High-throughput data analysis for detecting and identifying differences between samples in GC/MS-based metabolomic analyses

In metabolomics, the objective is to identify differences in metabolite profiles between samples. A widely used tool in metabolomics investigations is gas chromatography-mass spectrometry (GC/MS). More than 400 compounds can be detected in a single analysis, if overlapping GC/MS peaks are deconvoluted. However, the deconvolution process is time-consuming and difficult to automate, and additional processing is needed in order to compare samples. Therefore, there is a need to improve and automate the data processing strategy for data generated in GC/MS-based metabolomics; if not, the processing step will be a major bottleneck for high-throughput analyses. Here we describe a new semiautomated strategy using a hierarchical multivariate curve resolution approach that processes all samples simultaneously. The presented strategy generates (after appropriate treatment, e.g., multivariate analysis) tables of all the detected metabolites that differ in relative concentrations between samples. The processing of 70 samples took similar time to that of the GC/TOFMS analyses of the samples. The strategy has been validated using two different sets of samples: a complex mixture of standard compounds and Arabidopsis samples.     

Peptidyl Vinyl Ketone Irreversible Inhibitors of Rhodesain: Modifications of the P2 Fragment

In this paper, we report the design, synthesis and biological investigation of a series of peptidyl vinyl ketones obtained by modifying the P2 fragment of previously reported highly potent inhibitors of rhodesain, the main cysteine protease of Trypanosoma brucei rhodesiense. Investigation of the structure–activity relationship led us to identify new rhodesain inhibitors endowed with an improved selectivity profile (a selectivity index of up to 22 000 towards the target enzyme), and/or an improved antitrypanosomal activity in the sub-micromolar range.     

Towards patient‐centered packaging design: An industry perspective on processes,functions, and constraints

Medication packaging is essential to provide patients with guidance and correct use of their medicines for effective treatment. This research aims to increase knowledge about the medication packaging innovation process and its uptake towards patient‐centered packaging design. The study applied a qualitative research approach based on data from 25 in‐depth interviews with stakeholders involved in medication packaging design. The empirical data analysis revealed four themes that can improve and advance user‐centered packaging design: medication packaging innovation process, medication packaging functions and features, medication packaging design constraints, and patient‐centered medication packaging design. The findings suggest that medication packaging design is strongly affected by an emphasis on protective and safety packaging functions rather than on patients' needs. Packaging innovation usually is constrained by rigid incremental development processes, where compliance with regulations, extensive documentation, avoidance of manufacturing complexity, and considerations on cost prevail. These findings are discussed in relation to the three most evident trade‐offs for patient‐centered design: protection versus openability, utility versus cost, and complexity of manufacturability versus complexity of use. This research contributes with valuable input and additional evidence about the necessary shift to a user‐centered approach in a field that has not been design driven. This input complements previous research and provides an opportunity for industry decision makers and policy makers to lead patient‐centered packaging design that can benefit patients and relieve overloaded health care systems.     

Mass Spectrometric Analysis of Cerebrospinal Fluid Ubiquitin in Alzheimer's Disease and Parkinsonian Disorders

1 Purpose

Dysfunctional proteostasis, with decreased protein degradation and an accumulation of ubiquitin into aggregated protein inclusions, is a feature of neurodegenerative diseases. Identifying new potential biomarkers in cerebrospinal fluid (CSF) reflecting this process could contribute important information on pathophysiology.

2 Experimental design

A developed method combining SPE and PRM‐MS is employed to monitor the concentration of ubiquitin in CSF from subjects with Alzheimer's disease (AD), Parkinson's disease (PD), and progressive supranuclear palsy (PSP). Four independent cross‐sectional studies are conducted, studies 1–4, including controls (n = 86) and participants with AD (n = 60), PD (n = 15), and PSP (n = 11).

3 Results

The method shows a repeatability and intermediate precision not exceeding 6.1 and 7.9%, respectively. The determined LOD is 0.1 nm and the LOQ range between 0.625 and 80 nm . The CSF ubiquitin concentration is 1.2–1.5‐fold higher in AD patients compared with controls in the three independent AD‐control studies (Study 1, p < 0.001; Study 2, p < 0.001; and Study 3, p = 0.003). In the fourth study, there is no difference in PD or PSP, compared to controls.

4 Conclusion and clinical relevance

CSF ubiquitin may reflect dysfunctional proteostasis in AD. The described method can be used for further exploration of ubiquitin as a potential biomarker in neurodegenerative diseases.     

Automated reference-free detection of motion artifacts in magnetic resonance images

Objectives

Our objectives were to provide an automated method for spatially resolved detection and quantification of motion artifacts in MR images of the head and abdomen as well as a quality control of the trained architecture.

Materials and methods

T1-weighted MR images of the head and the upper abdomen were acquired in 16 healthy volunteers under rest and under motion. Images were divided into overlapping patches of different sizes achieving spatial separation. Using these patches as input data, a convolutional neural network (CNN) was trained to derive probability maps for the presence of motion artifacts. A deep visualization offers a human-interpretable quality control of the trained CNN. Results were visually assessed on probability maps and as classification accuracy on a per-patch, per-slice and per-volunteer basis.

Results

On visual assessment, a clear difference of probability maps was observed between data sets with and without motion. The overall accuracy of motion detection on a per-patch/per-volunteer basis reached 97%/100% in the head and 75%/100% in the abdomen, respectively.

Conclusion

Automated detection of motion artifacts in MRI is feasible with good accuracy in the head and abdomen. The proposed method provides quantification and localization of artifacts as well as a visualization of the learned content. It may be extended to other anatomic areas and used for quality assurance of MR images.

     

Nanoporous aluminum oxide membranes for filtration and biofunctionalization

Nanoporous aluminum oxide membranes with high open porosity are prepared by anodic oxidation. Conventional self-supporting as well as mechanically stabilized nanoporous membranes are produced from aluminum plates and microimprinted aluminum foils, respectively. The mechanically stabilized membranes are characterized by very thin membrane parts stabilized by surrounding thick bridges. The minimal thickness of these thin membranes with open pores on both sides is 1 microm, with a mean pore size of the parallel open pores of 185 nm. With these two kinds of membrane the flow rates for cross filtration can be tuned over a wide range. With the mechanically stabilized membranes, substantially higher flow rates are achieved and experiments that cannot be performed with thicker membranes become possible. The biofunctionalization of the pore walls with archaebacterial tetraether lipids is realized and proved using aminated semiconductor nanocrystals. The lipid layer deposited on the pore walls also changes the filtration properties.     

Rheological properties of aqueous α A12O3 suspensions: Influence of dispersant concentration

The effects of concentration of polyacrylic acid as a dispersant on rheological properties of aqueous alumina suspensions have been investigated under steady and oscillatory shear conditions. At solid volume fractions between 0.45 and 0.6, a high degree of particle stabilization is achieved when 0.2 wt% of polyacrylic acid is added. At lower dispersant concentrations, suspensions exhibit pronounced irreversible thixotropic behaviour, whereas at higher dispersant concentrations, time dependent effects on the flow properties are not detectable. When the saturation adsorption limit of the polyelectrolyte on Al₂O₃ is reached, further addition of the dispersant appreciably changes the flow behaviour, as well as the viscoelastic response of investigated suspensions. The data under steady shear are described by application of the generalized Casson model, and for the analysis of viscoelastic data the generalized Maxwell model is used.