miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data

Single-cell RNA-sequencing (scRNA-seq) has made it possible to profile gene expression in tissues at high resolution. An important preprocessing step prior to performing downstream analyses is to identify and remove cells with poor or degraded sample quality using quality control (QC) metrics. Two widely used QC metrics to identify a ‘low-quality’ cell are (i) if the cell includes a high proportion of reads that map to mitochondrial DNA (mtDNA) encoded genes and (ii) if a small number of genes are detected. Current best practices use these QC metrics independently with either arbitrary, uniform thresholds (e.g. 5%) or biological context-dependent (e.g. species) thresholds, and fail to jointly model these metrics in a data-driven manner. Current practices are often overly stringent and especially untenable on certain types of tissues, such as archived tumor tissues, or tissues associated with mitochondrial function, such as kidney tissue [1]. We propose a data-driven QC metric (miQC) that jointly models both the proportion of reads mapping to mtDNA genes and the number of detected genes with mixture models in a probabilistic framework to predict the low-quality cells in a given dataset. We demonstrate how our QC metric easily adapts to different types of single-cell datasets to remove low-quality cells while preserving high-quality cells that can be used for downstream analyses. Our software package is available at https://bioconductor.org/packages/miQC.     

Side-by-side comparison of horizontal subsurface flow and free water surface flow constructed wetlands and artificial neural network (ANN) modelling approach

A horizontal subsurface flow (HSSF) and a free water surface flow (FWSF) constructed wetlands (4 m² of each) were set up on the campus of Harran University, Sanliurfa, Turkey. The main objective of the research was to compare the performance of two systems to decide the better one for future planning of wastewater treatment system on the campus. Both of the wetland systems were planted with Phragmites australis and Canna indica. During the observation period (10 months), environmental conditions such as pH, temperature and total chemical oxygen demand (COD), soluble COD, total biochemical oxygen demand (BOD), soluble BOD, total suspended solids (TSS), total phosphate (TP), total nitrogen (TN) removal efficiencies of the systems were determined. According to the results, average yearly removal efficiencies for the HSSF and the FWSF, respectively, were as follows: total COD (75.7% and 69.9%), soluble COD (85.4% and 84.3%), total BOD (79.6% and 87.6%), soluble BOD (87.7% and 95.3%), TN (33.2% and 39.4%), and TP (31.5% and 6.5%). Soluble COD and BOD removal efficiencies of both systems increased gradually since the start-up. After nine months of operation, above 90% removal of organic matters were observed. The treatment performances of the HSSF were better than that of the FWSF with regard to the removal of suspended solids and total COD at especially high temperatures. In FWSF systems, COD concentrations extremely exceeded the discharge limit values due to high concentrations of algae in spring months.The performance of the two systems was modelled using an artificial neural network-back-propagation algorithm. The ANN model was competent at providing reasonable match between the measured and the predicted concentrations of total COD (R = 0.90 for HSSF and R = 0.96 for FWSF), soluble COD (R = 0.90 for HSSF and R = 0.74 for FWSF) and total BOD (R = 0.94 for HSSF and R = 0.84 for FWSF) in the effluents of constructed wetlands.     

Performance of sulfidogenic anaerobic baffled reactor (ABR) treating acidic and zinc-containing wastewater

The applicability of anaerobic baffled reactor (ABR) was investigated for the treatment of acidic (pH 4.5–7.0) wastewater containing sulfate (1000–2000 mg/L) and Zn (65–200 mg/L) at 35 °C. The ABR consisted of four equal stages and lactate was supplemented (COD/SO₄²⁻ = 0.67) as carbon and energy source for sulfate reducing bacteria (SRB). The robustness of the system was studied by decreasing pH and increasing Zn, COD, and sulfate loadings. Sulfate-reduction efficiency quickly increased during the startup period and reached 80% within 45 days. Decreasing feed pH, increasing feed sulfate and Zn concentrations did not adversely affect system performance as sulfate reduction and COD removal efficiencies were within 62–90% and 80–95%, respectively. Although feed pH was steadily decreased from 7.0 to 4.5, effluent pH was always within 6.8–7.5. Over 99% Zn removal was attained throughout the study due to formation of Zn-sulfide precipitate.     

Acoustic rhinometry in humans: accuracy of nasal passage area estimates, and ability to quantify paranasal sinus volume and ostium size.

A comprehensive study that compared acoustic rhinometry (AR) data to computed tomography (CT) data was performed to evaluate the accuracy of AR measurements in estimating nasal passage area and to assess its ability of quantifying paranasal sinus volume and ostium size in live humans. Twenty nasal passages of 10 healthy adults were examined by using AR and CT. Actual cross-sectional areas of the nasal cavity, sinus ostia sizes, and maxillary and frontal sinus volumes were determined from CT sections perpendicular to the curved acoustic axis of the nasal passage. Nasal cavity volume (from nostril to choana) calculated from the AR-derived area-distance curve was compared with that from the CT-derived area-distance curve. AR measurements were also done on pipe models that featured a side branch (Helmholtz resonator of constant volume but two different neck diameters) simulating a paranasal sinus. In the anterior nasal cavity, there was good agreement between the cross-sectional areas determined by AR and CT. However, posterior to the sinus ostia, AR overestimated cross-sectional area. The difference between AR nasal volume and CT nasal volume was much smaller than the combined volume of the maxillary and frontal sinuses. The results suggest that AR measurements of the healthy adult nasal cavity are reasonably accurate to the level of the paranasal sinus ostia. Beyond this point, AR overestimates cross-sectional area and provides no quantitative data for sinus volume or ostium size. The effects of paranasal sinuses and acoustic resonances in the nasal cavity are not accounted for in the present AR algorithms.     

Biologically Fe<Superscript>2+</Superscript> oxidizing fluidized bed reactor performance and controlling of Fe<Superscript>3+</Superscript> recycle during heap bioleaching: an artificial neural network-based model

The performance of a biological Fe²⁺ oxidizing fluidized bed reactor (FBR) was modeled by a popular neural network-back-propagation algorithm over a period of 220 days at 37 °C under different operational conditions. A method is proposed for modeling Fe³⁺ production in FBR and thereby managing the regeneration of Fe³⁺ for heap leaching application, based on an artificial neural network-back-propagation algorithm. Depending on output value, relevant control strategies and actions are activated, and Fe³⁺ production in FBR was considered as a critical output parameter. The modeling of effluent Fe³⁺ concentration was very successful, and an excellent match was obtained between the measured and the predicted concentrations.     

The effect of clopidogrel on apoptosis--an in vivo study

Clopidogrel is widely used in cardiovascular medicine, and is believed to play an important role in the pathogenesis of many cardiovascular disease processes. In particular, patients undergoing coronary stenting, who are commonly treated with clopidogrel, are candidates for in-stent restenosis. This is mainly caused by neointimal hyperplasia, so it is important to consider whether clopidogrel affects neointimal hyperplasia via apoptosis. Lymphocytes, especially T-cells, are known to play a key role in the initiation and formation of atherosclerotic plaques. The aim of this study was to investigate the effect of clopidogrel on human lymphocyte apoptosis, using a DNA fragmentation assay.     

Cutting edge: A common polymorphism impairs cell surface trafficking and functional responses of TLR1 but protects against leprosy

TLRs constitute an essential family of pattern recognition molecules that, through direct recognition of conserved microbial components, initiate inflammatory responses following infection. In this role, TLR1 enables host responses to a variety of bacteria, including pathogenic species of mycobacteria. In this study, we report that I602S, a common single nucleotide polymorphism within TLR1, is associated with aberrant trafficking of the receptor to the cell surface and diminished responses of blood monocytes to bacterial agonists. When expressed in heterologous systems, the TLR1 602S variant, but not the TLR1 602I variant, exhibits the expected deficiencies in trafficking and responsiveness. Among white Europeans, the 602S allele represents the most common single nucleotide polymorphism affecting TLR function identified to date. Surprisingly, the 602S allele is associated with a decreased incidence of leprosy, suggesting that Mycobacterium leprae subverts the TLR system as a mechanism of immune evasion.     

Azoramide improves mitochondrial dysfunction in palmitate-induced insulin resistant H9c2 cells

Molecular and Cellular Biochemistry - White adipose tissue (WAT) is the bulk of fatty tissues in humans. Enhancing the potential of WAT-derived stem cells (WATDCs) to generate cardiomyocytes may...