Batch effect confounding leads to strong bias in performance estimates obtained by cross-validation.

BACKGROUND: With the large amount of biological data that is currently publicly available, many investigators combine multiple data sets to increase the sample size and potentially also the power of their analyses. However, technical differences ("batch effects") as well as differences in sample composition between the data sets may significantly affect the ability to draw generalizable conclusions from such studies. FOCUS: The current study focuses on the construction of classifiers, and the use of cross-validation to estimate their performance. In particular, we investigate the impact of batch effects and differences in sample composition between batches on the accuracy of the classification performance estimate obtained via cross-validation. The focus on estimation bias is a main difference compared to previous studies, which have mostly focused on the predictive performance and how it relates to the presence of batch effects. DATA: We work on simulated data sets. To have realistic intensity distributions, we use real gene expression data as the basis for our simulation. Random samples from this expression matrix are selected and assigned to group 1 (e.g., 'control') or group 2 (e.g., 'treated'). We introduce batch effects and select some features to be differentially expressed between the two groups. We consider several scenarios for our study, most importantly different levels of confounding between groups and batch effects. METHODS: We focus on well-known classifiers: logistic regression, Support Vector Machines (SVM), k-nearest neighbors (kNN) and Random Forests (RF). Feature selection is performed with the Wilcoxon test or the lasso. Parameter tuning and feature selection, as well as the estimation of the prediction performance of each classifier, is performed within a nested cross-validation scheme. The estimated classification performance is then compared to what is obtained when applying the classifier to independent data.

Disseny d'una eina de gestió d'un planificador d'execucions batch

L'abast d'aquest projecte es centrarà en el disseny d'una eina de gestió d'un planificador d'execucions batch, que intentarà donar una solució independent de l'entorn on s'executen aquests processos i que servirà com a eina de suport a un equip d'analistes i dissenyadors que creïn o mantinguin aquests processos.

A Petri Nets-based Scheduling Methodology forMultipurpose Batch Plants.

This article presents an optimization methodology of batch production processes assembled by shared resources which rely on a mapping of state-events into time-events allowing in this way the straightforward use of a well consolidated scheduling policies developed for manufacturing systems. A technique to generate the timed Petri net representation from a continuous dynamic representation (Differential-Algebraic Equations systems (DAEs)) of the production system is presented together with the main characteristics of a Petri nets-based tool implemented for optimization purposes. This paper describes also how the implemented tool generates the coverability tree and how it can be pruned by a general purpose heuristic. An example of a distillation process with two shared batch resources is used to illustrate the optimization methodology proposed.

Control and Simulation of Batch Crystallization

Concerning process control of batch cooling crystallization the present work focused on the cooling profile and seeding technique. Secondly, the influence of additives on batch-wise precipitation process was investigated. Moreover, a Computational Fluid Dynamics (CFD) model for simulation of controlled batch cooling crystallization was developed. A novel cooling model to control supersaturation level during batch-wise cooling crystallization was introduced. The crystallization kinetics together with operating conditions, i.e. seed loading, cooling rate and batch time, were taken into account in the model. Especially, the supersaturation- and suspension density- dependent secondary nucleation was included in the model. The interaction between the operating conditions and their influence on the control target, i.e. the constant level of supersaturation, were studied with the aid of a numerical solution for the cooling model. Further, the batch cooling crystallization was simulated with the ideal mixing model and CFD model. The moment transformation of the population balance, together with the mass and heat balances, were solved numerically in the simulation. In order to clarify a relationship betweenthe operating conditions and product sizes, a system chart was developed for anideal mixing condition. The utilization of the system chart to determine the appropriate operating condition to meet a required product size was introduced. With CFD simulation, batch crystallization, operated following a specified coolingmode, was studied in the crystallizers having different geometries and scales. The introduced cooling model and simulation results were verified experimentallyfor potassium dihydrogen phosphate (KDP) and the novelties of the proposed control policies were demonstrated using potassium sulfate by comparing with the published results in the literature. The study on the batch-wise precipitation showed that immiscible additives could promote the agglomeration of a derivative of benzoic acid, which facilitated the filterability of the crystal product.

Towards desired crystalline product properties: In-situ monitoring of batch crystallization

The objective of industrial crystallization is to obtain a crystalline product which has the desired crystal size distribution, mean crystal size, crystal shape, purity, polymorphic and pseudopolymorphic form. Effective control of the product quality requires an understanding of the thermodynamics of the crystallizing system and the effects of operation parameters on the crystalline product properties. Therefore, obtaining reliable in-line information about crystal properties and supersaturation, which is the driving force of crystallization, would be very advantageous. Advanced techniques, such asRaman spectroscopy, attenuated total reflection Fourier transform infrared (ATR FTIR) spectroscopy, and in-line imaging techniques, offer great potential for obtaining reliable information during crystallization, and thus giving a better understanding of the fundamental mechanisms (nucleation and crystal growth) involved. In the present work, the relative stability of anhydrate and dihydrate carbamazepine in mixed solvents containing water and ethanol were investigated. The kinetics of the solvent mediated phase transformation of the anhydrate to hydrate in the mixed solvents was studied using an in-line Raman immersion probe. The effects of the operation parameters in terms of solvent composition, temperature and the use of certain additives on the phase transformation kineticswere explored. Comparison of the off-line measured solute concentration and the solid-phase composition measured by in-line Raman spectroscopy allowedthe identification of the fundamental processes during the phase transformation. The effects of thermodynamic and kinetic factors on the anhydrate/hydrate phase of carbamazepine crystals during cooling crystallization were also investigated. The effect of certain additives on the batch cooling crystallization of potassium dihydrogen phosphate (KDP) wasinvestigated. The crystal growth rate of a certain crystal face was determined from images taken with an in-line video microscope. An in-line image processing method was developed to characterize the size and shape of thecrystals. An ATR FTIR and a laser reflection particle size analyzer were used to study the effects of cooling modes and seeding parameters onthe final crystal size distribution of an organic compound C15. Based on the obtained results, an operation condition was proposed which gives improved product property in terms of increased mean crystal size and narrowersize distribution.

Short communication.Wood identification based on their common name and their transversal surface anatomy. Application to the batch from the expedition of Ruiz and Pavon

Aim of study: To identify species of wood samples based on common names and anatomical analyses of their transversal surfaces (without microscopic preparations). Area of study: Spain and South America Material and methods: The test was carried out on a batch of 15 lumber samples deposited in the Royal Botanical Garden in Madrid, from the expedition by Ruiz and Pavon (1777-1811). The first stage of the methodology is to search and to make a critical analysis of the databases which list common nomenclature along with scientific nomenclature. A geographic filter was then applied to the information resulting from the samples with a more restricted distribution. Finally an anatomical verification was carried out with a pocket microscope with a magnification of x40, equipped with a 50 micrometers resolution scale. Main results: The identification of the wood based exclusively on the common name is not useful due to the high number of alternative possibilities (14 for “naranjo”, 10 for “ébano”, etc.). The common name of one of the samples (“huachapelí mulato”) enabled the geographic origin of the samples to be accurately located to the shipyard area in Guayaquil (Ecuador). Given that Ruiz y Pavon did not travel to Ecuador, the specimens must have been obtained by Tafalla. It was possible to determine correctly 67% of the lumber samples from the batch. In 17% of the cases the methodology did not provide a reliable identification. Research highlights: It was possible to determine correctly 67% of the lumber samples from the batch and their geographic provenance. The identification of the wood based exclusively on the common name is not useful.

Treatment of micropollutants in municipal wastewater: study of a sequential batch biofilter

All the experimental part of this final project was done at Laboratoire de Biotechnologie Environnementale (LBE) from the École Polytechnique Fédérale de Lausanne (EPFL), Switzerland, during 6 months (November 2013- May 2014). A fungal biofilter composed of woodchips was designed in order to remove micropollutants from the effluents of waste water treatment plants. Two fungi were tested: Pleurotus ostreatus and Trametes versicolor in order to evaluate their efficiency for the removal of two micropollutants: the anti-inflammatory drug naproxen and the antibiotic sulfamethoxazole,. Although Trametes versicolor was able to degrade quickly naproxen, this fungus was not any more active after one week of operation in the filter. Pleurotus ostreatus was, on contrary, able to survive more than 3 months in the filter, showing good removal efficiencies of naproxen and sulfamethoxazole during all this period, in tap water but also in real treated municipal wastewater. Several other experiments have provided insight on the removal mechanisms of these micropollutants in the fungal biofilter (degradation and adsorption) and also allowed to model the removal trend. Fungal treatment with Pleurotus ostreatus grown on wood substrates appeared to be a promising solution to improve micropollutants removal in wastewater.

The Present State and a Development Plan of Cost Accounting in Batch Production of Wind Turbine Gears

The aim of this master’s thesis was to document the present state and to create a development plan for Moventas Wind’s cost accounting. The current cost accounting system was evaluated and most fundamental problems were chosen as areas of focus in development work. The development plan includes both short- and long-term development proposals for problems identified. This report presents two alternative models for product costing. Benchmarking of cost accounting practices and modern cost accounting theories were used in development of cost accounting. It was found that the current cost accounting system functions quite well and the adjustments in unit cost rate calculation have only a minor influence on costs of goods sold. An OEE-based standard cycle concept was also developed and it was found that the implementation of this new system is worthwhile in the long-term.

Retrieval of kinetic rates in reactions with semi batch liquid phase using ill-posed inverse problem theory

A neural network procedure to solve inverse chemical kinetic problems is discussed in this work. Rate constants are calculated from the product concentration of an irreversible consecutive reaction: the hydrogenation of Citral molecule, a process with industrial interest. Simulated and experimental data are considered. Errors in the simulated data, up to 7% in the concentrations, were assumed to investigate the robustness of the inverse procedure. Also, the proposed method is compared with two common methods in nonlinear analysis; the Simplex and Levenberg-Marquardt approaches. In all situations investigated, the neural network approach was numerically stable and robust with respect to deviations in the initial conditions or experimental noises.

Flow-batch analyser for preparation of calibration standard mixtures in simultaneous multicomponent spectrometric analysis

The application of multivariate calibration techniques to multicomponent analysis by UV-VIS molecular absorption spectrometry is a powerful tool for simultaneous determination of several chemical species. However, when this methodology is accomplished manually, it is slow and laborious, consumes high amounts of reagents and samples, is susceptible to contaminations and presents a high operational cost. To overcome these drawbacks, a flow-batch analyser is proposed in this work. This analyser was developed for automatic preparation of standard calibration and test (or validation) mixtures. It was applied to the simultaneous determination of Cu2+, Mn2+ and Zn2+ in polyvitaminic and polymineral pharmaceutical formulations, using 4-(2-piridilazo) resorcinol as reagent and a UV-VIS spectrophotometer with a photodiode array detector. The results obtained with the proposed system are in good agreement with those obtained by flame atomic absorption spectrometry, which was employed as reference method. With the proposed analyser, the preparation of calibration and test mixtures can be accomplished about four hours, while the manual procedure requires at least two days. Moreover, it consumes smaller amounts of reagents and samples than the manual procedure. After the preparation of calibration and test mixtures, 60 samples h-1 can be carried out with the proposed flow-batch analyser.

Kinetic behavior of nitrification in the post-treatment of poultry wastewater in a sequential batch reactor

A sequential batch reactor with suspended biomass and useful volume of 5 L was used in the removal of nutrients and organic matter in workbench scale under optimal conditions obtained by central composite rotational design (CCRD), with cycle time (CT) of 16 h (10.15 h, aerobic phase, and 4.35 h, anoxic phase) and carbon: nitrogen ratio (COD/NO2--N+NO3--N) equal to 6. Complete cycles (20), nitrification followed by denitrification, were evaluated to investigate the kinetic behavior of degradation of organic (COD) and nitrogenated (NH4+-N, NO2--N and NO3--N) matter present in the effluent from a bird slaughterhouse and industrial processing facility, as well as to evaluate the stability of the reactor using Shewhart control charts of individual measures. The results indicate means total inorganic nitrogen (NH4+-N+NO2- -N+NO3--N) removal of 84.32±1.59% and organic matter (COD) of 53.65±8.48% in the complete process (nitrification-denitrification) with the process under statistical control. The nitrifying activity during the aerobic phase estimated from the determination of the kinetic parameters had mean K1 and K2 values of 0.00381±0.00043 min-1 and 0.00381±0.00043 min-1, respectively. The evaluation of the kinetic behavior of the conversion of nitrogen indicated a possible reduction of CT in the anoxic phase, since removals of NO2--N and NO3--N higher than 90% were obtained with only 1 h of denitrification.

Performance of UASB reactors in two stages followed by post-treatment with activated sludge in wastewater batch of wet-processed coffee

In this study it was evaluated the efficiency of the treatment of wet-processed coffee wastewater in upflow anaerobic sludge blanket (UASB) reactors in two stages, in bench scale, followed by post-treatment with activated sludge in batch. The first UASB reactor was submitted to an hydraulic retention time (HRT) of 6.2 d and organic loading rates (OLR) of 2.3 and 4.5g CODtotal (L d)-1, and the second UASB reactor to HRT of 3.1 d with OLR of 0.4 and 1.4g CODtotal (L d)-1. The average values of the affluent CODtotal increased from 13,891 to 27,926mg L-1 and the average efficiencies of removal of the CODtotal decreased from 95 to 91%, respectively, in the UASB reactors in two stages. The volumetric methane production increased from 0.274 to 0.323L CH4 (L reactor d)-1 with increment in the OLR. The average concentrations of total phenols in the affluent were of 48 and 163mg L-1, and the removal efficiencies in the UASB reactors in two stages of 92 and 90%, respectively, and increased to 97% with post-treatment. The average values of the removal efficiencies of total nitrogen and phosphorus were of 57 to 80% and 44 to 60%, respectively, in the UASB reactors in two stages and increased to 91 and 84% with the post-treatment.

Anaerobic-aerobic treatment of swine wastewater in uasb and batch reactors in series

In this work it was evaluated the performance of two systems of swine wastewater treatment consisting of two-stage upflow anaerobic sludge blanket (UASB) reactors, with and without post-treatment in sequencing batch reactor (SBR), fed continuously, with aerobic phase. The UASB reactors in the first stage had 908 L in the sets I and II, and in the second stage 350 and 188 L, respectively. In the set II the post-treatment was performed in a SBR of 3,000 L. The hydraulic detention times in the anaerobic treatment systems were 100, 75 and 58 h in the set I; 87, 65 and 51 h in the set II; and 240 and 180 h in the SBR. The volumetric organic load applied in the first stage UASB reactors ranged from 6.9 to 12.6 g total COD (L d)-1 in the set I and 7.5 to 9.8 g total COD (L d)-1 in the set II. The average removal efficiencies of total COD, total phosphorus (Ptotal), and Kjeldahl and organic nitrogen (KN and Norg) in the anaerobic treatment systems were similar and reached maximum values of 97%, 64%, 68%, and 98%. In the SBR, the removal efficiencies of total COD and thermotolerant coliforms were up to 62 and 92% resulting, respectively, in effluent concentrations of 135 mg L-1 and 2x10(4)MPN (100 mL)-1. For Ptotal, total nitrogen (TN) and Norg, the average removal efficiencies in the SBR were up to 58, 25 and 73%, respectively.

Application of response surface methodology to study the biological removal of nitrogen from effluent of cattle slaughterhouse in a sequencing batch reactor

The aim of this study was to evaluate the efficiency of a sequencing batch reactor (SBR) on biological removal of nitrogen from cattle slaughterhouse wastewater by nitrification/denitrification processes. The effects of initial concentration of ammoniacal nitrogen were investigated at 100; 150 and 200 mg L-1 and air flow rate at 0.125; 0.375 and 0.625 L min¹ Lreactor-1 on the nitrogen compounds removal, by a Central Composite Rotational Design (CCRD) configuration. There were variations from 9.2 to 94.9%, 4.0 to 19.6% and 20.8 to 92.0% in the conversion of ammoniacal nitrogen to nitrate and nitrite concentration and removal of total nitrogen, respectively. The increase of air flow rate and decrease of the initial concentration of ammoniacal nitrogen resulted in higher efficiencies of total nitrogen removal, as well as the conversion of ammoniacal nitrogen to nitrate. During the pre-established intervals of this study, the removal and conversion efficiencies of nitrogen compounds above 85% were achieved in air flow rate variations from 0.375 to 0.725 L min-1 Lreactor-1 and initial concentration of ammoniacal nitrogen from 80 to 200 mg L-1. On denitrification process, we obtained efficiencies from 91.5 to 96.9% on the removal of nitrite/nitrate and from 78.3 to 87.9% on the removal of organic matter.

Effect of cycle time and airflow in biological nitrogen removal from poultry slaughterhouse wastewater using sequencing batch reactor

This study aimed to evaluate the influence of airflow (0.25, 0.50 and 0.75 L.L-1.min-1) and cycle time (10.45 h, 14.25 h and 17.35 h) on a sequencing batch reactor (SBR) performance in promoting nitrification and denitrification of poultry slaughterhouse wastewater. The operational stages included feeding, aerobic and anoxic reactions, sedimentation and discharge. SBR was operated in a laboratory scale with a working volume of 4 L, keeping 25% of biomass retained inside the reactor as inoculum for the next batch. In the anoxic stage, C: N ratio was maintained between 5 and 6 by adding cassava starch wastewater. A factorial design (22) with five repetitions was designed at the central point to evaluate the influence of cycle time and airflow on total inorganic nitrogen removal (N-NH4++N-NO2-+N-NO3-) and in the whole process (nitrification and denitrification). The highest total inorganic nitrogen removal (93.3%) was observed for airflow of 0.25 L.L-1.min‑1 and a cycle time of 14.25 h. At the end of the experiment, the sludge inside the reactor was characterized by fluorescent in situ hybridization (FISH), indicating the presence of ammonia and nitrite oxidizing bacteria.