A new optimization strategy for MALDI FTICR MS tissue analysis for untargeted metabolomics using experimental design and data modeling

2019 ◽  
Vol 411 (17) ◽  
pp. 3891-3903 ◽  
Author(s):  
Justine Ferey ◽  
Florent Marguet ◽  
Annie Laquerrière ◽  
Stéphane Marret ◽  
Isabelle Schmitz-Afonso ◽  
...  
2020 ◽  
Vol 19 (6) ◽  
pp. 923-939
Author(s):  
Jeng-Fung Hung ◽  
Chun-Yen Tsai

Previous studies on the effectiveness of virtual laboratories for learning have shown inconsistent results over the past decade. The purpose of this research was to explore the effects of a virtual laboratory and meta-cognitive scaffolding on students' data modeling competences. A quasi-experimental design was used. Three classes of eighth graders from southern Taiwan participated in this research and were assigned to the Experimental Group Ⅰ (EG Ⅰ), the Experimental Group Ⅱ (EG Ⅱ), and the Control Group (CG). EG Ⅰ (n=25) received the virtual laboratory and meta-cognitive scaffolding in the teaching and learning. EG Ⅱ (n=28) received the virtual laboratory only in the teaching and learning. The CG (n=27) received the lecture with the cookbook laboratory. The teaching unit was Heat and Specific Heat, and the teaching time for the three groups was six lessons (of 45 minutes each). The Data Modeling Competences Test (DMCT) designed by the research team was used as the data collection instrument. The results showed that the virtual laboratory and meta-cognitive scaffolding had effects on students' data modeling competences. This research shows the importance of the meta-cognitive scaffolding strategy for virtual laboratories when conducting data modeling teaching. Keywords: data modeling, quasi-experimental design, meta-cognitive scaffolding, virtual laboratory


2021 ◽  
Author(s):  
Moataz Dowaidar

The value of systems biology in cardiology is becoming more recognized. There has been a tremendous rise in the number of articles in the last two decades, as publicly available datasets have been provided online and high-throughput tissue analysis has become more prevalent. In animal models, however, the future of cardiovascular medicine is less likely to be reanalyzing data and more likely to be investigating the function of GWAS-identified SNPs or network change using informatics and gene-editing technologies. These techniques, when combined with other omics interrogations and rigorous experimental design, have the potential to improve our understanding of gene-to-disease pathways.Systems biology is a method for studying large amounts of multidimensional data generated by omics technologies and, more broadly, the transition to big data in health care.Cross-validation of the various technological platforms is critical because omics studies are prone to bias and overinterpretation.Investigators must carefully determine which publicly accessible datasets, if any, to employ while conducting a systems analysis. Despite the fact that network theory and machine learning may yield amazing outcomes, these methods are not yet standardized. The studies mentioned here are excellent examples, in part because they use empirical models to support emergent systems biology results. In the few successful cases, careful experimental design, including interventional research and clinical trials, is required, in addition to the insights supplied by bioinformatics analysis of omics approaches. While it may be tempting to use emergent qualities to capture these new discoveries in more fundamental concepts, we agree with the English philosopher William of Ockham when he says, "It is futile to do with more things what can be done with fewer."


HortScience ◽  
1997 ◽  
Vol 32 (3) ◽  
pp. 485B-485
Author(s):  
Mohammad Baqir ◽  
Richard L. Harkess

On 2 Feb. 1996, rooted cuttings of Pelargonium × hortorum L. H. Bailey cvs. Tango and Blues were planted in 750-cm3 (14 cm in diameter) pots containing peatmoss mixed with shredded tire rubber (2–6.0 mm particle size) at 0%, 20%, 40%, 60%, or 80%. Plants were irrigated by hand, drip, or ebb-and-fl ood, and were arranged in a split-plot experimental design. A wetting agent (Aqua Gro 2000 L, Aquatrols Corporation, Cherry Hill, N.J.) was mixed at the rate of 6 ml per 3750 ml of water and 120 ml of solution was applied to each plant. Greenhouse studies indicated that geraniums could be grown successfully in media containing up to 20% shredded tire rubber by volume when irrigated by hand. Plants grown in media containing more than 20% rubber were observed to be slow-growing and chlorotic. Tissue analysis of the plants indicated significantly increased levels of zinc in plants grown in media containing high percentages of rubber. Geraniums grown in media containing 80% rubber and irrigated using ebb-and-fl ood benches had the significantly highest levels of foliar zinc. Media porosity, percent air space, and bulk density increased, while water holding capacity decreased with increasing amounts of shredded tire rubber added to the media.


2019 ◽  
Vol 20 (2) ◽  
pp. 446 ◽  
Author(s):  
Abdellah Tebani ◽  
Lenaig Abily-Donval ◽  
Isabelle Schmitz-Afonso ◽  
Monique Piraud ◽  
Jérôme Ausseil ◽  
...  

Metabolic phenotyping is poised as a powerful and promising tool for biomarker discovery in inherited metabolic diseases. However, few studies applied this approach to mcopolysaccharidoses (MPS). Thus, this innovative functional approach may unveil comprehensive impairments in MPS biology. This study explores mcopolysaccharidosis VI (MPS VI) or Maroteaux–Lamy syndrome (OMIM #253200) which is an autosomal recessive lysosomal storage disease caused by the deficiency of arylsulfatase B enzyme. Urine samples were collected from 16 MPS VI patients and 66 healthy control individuals. Untargeted metabolomics analysis was applied using ultra-high-performance liquid chromatography combined with ion mobility and high-resolution mass spectrometry. Furthermore, dermatan sulfate, amino acids, carnitine, and acylcarnitine profiles were quantified using liquid chromatography coupled to tandem mass spectrometry. Univariate analysis and multivariate data modeling were used for integrative analysis and discriminant metabolites selection. Pathway analysis was done to unveil impaired metabolism. The study revealed significant differential biochemical patterns using multivariate data modeling. Pathway analysis revealed that several major amino acid pathways were dysregulated in MPS VI. Integrative analysis of targeted and untargeted metabolomics data with in silico results yielded arginine-proline, histidine, and glutathione metabolism being the most affected. This study is one of the first metabolic phenotyping studies of MPS VI. The findings might shed light on molecular understanding of MPS pathophysiology to develop further MPS studies to enhance diagnosis and treatments of this rare condition.


2018 ◽  
Vol 41 ◽  
Author(s):  
Wei Ji Ma

AbstractGiven the many types of suboptimality in perception, I ask how one should test for multiple forms of suboptimality at the same time – or, more generally, how one should compare process models that can differ in any or all of the multiple components. In analogy to factorial experimental design, I advocate for factorial model comparison.


2019 ◽  
Vol 42 ◽  
Author(s):  
J. Alfredo Blakeley-Ruiz ◽  
Carlee S. McClintock ◽  
Ralph Lydic ◽  
Helen A. Baghdoyan ◽  
James J. Choo ◽  
...  

Abstract The Hooks et al. review of microbiota-gut-brain (MGB) literature provides a constructive criticism of the general approaches encompassing MGB research. This commentary extends their review by: (a) highlighting capabilities of advanced systems-biology “-omics” techniques for microbiome research and (b) recommending that combining these high-resolution techniques with intervention-based experimental design may be the path forward for future MGB research.


1978 ◽  
Vol 48 ◽  
pp. 7-29
Author(s):  
T. E. Lutz

This review paper deals with the use of statistical methods to evaluate systematic and random errors associated with trigonometric parallaxes. First, systematic errors which arise when using trigonometric parallaxes to calibrate luminosity systems are discussed. Next, determination of the external errors of parallax measurement are reviewed. Observatory corrections are discussed. Schilt’s point, that as the causes of these systematic differences between observatories are not known the computed corrections can not be applied appropriately, is emphasized. However, modern parallax work is sufficiently accurate that it is necessary to determine observatory corrections if full use is to be made of the potential precision of the data. To this end, it is suggested that a prior experimental design is required. Past experience has shown that accidental overlap of observing programs will not suffice to determine observatory corrections which are meaningful.


2011 ◽  
Vol 20 (4) ◽  
pp. 109-113
Author(s):  
Karen Copple ◽  
Rajinder Koul ◽  
Devender Banda ◽  
Ellen Frye

Abstract One of the instructional techniques reported in the literature to teach communication skills to persons with autism is video modeling (VM). VM is a form of observational learning that involves watching and imitating the desired target behavior(s) exhibited by the person on the videotape. VM has been used to teach a variety of social and communicative behaviors to persons with developmental disabilities such as autism. In this paper, we describe the VM technique and summarize the results of two single-subject experimental design studies that investigated the acquisition of spontaneous requesting skills using a speech generating device (SGD) by persons with autism following a VM intervention. The results of these two studies indicate that a VM treatment package that includes a SGD as one of its components can be effective in facilitating communication in individuals with autism who have little or no functional speech.


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