Data Analysis in Transcriptomics and Metabolomics Clinical Applications

2018 ◽  
pp. 613-641
Author(s):  
Hector Gallart-Ayala ◽  
José Fernández-Navarro ◽  
Antonio Checa
Keyword(s):  
Data Analysis ◽  
Clinical Applications

scholarly journals A beginner’s guide to mass spectrometry–based proteomics

2020 ◽  
Vol 42 (5) ◽  
pp. 64-69
Author(s):  
Ankit Sinha ◽  
Matthias Mann
Keyword(s):  
Analytical Chemistry ◽  
Mass Spectrometry ◽  
Data Analysis ◽  
Sample Preparation ◽  
Single Cell Analysis ◽  
Clinical Applications ◽  
Preparation Process ◽  
Cell Analysis ◽  
Analysis Strategies ◽  
Quantitative Profiling

Mass spectrometry (MS)-based proteomics is the most comprehensive approach for the quantitative profiling of proteins, their interactions and modifications. It is a challenging topic as a firm grasp requires expertise in biochemistry for sample preparation, analytical chemistry for instrumentation and computational biology for data analysis. In this short guide, we highlight the various components of a mass spectrometer, the sample preparation process for conversion of proteins into peptides, and quantification and analysis strategies. The advancing technology of MS-based proteomics now opens up opportunities in clinical applications and single-cell analysis.

scholarly journals Sepsis: deriving biological meaning and clinical applications from high-dimensional data

2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Alex R. Schuurman ◽  
Tom D. Y. Reijnders ◽  
Robert F. J. Kullberg ◽  
Joe M. Butler ◽  
Tom van der Poll ◽  
...  
Keyword(s):  
Data Analysis ◽  
Clinical Care ◽  
High Dimensional Data ◽  
Clinical Applications ◽  
High Dimensional ◽  
Omics Technologies ◽  
Current Trends ◽  
Omics Integration ◽  
Biological Meaning ◽  
Future Challenges

AbstractThe pathophysiology of sepsis is multi-facetted and highly complex. As sepsis is a leading cause of global mortality that still lacks targeted therapies, increased understanding of its pathogenesis is vital for improving clinical care and outcomes. An increasing number of investigations seeks to unravel the complexity of sepsis through high-dimensional data analysis, enabled by advances in -omics technologies. Here, we summarize progress in the following major -omics fields: genomics, epigenomics, transcriptomics, proteomics, lipidomics, and microbiomics. We describe what these fields can teach us about sepsis, and highlight current trends and future challenges. Finally, we focus on multi-omics integration, and discuss the challenges in deriving biological meaning and clinical applications from these types of data.

scholarly journals Some Points to Consider in a Task-Based fMRI Study: A Guideline for Beginners

2020 ◽  
Author(s):  
Seyed Amir Hossein Batouli ◽  
Minoo Sisakhti
Keyword(s):  
Magnetic Resonance Imaging ◽  
Data Analysis ◽  
Magnetic Resonance ◽  
Brain Function ◽  
Clinical Applications ◽  
Careful Consideration ◽  
Functional Magnetic Resonance ◽  
Resonance Imaging ◽  
Fmri Study ◽  
Data Analysis Methods

Functional Magnetic Resonance Imaging (fMRI) is a technique widely used to probe brain function, and has shown many research and clinical applications. Despite its popularity and strength, performing an fMRI study needs careful consideration of the design of the experiment, as well as the techniques and methodologies implemented in it, due to the high potential of these factors to alter the outputs of the study. The influences of the demographics of the participants, stimuli design, image acquisition, and data analysis methods on the fMRI results are illustrated previously. Therefore, it is of utmost significance to have an understanding of the critical considerations when designing an fMRI study. In this manuscript, by reviewing the methodology of over one hundred task-based fMRI studies, around 300 substantial tips regarding the different stages of an fMRI experiment are gathered. These could only be found scattered through the literature, and such a collection would act as a guideline for the beginners in the field of fMRI.

scholarly journals Accuracy evaluation of tridimensional images performed by portable stereophotogrammetric system

2019 ◽  
Vol 48 ◽  
Author(s):  
Alvaro Augusto JUNQUEIRA-JÚNIOR ◽  
Laís Valencise MAGRI ◽  
Mateus Sgobi CAZAL ◽  
Aline Akemi MORI ◽  
Ana Maria Bettoni RODRIGUES DA SILVA ◽  
...  
Keyword(s):  
Data Analysis ◽  
Quantitative Analysis ◽  
Clinical Applications ◽  
Dental Occlusion ◽  
Accuracy Evaluation ◽  
Clinical Environment ◽  
Direct Evaluation ◽  
Facial Analysis ◽  
Facial Harmony ◽  
Portable System

Abstract Introduction Human facial characteristics vary according to individual dental occlusion, facial harmony, orofacial musculature and the format and configuration of craniofacial structures. Traditionally, anthropometric measurements have been acquired through direct evaluation of subjects in a clinical environment using calipers and metric tapes to measure distances between arches and landmarks. Scientific breakthroughs have enabled the digitization of data and introduced the possibility of quick, precise, radiation-free acquisitions; details can be archived for future analysis and easily shared with patients and colleagues. Among new facial analysis methods, the stereophotogrammetry technique has emerged, which uses a group of cameras to take many photographs of a subject in rapid succession from multiple angles. Nowadays, portable stereophotogrammetric systems are being proposed, as they are more practical and easier to use. Objective The aim of this work was to analyze the accuracy and reproducibility of a portable 3D stereophotogrammetric system (Vectra H1, Canfield, Fairfield, NJ, USA) in measuring soft facial tissues of 30 participants, defining measures of a cube and comparing these measurements with those obtained by a set 3D stereophotogrammetric system (Vectra M3, Canfield, Fairfield, NJ, USA) with previously validated accuracy and reproducibility through quantitative analysis of possible errors. Material and method Thirty temporary landmarks were used to measure (in mm) 34 distances in 30 participants (n = 30). Regarding the cube, 12 angles and 9 linear distances were evaluated. Result The results obtained by the established methodology indicated that the Vectra H1 portable system has shown accuracy and reproducibility equal to that of the Vectra M3 set system. Conclusion Data analysis and correlation to literature findings show Vectra H1's capability to reliably capture tridimensional images, which makes it practical for use in diverse clinical applications.

Multivariate approaches for SERS data analysis in clinical applications

2022 ◽  
pp. 395-431
Author(s):  
Duo Lin ◽  
Sufang Qiu ◽  
Yang Chen ◽  
Shangyuan Feng ◽  
Haishan Zeng
Keyword(s):  
Data Analysis ◽  
Clinical Applications ◽  
Multivariate Approaches

From experimental data analysis and modeling to clinical applications

1997 ◽  
Vol 18 (15) ◽  
pp. I-I
Author(s):  
Ron D. Appel ◽  
Michael J. Dunn ◽  
Denis F. Hochstrasser
Keyword(s):  
Experimental Data ◽  
Data Analysis ◽  
Clinical Applications ◽  
Experimental Data Analysis

scholarly journals Beyond Messiaen’s birds: the post-verbal world of dementia

2019 ◽  
Vol 46 (1) ◽  
pp. 73-83
Author(s):  
Stuart Wood
Keyword(s):  
Data Analysis ◽  
Medical Humanities ◽  
Research Method ◽  
Clinical Applications ◽  
Dementia Care ◽  
Ethnographic Study ◽  
Important Advance ◽  
Healthcare Settings ◽  
Musical Transcription ◽  
Medical And Healthcare

This paper investigates the use of verbatim musical transcription as a research method in dementia care. It reports on an art-based ethnographic study (Aesthetic Research in Everyday Life (Aeriel)) in which verbatim transcription was applied to everyday interactions in dementia care, making use of musical—instead of verbal—notation. Starting from the notion that medical and healthcare settings can be sites of ‘found performance’, the paper reviews literature relating to artistic methodologies within medical humanities, music, ethnography and dementia care. From this review, it proposes a research design and method of verbatim musical transcription as a potential avenue of investigating communication between carer and cared for in dementia care. The paper offers an illustrative example from Aeriel and draws conclusions from the synthesis of verbal and musical data analysis. Findings indicate an important advance in studies of dementia care communication towards a concept of the ‘post-verbal’ enabled by a musical research method and the clinical applications that it offers.

Microchemical imaging in biomedical research

1992 ◽  
Vol 50 (2) ◽  
pp. 1118-1119
Author(s):  
P. Ingram
Keyword(s):  
Data Analysis ◽  
Electron Probe ◽  
The Other ◽  
X Ray ◽  
Cell Element ◽  
Physiological Information ◽  
Functional States ◽  
Elemental Maps ◽  
Electron Energy Loss ◽  
Secondary Ion

It is well established that unique physiological information can be obtained by rapidly freezing cells in various functional states and analyzing the cell element content and distribution by electron probe x-ray microanalysis. (The other techniques of microanalysis that are amenable to imaging, such as electron energy loss spectroscopy, secondary ion mass spectroscopy, particle induced x-ray emission etc., are not addressed in this tutorial.) However, the usual processes of data acquisition are labor intensive and lengthy, requiring that x-ray counts be collected from individually selected regions of each cell in question and that data analysis be performed subsequent to data collection. A judicious combination of quantitative elemental maps and static raster probes adds not only an additional overall perception of what is occurring during a particular biological manipulation or event, but substantially increases data productivity. Recent advances in microcomputer instrumentation and software have made readily feasible the acquisition and processing of digital quantitative x-ray maps of one to several cells.

Specimen Preparation for Clinical Applications of X-Ray Microanalysis

1990 ◽  
Vol 48 (2) ◽  
pp. 328-329
Author(s):  
J.D. Shelburne ◽  
G.M. Roomans
Keyword(s):  
Carbon Coating ◽  
Clinical Applications ◽  
Point Of View ◽  
Practical Significance ◽  
Sweat Test ◽  
Specimen Preparation ◽  
Tissue Preparation ◽  
X Ray ◽  
Gallbladder Stones ◽  
Clinical Problems

Proper preparative procedures are a prerequisite for the validity of the results of x-ray microanalysis of biological tissue. Clinical applications of x-ray microanalysis are often concerned with diagnostic problems and the results may have profound practical significance for the patient. From this point of view it is especially important that specimen preparation for clinical applications is carried out correctly.Some clinical problems require very little tissue preparation. Hair, nails, and kidney and gallbladder stones may be examined and analyzed after carbon coating. High levels of zinc or copper in hair may be indicative of dermatological or systemic diseases. Nail clippings may be analyzed (as an alternative to the more conventional sweat test) to confirm a diagnosis of cystic fibrosis. X-ray microanalysis in combination with scanning electron microscopy has been shown to be the most reliable method for the identification of the components of kidney or gallbladder stones.A quantitatively very important clinical application of x-ray microanalysis is the identification and quantification of asbestos and other exogenous particles in lung.

Reduction of Potassium in Kidney Proximal Tubules to Aid in Electron Probe X-Ray Microanalysis of Calcium

1985 ◽  
Vol 43 ◽  
pp. 474-475
Author(s):  
A. LeFurgey ◽  
P. Ingram ◽  
L.J. Mandel
Keyword(s):  
Smooth Muscle ◽  
Proximal Tubule ◽  
Electron Probe ◽  
Clinical Applications ◽  
Proximal Tubules ◽  
Rabbit Kidney ◽  
Target Cells ◽  
X Ray ◽  
Freeze Dried

For quantitative determination of subcellular Ca distribution by electron probe x-ray microanalysis, decreasing (and/or eliminating) the K content of the cell maximizes the ability to accurately separate the overlapping K Kß and Ca Kα peaks in the x-ray spectra. For example, rubidium has been effectively substituted for potassium in smooth muscle cells, thus giving an improvement in calcium measurements. Ouabain, a cardiac glycoside widely used in experimental and clinical applications, inhibits Na-K ATPase at the cell membrane and thus alters the cytoplasmic ion (Na,K) content of target cells. In epithelial cells primarily involved in active transport, such as the proximal tubule of the rabbit kidney, ouabain rapidly (t1/2= 2 mins) causes a decrease2 in intracellular K, but does not change intracellular total or free Ca for up to 30 mins. In the present study we have taken advantage of this effect of ouabain to determine the mitochondrial and cytoplasmic Ca content in freeze-dried cryosections of kidney proximal tubule by electron probe x-ray microanalysis.

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