO2 nanoparticles (up to 50 mg L-1) from the effluent.

Searching CA Condensates, On-Line and Batch.

ERIC Educational Resources Information Center

Kaminecki, Ronald M.; And Others

Batch mode processing is compared, using cost-effectiveness, with on-line processing for computer-aided searching of chemical abstracts. Consideration for time, need, coverage, and adaptability are found to be the criteria by which a searcher selects a method, and sometimes both methods are used. There is a tradeoff between batch mode's slower…

Effect of pine bark on the biotransformation of trinitrotoluene and on the bacterial community structure in a batch experiment.

PubMed

Chusova, Olga; Nolvak, Hiie; Nehrenheim, Emma; Truu, Jaak; Odlare, Monica; Oopkaup, Kristjan; Truu, Marika

2014-01-01

Pine bark, a low-cost industrial residue, has been suggested as a promising substitute for granular activated carbon in the on-site treatment of water contaminated with 2,4,6-trinitrotoluene (TNT). However, the complex organic structure and indigenous microbial community of pine bark have thus far not been thoroughly described in the context of TNT-contaminated water treatment. This two-week batch study examined the removal efficiency ofTNT from water by (1) adsorption on pine bark and (2) simultaneous adsorption on pine bark and biotransformation by specialized TNT-biotransforming microbial inocula. The bacterial community composition of experimental batches, inocula and pine bark, was profiled by Illumina sequencing of the V6 region of the 16S rRNA gene. The results revealed that the inocula and experimental batches were dominated by phylotypes belonging to the Enterobacteriaceae family and that the tested inocula had good potential for TNT biotransformation. The type of applied inocula had the most profound effect on the TNT-transforming bacterial community structure in the experimental batches. The indigenous microbial community of pine bark harboured phylotypes that also have a potential to degrade TNT. Altogether, the combination of a specialized inoculum and pine bark proved to be the most efficient treatment option for TNT-contaminated water.

Preparative Protein Production from Inclusion Bodies and Crystallization: A Seven-Week Biochemistry Sequence

ERIC Educational Resources Information Center

Peterson, Megan J.; Snyder, W. Kalani; Westerman, Shelley; McFarland, Benjamin J.

2011-01-01

We describe how to produce and purify proteins from "Escherichia coli" inclusion bodies by adapting versatile, preparative-scale techniques to the undergraduate laboratory schedule. This 7-week sequence of experiments fits into an annual cycle of research activity in biochemistry courses. Recombinant proteins are expressed as inclusion bodies,…

Fast laboratory-based micro-computed tomography for pore-scale research: Illustrative experiments and perspectives on the future

NASA Astrophysics Data System (ADS)

Bultreys, Tom; Boone, Marijn A.; Boone, Matthieu N.; De Schryver, Thomas; Masschaele, Bert; Van Hoorebeke, Luc; Cnudde, Veerle

2016-09-01

Over the past decade, the wide-spread implementation of laboratory-based X-ray micro-computed tomography (micro-CT) scanners has revolutionized both the experimental and numerical research on pore-scale transport in geological materials. The availability of these scanners has opened up the possibility to image a rock's pore space in 3D almost routinely to many researchers. While challenges do persist in this field, we treat the next frontier in laboratory-based micro-CT scanning: in-situ, time-resolved imaging of dynamic processes. Extremely fast (even sub-second) micro-CT imaging has become possible at synchrotron facilities over the last few years, however, the restricted accessibility of synchrotrons limits the amount of experiments which can be performed. The much smaller X-ray flux in laboratory-based systems bounds the time resolution which can be attained at these facilities. Nevertheless, progress is being made to improve the quality of measurements performed on the sub-minute time scale. We illustrate this by presenting cutting-edge pore scale experiments visualizing two-phase flow and solute transport in real-time with a lab-based environmental micro-CT set-up. To outline the current state of this young field and its relevance to pore-scale transport research, we critically examine its current bottlenecks and their possible solutions, both on the hardware and the software level. Further developments in laboratory-based, time-resolved imaging could prove greatly beneficial to our understanding of transport behavior in geological materials and to the improvement of pore-scale modeling by providing valuable validation.

Comparison of batch sorption tests, pilot studies, and modeling for estimating GAC bed life.

PubMed

Scharf, Roger G; Johnston, Robert W; Semmens, Michael J; Hozalski, Raymond M

2010-02-01

Saint Paul Regional Water Services (SPRWS) in Saint Paul, MN experiences annual taste and odor episodes during the warm summer months. These episodes are attributed primarily to geosmin that is produced by cyanobacteria growing in the chain of lakes used to convey and store the source water pumped from the Mississippi River. Batch experiments, pilot-scale experiments, and model simulations were performed to determine the geosmin removal performance and bed life of a granular activated carbon (GAC) filter-sorber. Using batch adsorption isotherm parameters, the estimated bed life for the GAC filter-sorber ranged from 920 to 1241 days when challenged with a constant concentration of 100 ng/L of geosmin. The estimated bed life obtained using the AdDesignS model and the actual pilot-plant loading history was 594 days. Based on the pilot-scale GAC column data, the actual bed life (>714 days) was much longer than the simulated values because bed life was extended by biological degradation of geosmin. The continuous feeding of high concentrations of geosmin (100-400 ng/L) in the pilot-scale experiments enriched for a robust geosmin-degrading culture that was sustained when the geosmin feed was turned off for 40 days. It is unclear, however, whether a geosmin-degrading culture can be established in a full-scale filter that experiences taste and odor episodes for only 1 or 2 months per year. The results of this research indicate that care must be exercised in the design and interpretation of pilot-scale experiments and model simulations for predicting taste and odor removal in full-scale GAC filter-sorbers. Adsorption and the potential for biological degradation must be considered to estimate GAC bed life for the conditions of intermittent geosmin loading typically experienced by full-scale systems. (c) 2009 Elsevier Ltd. All rights reserved.

DESTRUCTION OF TETRAPHENYLBORATE IN TANK 48H USING WET AIR OXIDATION BATCH BENCH SCALE AUTOCLAVE TESTING WITH ACTUAL RADIOACTIVE TANK 48H WASTE

DOE Office of Scientific and Technical Information (OSTI.GOV)

Adu-Wusu, K; Paul Burket, P

2009-03-31

Wet Air Oxidation (WAO) is one of the two technologies being considered for the destruction of Tetraphenylborate (TPB) in Tank 48H. Batch bench-scale autoclave testing with radioactive (actual) Tank 48H waste is among the tests required in the WAO Technology Maturation Plan. The goal of the autoclave testing is to validate that the simulant being used for extensive WAO vendor testing adequately represents the Tank 48H waste. The test objective was to demonstrate comparable test results when running simulated waste and real waste under similar test conditions. Specifically: (1) Confirm the TPB destruction efficiency and rate (same reaction times) obtainedmore » from comparable simulant tests, (2) Determine the destruction efficiency of other organics including biphenyl, (3) Identify and quantify the reaction byproducts, and (4) Determine off-gas composition. Batch bench-scale stirred autoclave tests were conducted with simulated and actual Tank 48H wastes at SRNL. Experimental conditions were chosen based on continuous-flow pilot-scale simulant testing performed at Siemens Water Technologies Corporation (SWT) in Rothschild, Wisconsin. The following items were demonstrated as a result of this testing. (1) Tetraphenylborate was destroyed to below detection limits during the 1-hour reaction time at 280 C. Destruction efficiency of TPB was > 99.997%. (2) Other organics (TPB associated compounds), except biphenyl, were destroyed to below their respective detection limits. Biphenyl was partially destroyed in the process, mainly due to its propensity to reside in the vapor phase during the WAO reaction. Biphenyl is expected to be removed in the gas phase during the actual process, which is a continuous-flow system. (3) Reaction byproducts, remnants of MST, and the PUREX sludge, were characterized in this work. Radioactive species, such as Pu, Sr-90 and Cs-137 were quantified in the filtrate and slurry samples. Notably, Cs-137, boron and potassium were shown as soluble as

DNA fingerprinting, DNA barcoding, and next generation sequencing technology in plants.

PubMed

Sucher, Nikolaus J; Hennell, James R; Carles, Maria C

2012-01-01

DNA fingerprinting of plants has become an invaluable tool in forensic, scientific, and industrial laboratories all over the world. PCR has become part of virtually every variation of the plethora of approaches used for DNA fingerprinting today. DNA sequencing is increasingly used either in combination with or as a replacement for traditional DNA fingerprinting techniques. A prime example is the use of short, standardized regions of the genome as taxon barcodes for biological identification of plants. Rapid advances in "next generation sequencing" (NGS) technology are driving down the cost of sequencing and bringing large-scale sequencing projects into the reach of individual investigators. We present an overview of recent publications that demonstrate the use of "NGS" technology for DNA fingerprinting and DNA barcoding applications.

The Long Non-Coding RNA Transcriptome Landscape in CHO Cells Under Batch and Fed-Batch Conditions.

PubMed

Vito, Davide; Smales, C Mark

2018-05-21

The role of non-coding RNAs in determining growth, productivity and recombinant product quality attributes in Chinese hamster ovary (CHO) cells has received much attention in recent years, exemplified by studies into microRNAs in particular. However, other classes of non-coding RNAs have received less attention. One such class are the non-coding RNAs known collectively as long non-coding RNAs (lncRNAs). We have undertaken the first landscape analysis of the lncRNA transcriptome in CHO using a mouse based microarray that also provided for the surveillance of the coding transcriptome. We report on those lncRNAs present in a model host CHO cell line under batch and fed-batch conditions on two different days and relate the expression of different lncRNAs to each other. We demonstrate that the mouse microarray was suitable for the detection and analysis of thousands of CHO lncRNAs and validated a number of these by qRT-PCR. We then further analysed the data to identify those lncRNAs whose expression changed the most between growth and stationary phases of culture or between batch and fed-batch culture to identify potential lncRNA targets for further functional studies with regard to their role in controlling growth of CHO cells. We discuss the implications for the publication of this rich dataset and how this may be used by the community. This article is protected by copyright. All rights reserved.

Universal sequence map (USM) of arbitrary discrete sequences

PubMed Central

2002-01-01

Background For over a decade the idea of representing biological sequences in a continuous coordinate space has maintained its appeal but not been fully realized. The basic idea is that any sequence of symbols may define trajectories in the continuous space conserving all its statistical properties. Ideally, such a representation would allow scale independent sequence analysis – without the context of fixed memory length. A simple example would consist on being able to infer the homology between two sequences solely by comparing the coordinates of any two homologous units. Results We have successfully identified such an iterative function for bijective mappingψ of discrete sequences into objects of continuous state space that enable scale-independent sequence analysis. The technique, named Universal Sequence Mapping (USM), is applicable to sequences with an arbitrary length and arbitrary number of unique units and generates a representation where map distance estimates sequence similarity. The novel USM procedure is based on earlier work by these and other authors on the properties of Chaos Game Representation (CGR). The latter enables the representation of 4 unit type sequences (like DNA) as an order free Markov Chain transition table. The properties of USM are illustrated with test data and can be verified for other data by using the accompanying web-based tool:http://bioinformatics.musc.edu/~jonas/usm/. Conclusions USM is shown to enable a statistical mechanics approach to sequence analysis. The scale independent representation frees sequence analysis from the need to assume a memory length in the investigation of syntactic rules. PMID:11895567

40 CFR 63.1322 - Batch process vents-reference control technology.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 11 2010-07-01 2010-07-01 true Batch process vents-reference control technology. 63.1322 Section 63.1322 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR... Batch process vents—reference control technology. (a) Batch process vents. The owner or operator of a...

40 CFR 63.1322 - Batch process vents-reference control technology.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 12 2013-07-01 2013-07-01 false Batch process vents-reference control... (CONTINUED) National Emission Standards for Hazardous Air Pollutant Emissions: Group IV Polymers and Resins § 63.1322 Batch process vents—reference control technology. (a) Batch process vents. The owner or...

40 CFR 63.1322 - Batch process vents-reference control technology.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 12 2012-07-01 2011-07-01 true Batch process vents-reference control technology. 63.1322 Section 63.1322 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR... Batch process vents—reference control technology. (a) Batch process vents. The owner or operator of a...

40 CFR 63.1322 - Batch process vents-reference control technology.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 12 2014-07-01 2014-07-01 false Batch process vents-reference control technology. 63.1322 Section 63.1322 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR... § 63.1322 Batch process vents—reference control technology. (a) Batch process vents. The owner or...

40 CFR 63.1322 - Batch process vents-reference control technology.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 11 2011-07-01 2011-07-01 false Batch process vents-reference control technology. 63.1322 Section 63.1322 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR... Batch process vents—reference control technology. (a) Batch process vents. The owner or operator of a...

Establishment of replacement batches for heparin low-molecular-mass for calibration CRS, and the International Standard Low Molecular Weight Heparin for Calibration.

PubMed

Mulloy, B; Heath, A; Behr-Gross, M-E

2007-12-01

An international collaborative study involving fourteen laboratories has taken place, organised by the European Directorate for the Quality of Medicines & HealthCare (EDQM) with National Institute for Biological Standards & Control (NIBSC) (in its capacity as a World Health Organisation (WHO) Laboratory for Biological Standardisation) to provide supporting data for the establishment of replacement batches of Heparin Low-Molecular-Mass (LMM) for Calibration Chemical Reference Substance (CRS), and of the International Reference Reagent (IRR) Low Molecular Weight Heparin for Molecular Weight Calibration. A batch of low-molecular-mass heparin was donated to the organisers and candidate preparations of freeze-dried heparin were produced at NIBSC and EDQM. The establishment study was organised in two phases: a prequalification (phase 1, performed in 3 laboratories in 2005) followed by an international collaborative study (phase 2). In phase 2, started in March 2006, molecular mass parameters were determined for seven different LMM heparin samples using the current CRS batch and two batches of candidate replacement material with a defined number average relative molecular mass (Mn) of 3,700, determined in phase 1. The values calculated using the candidates as standard were systematically different from values calculated using the current batch with its assigned number-average molecular mass (Mna) of 3,700. Using raw data supplied by participants, molecular mass parameters were recalculated using the candidates as standard with values for Mna of 3,800 and 3,900. Values for these parameters agreed more closely with those calculated using the current batch supporting the fact that the candidates, though similar to batch 1 in view of the production processes used, differ slightly in terms of molecular mass distribution. Therefore establishment of the candidates was recommended with an assigned Mna value of 3,800 that is both consistent with phase 1 results and guarantees

Atomic-batched tensor decomposed two-electron repulsion integrals

NASA Astrophysics Data System (ADS)

Schmitz, Gunnar; Madsen, Niels Kristian; Christiansen, Ove

2017-04-01

We present a new integral format for 4-index electron repulsion integrals, in which several strategies like the Resolution-of-the-Identity (RI) approximation and other more general tensor-decomposition techniques are combined with an atomic batching scheme. The 3-index RI integral tensor is divided into sub-tensors defined by atom pairs on which we perform an accelerated decomposition to the canonical product (CP) format. In a first step, the RI integrals are decomposed to a high-rank CP-like format by repeated singular value decompositions followed by a rank reduction, which uses a Tucker decomposition as an intermediate step to lower the prefactor of the algorithm. After decomposing the RI sub-tensors (within the Coulomb metric), they can be reassembled to the full decomposed tensor (RC approach) or the atomic batched format can be maintained (ABC approach). In the first case, the integrals are very similar to the well-known tensor hypercontraction integral format, which gained some attraction in recent years since it allows for quartic scaling implementations of MP2 and some coupled cluster methods. On the MP2 level, the RC and ABC approaches are compared concerning efficiency and storage requirements. Furthermore, the overall accuracy of this approach is assessed. Initial test calculations show a good accuracy and that it is not limited to small systems.

Atomic-batched tensor decomposed two-electron repulsion integrals.

PubMed

Schmitz, Gunnar; Madsen, Niels Kristian; Christiansen, Ove

2017-04-07

We present a new integral format for 4-index electron repulsion integrals, in which several strategies like the Resolution-of-the-Identity (RI) approximation and other more general tensor-decomposition techniques are combined with an atomic batching scheme. The 3-index RI integral tensor is divided into sub-tensors defined by atom pairs on which we perform an accelerated decomposition to the canonical product (CP) format. In a first step, the RI integrals are decomposed to a high-rank CP-like format by repeated singular value decompositions followed by a rank reduction, which uses a Tucker decomposition as an intermediate step to lower the prefactor of the algorithm. After decomposing the RI sub-tensors (within the Coulomb metric), they can be reassembled to the full decomposed tensor (RC approach) or the atomic batched format can be maintained (ABC approach). In the first case, the integrals are very similar to the well-known tensor hypercontraction integral format, which gained some attraction in recent years since it allows for quartic scaling implementations of MP2 and some coupled cluster methods. On the MP2 level, the RC and ABC approaches are compared concerning efficiency and storage requirements. Furthermore, the overall accuracy of this approach is assessed. Initial test calculations show a good accuracy and that it is not limited to small systems.

Synthesis of Cyclic α-Diazo-β-keto Sulfoxides in Batch and Continuous Flow.

PubMed

McCaw, Patrick G; Buckley, Naomi M; Eccles, Kevin S; Lawrence, Simon E; Maguire, Anita R; Collins, Stuart G

2017-04-07

Diazo transfer to β-keto sulfoxides to form stable isolable α-diazo-β-keto sulfoxides has been achieved for the first time. Both monocyclic and benzofused ketone derived β-keto sulfoxides were successfully explored as substrates for diazo transfer. Use of continuous flow leads to isolation of the desired compounds in enhanced yields relative to standard batch conditions, with short reaction times, increased safety profile, and potential to scale up.

Production of laccase by Coriolus versicolor and its application in decolorization of dyestuffs: (I). Production of laccase by batch and repeated-batch processes.

PubMed

Lin, Jian-Ping; Wei, Lian; Xia, Li-Ming; Cen, Pei-Lin

2003-01-01

The production of laccase by Coriolus versicolor was studied. The effect of cultivation conditions on laccase production by Coriolus versicolor was examined to obtain optimal medium and cultivation conditions. Both batch and repeated-batch processes were performed for laccase production. In repeated-batch fermentation with self-immobilized mycelia, total of 14 cycles were performed with laccase activity in the range between 3.4 and 14.8 U/ml.

Laboratory and pilot-scale field experiments for application of iron oxide nanoparticle-loaded chitosan composites to phosphate removal from natural water.

PubMed

Kim, Jae-Hyun; Kim, Song-Bae; Lee, Sang-Hyup; Choi, Jae-Woo

2018-03-01

The aim of this study was to apply iron oxide nanoparticle-chitosan (ION-chitosan) composites to phosphate removal from natural water collected from the Seoho Stream in Suwon, Republic of Korea. Laboratory batch experiments showed that phosphate removal by the ION-chitosan composites was not sensitive to pH changes between pH values of 5.0 and 9.0. During six cycles of adsorption-desorption, the composites could be successfully regenerated with 5 mM NaOH solution and reused for phosphate removal. Laboratory fixed-bed column experiments (column height = 10 and 20 cm, inner diameter = 2.5 cm, flow rate = 8.18 and 16.36 mL/min) demonstrated that the composites could be successfully applied for phosphate removal under dynamic flow conditions. A pilot-scale field experiment was performed in a pilot plant, which was mainly composed of chemical reactor/dissolved air flotation and an adsorption tower, built nearby the Seoho Stream. The natural water was pumped from the Seoho Stream into the pilot plant, passed through the chemical reactor/dissolved air flotation process, and then introduced into the adsorption tower (height = 100 cm, inner diameter = 45 cm, flow rate = 7.05 ± 0.18 L/min) for phosphate removal via the composites (composite volume = 80 L, composite weight = 85.74 kg). During monitoring of the adsorption tower (33 days), the influent total phosphorus (T-P) concentration was in the range of 0.020-0.046 mgP/L, whereas the effluent T-P concentration was in the range of 0.010-0.028 mgP/L. The percent removal of T-P in the adsorption tower was 52.3% with a phosphate removal capacity of 0.059 mgP/g.

Multilocus sequence typing of total-genome-sequenced bacteria.

PubMed

Larsen, Mette V; Cosentino, Salvatore; Rasmussen, Simon; Friis, Carsten; Hasman, Henrik; Marvig, Rasmus Lykke; Jelsbak, Lars; Sicheritz-Pontén, Thomas; Ussery, David W; Aarestrup, Frank M; Lund, Ole

2012-04-01

Accurate strain identification is essential for anyone working with bacteria. For many species, multilocus sequence typing (MLST) is considered the "gold standard" of typing, but it is traditionally performed in an expensive and time-consuming manner. As the costs of whole-genome sequencing (WGS) continue to decline, it becomes increasingly available to scientists and routine diagnostic laboratories. Currently, the cost is below that of traditional MLST. The new challenges will be how to extract the relevant information from the large amount of data so as to allow for comparison over time and between laboratories. Ideally, this information should also allow for comparison to historical data. We developed a Web-based method for MLST of 66 bacterial species based on WGS data. As input, the method uses short sequence reads from four sequencing platforms or preassembled genomes. Updates from the MLST databases are downloaded monthly, and the best-matching MLST alleles of the specified MLST scheme are found using a BLAST-based ranking method. The sequence type is then determined by the combination of alleles identified. The method was tested on preassembled genomes from 336 isolates covering 56 MLST schemes, on short sequence reads from 387 isolates covering 10 schemes, and on a small test set of short sequence reads from 29 isolates for which the sequence type had been determined by traditional methods. The method presented here enables investigators to determine the sequence types of their isolates on the basis of WGS data. This method is publicly available at www.cbs.dtu.dk/services/MLST.

Large-scale sequencing trials begin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Roberts, L.

1990-12-07

As genome sequencing gets under way, investigators are grappling not just with new techniques but also with questions about what is acceptable accuracy and when data should be released. Four groups are embarking on projects that could make or break the human genome project. They are setting out to sequence the longest stretches of DNA ever tackled-several million bases each-and to do it faster and cheaper than anyone has before. If these groups can't pull it off, then prospects for knocking off the entire human genome, all 3 billion bases, in 15 years and for $3 billion will look increasinglymore » unlikely. Harvard's Walter Gilbert, is first tackling the genome of Mycoplasma capricolum. At Stanford, David Botstein and Ron Davis are sequencing Saccharomyces cerevisiae. In a collaborative effort, Robert Waterson at Washington University and John Sulston at the Medical Research Council lab in Cambridge, England, have already started on the nematode Caenorhabditis elegans. And in the only longstanding project of the bunch, University of Wisconsin geneticist Fred Blattner is already several hundred kilobases into the Escherichia coli genome.« less

Laboratory and Pilot Scale Evaluation of Coagulation, Clarification, and Filtration for Upgrading Sewage Lagoon Effluents.

DTIC Science & Technology

1980-08-01

AD-AGAB 906 ARMY ENGINEER WATERWAYS EXPERIMENT STATION VICKSBURG--ETC FIG 14/2 LABORATORY AND PILOT SCALE EVALUATION OF COAGULATION, CLARIFICA -ETC U...FILTRATION FOR LWGRADING JEWAGE LAGOON EFFLUENTS~ w IL j0 ( M John ullinane, Jr., Richard A. hafer (0 Environmental Laboratory gel U. S. Army Engineer ...Shafer 9. PERFORMING ORGANIZATION NAME AND ADORESS SO. PROGRAM ELEMENT, PROJECT, TASK AREA a WORK UNIT NUMBERS U. S. Army Engineer Waterways Experiment

Actual distribution of Cronobacter spp. in industrial batches of powdered infant formula and consequences for performance of sampling strategies.

PubMed

Jongenburger, I; Reij, M W; Boer, E P J; Gorris, L G M; Zwietering, M H

2011-11-15

The actual spatial distribution of microorganisms within a batch of food influences the results of sampling for microbiological testing when this distribution is non-homogeneous. In the case of pathogens being non-homogeneously distributed, it markedly influences public health risk. This study investigated the spatial distribution of Cronobacter spp. in powdered infant formula (PIF) on industrial batch-scale for both a recalled batch as well a reference batch. Additionally, local spatial occurrence of clusters of Cronobacter cells was assessed, as well as the performance of typical sampling strategies to determine the presence of the microorganisms. The concentration of Cronobacter spp. was assessed in the course of the filling time of each batch, by taking samples of 333 g using the most probable number (MPN) enrichment technique. The occurrence of clusters of Cronobacter spp. cells was investigated by plate counting. From the recalled batch, 415 MPN samples were drawn. The expected heterogeneous distribution of Cronobacter spp. could be quantified from these samples, which showed no detectable level (detection limit of -2.52 log CFU/g) in 58% of samples, whilst in the remainder concentrations were found to be between -2.52 and 2.75 log CFU/g. The estimated average concentration in the recalled batch was -2.78 log CFU/g and a standard deviation of 1.10 log CFU/g. The estimated average concentration in the reference batch was -4.41 log CFU/g, with 99% of the 93 samples being below the detection limit. In the recalled batch, clusters of cells occurred sporadically in 8 out of 2290 samples of 1g taken. The two largest clusters contained 123 (2.09 log CFU/g) and 560 (2.75 log CFU/g) cells. Various sampling strategies were evaluated for the recalled batch. Taking more and smaller samples and keeping the total sampling weight constant, considerably improved the performance of the sampling plans to detect such a type of contaminated batch. Compared to random sampling

GenBank.

PubMed

Benson, Dennis A; Karsch-Mizrachi, Ilene; Lipman, David J; Ostell, James; Sayers, Eric W

2010-01-01

GenBank is a comprehensive database that contains publicly available nucleotide sequences for more than 300,000 organisms named at the genus level or lower, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole genome shotgun (WGS) and environmental sampling projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the European Molecular Biology Laboratory Nucleotide Sequence Database in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through the NCBI Entrez retrieval system, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bi-monthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI homepage: www.ncbi.nlm.nih.gov.

The sequence of sequencers: The history of sequencing DNA

PubMed Central

Heather, James M.; Chain, Benjamin

2016-01-01

Determining the order of nucleic acid residues in biological samples is an integral component of a wide variety of research applications. Over the last fifty years large numbers of researchers have applied themselves to the production of techniques and technologies to facilitate this feat, sequencing DNA and RNA molecules. This time-scale has witnessed tremendous changes, moving from sequencing short oligonucleotides to millions of bases, from struggling towards the deduction of the coding sequence of a single gene to rapid and widely available whole genome sequencing. This article traverses those years, iterating through the different generations of sequencing technology, highlighting some of the key discoveries, researchers, and sequences along the way. PMID:26554401