An Efficient Algorithm for the Detection of Outliers in Mislabeled Omics Data

High dimensionality and noise have made it difficult to detect related biomarkers in omics data. Through previous study, penalized maximum trimmed likelihood estimation is effective in identifying mislabeled samples in high-dimensional data with mislabeled error. However, the algorithm commonly used in these studies is the concentration step (C-step), and the C-step algorithm that is applied to robust penalized regression does not ensure that the criterion function is gradually optimized iteratively, because the regularized parameters change during the iteration. This makes the C-step algorithm runs very slowly, especially when dealing with high-dimensional omics data. The AR-Cstep (C-step combined with an acceptance-rejection scheme) algorithm is proposed. In simulation experiments, the AR-Cstep algorithm converged faster (the average computation time was only 2% of that of the C-step algorithm) and was more accurate in terms of variable selection and outlier identification than the C-step algorithm. The two algorithms were further compared on triple negative breast cancer (TNBC) RNA-seq data. AR-Cstep can solve the problem of the C-step not converging and ensures that the iterative process is in the direction that improves criterion function. As an improvement of the C-step algorithm, the AR-Cstep algorithm can be extended to other robust models with regularized parameters.

Electrochemical Degradation of Carbamazepine: A Case Study of Quantification of “10, 11 Dihydro-10 Hydroxy Carbamazepine And 10, 11-Epoxycarbamazepine” As The Main By-Products Using LC-TOF/MS.

Carbamazepine (CBZ) is one of the most widely used antiepileptic drugs in Malaysia, so, it was detected in wastewater frequently. The electrochemical treatment process has been applied for the degradation of CBZ using graphite-PVC as an anode. However, two main by-products, namely, 10,11-dihydro10-hydroxy carbamazepine (HDX-CBZ) and 10,11-epoxycarbamazepine (EPX-CBZ) have been analysed and quantified using liquid chromatography-time of flight/mass spectrometry (LC-TOF/MS). HDX-CBZ and EPX-CBZ were analysed in positive ionisation mode and were separated chromatographically using 5 mm, 2 mm´150 mm C18 column at a flow rate of 0.3 mL/min. To improve sensitivity and detectability, SPE was applied as a pre-concentration step for the treated carbamazepine samples to extract and pre-concentrate HDX-CBZ and EPX-CBZ. However, three different solvents, namely, methyl tertiary butyl ether, acetone and methanol, have been optimized to enhance the recovery. The recovery was 85% and 92% for HDX-CBZ and EPX-CBZ, respectively, in the presence of methanol. The limit of quantification (LOQ) was 0.588 and 0.109 µg/L for both by-products, respectively. The concentration of HDX-CBZ and EPX-CBZ was 343 and 144 μg/L, respectively, after 20 min of treatment, then, it was decreased to 17.2 and 9.8 μg/L at 40 min. Finally, both by-products were eliminated after 60 min.

Mengovirus as Process Control Virus in the Monitoring of Genomic RNA and Infectivity of Enteric Viruses in Water Matrices

The present study, developed in the scope of a survey to monitor enteric viruses in natural surface water and drinking water sources, addressed the suitability of mengovirus to assess viral recovery rates at two steps of the water sampling process. In a pilot campaign comprising two samples from each type of water source, when mengovirus was added after the filtration/primary concentration step, the recovery rates of viral RNA were higher than 18% and identical for both water matrices. In a one-year sampling campaign, where mengovirus was present along the whole sample processing (addition in the filtration/primary concentration step), significantly different recovery rates were observed between water matrices: usually higher than 1% in drinking water and under 1% in surface water. The results suggest the first stage of the water sampling process and the type of water matrix are the most influential factors for viral RNA recovery. This study also addressed and evidenced mengovirus replication and titration in Vero E6 cultures and showed infectious mengovirus to be recovered from samples of both types of water matrix. These results anticipate a more comprehensive applicability of mengovirus as a process control virus in the monitoring of viruses in water, extended to viral infectivity.

Impact and feasibility of a membrane pre-concentration step in kraft recovery

Emerging robust membrane systems can perform the first section of black liquor (BL) concentration by separating clean water from the black liquor stream using only mechanical pressure. By doing so, they can reduce the steam and energy required for BL concentration. Because of the high osmotic pressure of strong BL, a membrane system would not replace evaporators but would operate in series, performing the first section of BL concentration. In this work, we use a multi-effect evaporator (MEE) model to quantify the steam and energy savings associated with installing membrane systems of different sizes. When maintaining a constant BL solids throughput, we find that a pulp mill could reduce steam usage in its evaporators by up to 65%. Alternatively, a membrane system could also serve to increase BL throughput of the recovery train. We find that a membrane system capable of concentrating BL to 25% could double the BL solids throughput of a mill’s evaporators at the same steam usage. We also demonstrate that installing a membrane system before an MEE would minimally affect key operating parameters such as steam pressures and BL solids concentrations in each effect. This indicates that installing a membrane pre-concentration system would be nonintrusive to a mill’s operations.

Rhenium distribution and behaviour in the salinity gradient of a highly stratified estuary and pristine riverine waters

The abundance and distribution of dissolved Re (DRe) has been determined in the freshwater part of the Krka River (Croatia), draining the karstic carbonate landscape, as well as in the salinity gradient of its highly stratified estuary. Due to low DRe concentration, the batch procedure consisting of pre-concentration step using an anion exchange resin (Dovex) and analysis of DRe in 8 M HNO 3 eluate using a high resolution inductively coupled plasma mass spectrometry (HR ICP-MS) was adopted. Due to the potential inconsistent recoveries, ranging from 60% to 87%, the quantification was performed by using the isotope dilution (ID) technique. The DRe concentration in the Krka River basically increased in the downstream direction, with the 6.2 pM at the spring site, reaching 11.9 pM before the estuarine region. The weathering of the surrounding carbonate lithology is assumed as the source of natural Re. The two specific anomalies were registered: a strong increase in DRe concentration due to the anthropogenic input near the town of Knin (27.5 pM) and a decrease at downstream site caused by the subterranean input of freshwater of the Zrmanja River leading to relatively low DRe concentration (8.5 pM). In the estuarine segment, a near-conservative behavior of DRe was found in the salinity gradient of the upper surface layer, with the DRe concentration ranging from 18 to 38 pM. An anthropogenic supply was suggested within the estuarine segment close to the urban area causing a small positive deviation from the conservative line. In the bottom seawater layer, a minor decrease of DRe concentration in the most upstream estuarine regions was evidenced, implying a potential weak scavenging of Re.

Does each bead count? A reduced-cost approach for recovering waterborne protozoa from challenge water using immunomagnetic separation

Giardia duodenalis and Cryptosporidium spp. are two of the most prominent aetiological agents of waterborne diseases. Therefore, efficient and affordable methodologies for identifying and quantifying these parasites in water are increasingly necessary. USEPA Method 1623.1 is a widely used and validated protocol for detecting these parasites in water samples. It consists of a concentration step, followed by parasite purification and visualization by immunofluorescence microscopy. Although efficient, this method has a high cost particularly due to the immunomagnetic separation (IMS) step, which is most needed with complex and highly contaminated samples. Based on this, the present study aimed to determine whether it is possible to maintain the efficiency of Method 1623.1 while reducing the amount of beads per reaction, using as a matrix the challenge water recommended by the World Health Organization. As for Giardia cysts, a satisfactory recovery efficiency (RE) was obtained using 50% less IMS beads. This was evaluated both with a commercial cyst suspension (56.1% recovery) and an analytical quality assessment (47.5% recovery). Although RE rates obtained for Cryptosporidium parvum did not meet Method 1623.1 criteria in any of the experimental conditions tested, results presented in this paper indicated the relevance of the described adaptations, even in challenge water.

Evaluating volume reduction of clarified acid bovine milk whey via falling film vacuum evaporation

This research evaluates the effect of falling film vacuum evaporation on the characteristics of clarified acid bovine milk whey. The clarified acid whey was obtained by microfiltration (ceramic membranes, 0.2 µm cut-off, ∆TMP: 2 bar) and concentrated by a falling film evaporator. The clarified whey composition was mainly protein (0.32 ± 0.06 % w/w), ashes (0.56 ± 0.08 % w/w), soluble solids (5 ± 1 % w/w), and turbidity (16 ± 5 NTU). During the concentration step, the number of cycles changed notoriously for each volume reduction factor (VRF), being four the highest value achieved, with an average number of cycles of 18. The characteristics of concentrates were not affected by differences in the number of cycles, increasing proportionally with the VRF; it could be noticed in the final content that protein, ashes, and °Bx increased linearly around 3.5 times the initial composition. However, turbidity was different for each VRF because of heat treatment during the concentration stage (above 60 °C). A thermal treatment step after ricotta preparation would be advisable to remove the remaining protein. Tukey’s test was carried out at a 95 % CI, revealing statistical differences among means; therefore, there was a change in the characteristics of the final concentrated whey. Regarding color (absorbance), there were no considerable changes during the concentration process.

Evaluation of different stool extraction methods for metabolomics measurements in human fecal samples

BackgroundMeasurement of metabolomics in human stool samples is of great interest for a broad range of applications in biomedical research including early detection of colorectal neoplasms. However, due to the complexity of metabolites there is no consensus on how to process samples for stool metabolomics measurements to obtain a broad coverage of hydrophilic and hydrophobic substances.MethodsWe used frozen stool samples (50mg) from healthy study participants. Stool samples were processed after thawing using 8 different processing protocols and different solvents. Metabolites were measured afterwards using the MxP® Quant 500 kit (Biocrates). The best performing protocol was subsequently applied to compare stool samples of participants with different dietary habits.ResultsIn this study, we were able to determine up to 340 metabolites of various chemical classes extracted from stool samples of healthy study participants with 8 different protocols. Polar metabolites such as amino acids could be measured with each method while other metabolite classes, particular lipid species, are more dependent on the solvent or combination of solvents used. Only a small number of triglycerides or acylcarnitines were detected in human feces. Extraction efficiency was higher for protocols using isopropanol or those using ethanol or methanol and MTBE including an evaporation and concentration step than for other protocols. We detected significant fecal metabolite differences between vegetarians, semi-vegetarians and non-vegetarians.ConclusionFor the evaluation of metabolites in fecal samples we found protocols using solvents like isopropanol and those using ethanol or methanol and MTBE including an evaporation and concentration step to be superior over others tested in this study.

Simultaneous Pre-Concentration and HPLC-MS/MS Quantification of Phycotoxins and Cyanotoxins in Inland and Coastal Waters

The purpose of this study was to set up a sensitive method for the simultaneous determination of phycotoxins and cyanotoxins—Emerging pollutants with different structures and harmful properties (hepatotoxicity, neurotoxicity and cytotoxicity)—In environmental waters. Due to the low concentrations detected in these samples, a pre-concentration step is required and here it was performed in a single step with a commercial cartridge (Strata™-X), achieving enrichment factors up to 200 and satisfactory recovery (R = 70–118%) in different aqueous matrices. After solid-phase extraction (SPE), toxins were separated and quantified by High Performance Liquid Chromatography- Heated ElectroSpray Ionisation Tandem Mass Spectrometry (HPLC-HESI-MS/MS) in Multiple Reaction Monitoring (MRM) mode. An analytical evaluation of the proposed method was done based on the analytical figures of merit, such as precision and trueness, linearity, selectivity, and sensitivity, and it turned out to be a robust tool for the quantification of ng L−1 levels, phycotoxins and cyanotoxins in both freshwater and saltwater samples.

Characterization of Arabica and Robusta Coffees by Ion Mobility Sum Spectrum

Aroma is one of the main characteristics of coffee specimens. Different mixtures of Arabica and Robusta coffees are usually found in the market to offer specific aroma or flavor profiles to consumers. However, the mixed samples or their proportions are not always identified in the product labels. Since the price of Arabica is much higher than that of Robusta, this lack of information is not only an economical issue but a possible fraud to consumers, besides the potential allergic reaction that these mixtures may trigger in some individuals. In this paper, two sample preparation techniques were compared before the analysis of the total volatile organic compounds (VOCs) found in Robusta, Arabica, and in the mixture from both coffee types. The comparison of the signals obtained from the analyses showed that the VOCs concentration levels obtained from the headspace (HS) analyses were clearly higher than those obtained from the pre-concentration step where an adsorbent, an active charcoal strip (ACS + HS), was used. In the second part of this study, the possibility of using the headspace gas-chromatography ion mobility spectrometry (HS-GC-IMS) for the discrimination between Arabica, Robusta, and mixed coffee samples (n = 30) was evaluated. The ion mobility sum spectrum (IMSS) obtained from the analysis of the HS was used in combination with pattern recognition techniques, namely linear discrimination analysis (LDA), as an electronic nose. The identification of individual compounds was not carried out since chromatographic information was not used. This novel approach allowed the correct discrimination (100%) of all of the samples. A characteristic fingerprint for each type of coffee for a fast and easy identification was also developed. In addition, the developed method is ecofriendly, so it is a good alternative to traditional approaches.