The Value of Whole-Genome Sequencing for Mitochondrial DNA Population Studies: Strategies and Criteria for Extracting High-Quality Mitogenome Haplotypes

Whole-genome sequencing (WGS) data present a readily available resource for mitochondrial genome (mitogenome) haplotypes that can be utilized for genetics research including population studies. However, the reconstruction of the mitogenome is complicated by nuclear mitochondrial DNA (mtDNA) segments (NUMTs) that co-align with the mtDNA sequences and mimic authentic heteroplasmy. Two minimum variant detection thresholds, 5% and 10%, were assessed for the ability to produce authentic mitogenome haplotypes from a previously generated WGS dataset. Variants associated with NUMTs were detected in the mtDNA alignments for 91 of 917 (~8%) Swedish samples when the 5% frequency threshold was applied. The 413 observed NUMT variants were predominantly detected in two regions (nps 12,612–13,105 and 16,390–16,527), which were consistent with previously documented NUMTs. The number of NUMT variants was reduced by ~97% (400) using a 10% frequency threshold. Furthermore, the 5% frequency data were inconsistent with a platinum-quality mitogenome dataset with respect to observed heteroplasmy. These analyses illustrate that a 10% variant detection threshold may be necessary to ensure the generation of reliable mitogenome haplotypes from WGS data resources.     

Rapid Discrimination of Neuromyelitis Optica Spectrum Disorder and Multiple Sclerosis Using Machine Learning on Infrared Spectra of Sera

Neuromyelitis optica spectrum disorder (NMOSD) and multiple sclerosis (MS) are both autoimmune inflammatory and demyelinating diseases of the central nervous system. NMOSD is a highly disabling disease and rapid introduction of the appropriate treatment at the acute phase is crucial to prevent sequelae. Specific criteria were established in 2015 and provide keys to distinguish NMOSD and MS. One of the most reliable criteria for NMOSD diagnosis is detection in patient’s serum of an antibody that attacks the water channel aquaporin-4 (AQP-4). Another target in NMOSD is myelin oligodendrocyte glycoprotein (MOG), delineating a new spectrum of diseases called MOG-associated diseases. Lastly, patients with NMOSD can be negative for both AQP-4 and MOG antibodies. At disease onset, NMOSD symptoms are very similar to MS symptoms from a clinical and radiological perspective. Thus, at first episode, given the urgency of starting the anti-inflammatory treatment, there is an unmet need to differentiate NMOSD subtypes from MS. Here, we used Fourier transform infrared spectroscopy in combination with a machine learning algorithm with the aim of distinguishing the infrared signatures of sera of a first episode of NMOSD from those of a first episode of relapsing-remitting MS, as well as from those of healthy subjects and patients with chronic inflammatory demyelinating polyneuropathy. Our results showed that NMOSD patients were distinguished from MS patients and healthy subjects with a sensitivity of 100% and a specificity of 100%. We also discuss the distinction between the different NMOSD serostatuses. The coupling of infrared spectroscopy of sera to machine learning is a promising cost-effective, rapid and reliable differential diagnosis tool capable of helping to gain valuable time in patients’ treatment.     

Extraction of Bitter Acids from Hops and Hop Products Using Pressurized Solvent Extraction (PSE)

The EBC method 7.7, currently used for determination of bitter acids in hop products, is a time‐consuming and laborious extraction technique. In this paper, our aim was to propose a new extraction method based on Pressurized Solvent Extraction (PSE) sometimes also called Pressurized Fluid Extraction (PFE) or Accelerated Solvent Extraction (ASE). Compared to conventional extractions, PSE offers a number of important benefits. PSE on OnePSE^® automated extractor was used for extraction of α‐ and β‐acids from hops and hop products and the parameters influencing extraction efficiency and the influence of the sample preparation method were studied. The quantitative determination of α‐ and β‐acids in the extracts was accomplished by using an HPLC apparatus equipped with diode array detector. The experimental results were compared with those obtained by the standard EBC 7.7 method and the two methods were found to be fully compatible     

Estimation of Intrinsic Volumes from Digital Grey-Scale Images

Local algorithms are common tools for estimating intrinsic volumes from black-and-white digital images. However, these algorithms are typically biased in the design based setting, even when the resolution tends to infinity. Moreover, images recorded in practice are most often blurred grey-scale images rather than black-and-white. In this paper, an extended definition of local algorithms, applying directly to grey-scale images without thresholding, is suggested. We investigate the asymptotics of these new algorithms when the resolution tends to infinity and apply this to construct estimators for surface area and integrated mean curvature that are asymptotically unbiased in certain natural settings.     

Disentangling Water Usage in the European Union: A Decomposition Analysis

The Water Framework Directive (WFD) defines common objectives for water resources throughout the European Union (EU). Given this general approach to water preservation and water policy, the objective of this paper is to analyse whether common patterns of water consumption exist within Europe. In particular, our study uses two methods to reveal the reasons behind sectoral water use in all EU countries. The first method is based on an accounting indicator that calculates the water intensity of an economy as the sum of sectoral water intensities. The second method is a subsystem input-output model that divides total water use into different income channels within the production system. The application uses data for the years 2005 and 2009 on water consumption in the production system of the 27 countries of the EU. From our analysis it emerges that EU countries are characterized by very different patterns of water consumption. In particular water consumption by the agriculture sector is extremely high in Central/Eastern Europe, relative to the rest of Europe. In most countries, the water used by the fuel, power and water sector is consumed to satisfy domestic final demand. However, our analysis shows that for some countries exports from this sector are an important driver of water consumption. Focusing on the agricultural sector, the decomposition analysis suggests that water usage in Mediterranean countries is mainly driven by final demand for, and exports of, agricultural products. In Central/Eastern Europe domestic final demand is the main driver of water consumption, but in this region the proportion of water use driven by demand for exports is increasing over time. Given these heterogeneous water consumption patterns, our analysis suggests that Mediterranean and Central/Eastern European countries should adopt specific water policies in order to achieve efficient levels of water consumption in the European Union.     

A Review on the Effects of Supercritical Carbon Dioxide on Enzyme Activity

Different types of enzymes such as lipases, several phosphatases, dehydrogenases, oxidases, amylases and others are well suited for the reactions in SC-CO₂. The stability and the activity of enzymes exposed to carbon dioxide under high pressure depend on enzyme species, water content in the solution and on the pressure and temperature of the reaction system. The three-dimensional structure of enzymes may be significantly altered under extreme conditions, causing their denaturation and consequent loss of activity. If the conditions are less adverse, the protein structure may be largely retained. Minor structural changes may induce an alternative active protein state with altered enzyme activity, specificity and stability.     

The Effects of Ni-Plating and Prolonged High Temperature Oxidation at 1423 K (1150 °C) on a CMSX-10 Single-Crystal Ni-Based Super-Alloy and Coating System

A hypothesis was investigated, to assess if Ni-plating a 3rd-generation single-crystal alloy could favorably alter the diffusion profile of critical elements such that brittle, deleterious topologically close-packed (TCP) phases did not form or at least the extent to which they did was reduced. In conjunction with delaying the onset of these phases, it was hoped that more favorable alternatives could be promoted, such as martensite (β′). This study showed that Ni-plating did have some positive effects on the super-alloy/coating system. While the coating produced on the Ni-plated alloy was thinner, it retained a higher Al content than its unplated counterpart when subjected to oxidation. The retention of Al within the coating delayed the phase evolution of the coating from a β or β + β′ to a γ′-dominant coating as the Ni-plated system had a greater driving force for Ni and Al diffusion, which helped to establish the Ni-rich diffusion barrier that entrapped Al in the coating. Unfortunately, Ni-plating does not sufficiently alter the diffusion profiles within the alloy to prevent precipitation of the TCP phases. Four pairs of the CMSX-10 alloy were used for this study. While they were all aluminized, only half of them, one in each pair, were Ni plated prior to aluminizing. Three of the four pairs were then oxidized at 1423 K (1150 °C), while the first pair was kept as a standard. X-ray diffraction, scanning electron microscopy, and energy dispersive X-ray spectroscopy were used to characterize each alloy-coating system in an effort to better understand their performance under high temperature oxidation.     

A comprehensive study of the loss of enzyme activity in a continuous membrane reactor – application to starch hydrolysis

Loss of enzyme activity is a problem associated with enzymatic reactions in continuous recycled membrane reactors (CRMR). It may result from catalyst leakage and also enzyme denaturation due to the effects of pH, temperature, shear effects or adsorption/deposit on membrane. In this study, the relative importance of these various factors has been assessed in order to reduce their adverse effects on starch hydrolysis in a CRMR. The effects of temperature and denaturation by adsorption/deposit on membrane were the most limiting phenomena. Reducing the temperature to overcome thermal denaturation was not a practical solution since this increases viscosity and thereby decreases permeate flux and reactor performance. Insofar that adsorption/deposit of enzymes on the membrane is directly linked to membrane fouling, back‐flushing or regularly purging retentate should reduce this phenomenon by lowering accumulation of high molecular weight products. © 2001 Society of Chemical Industry