Development of an R script for simple lipidomic and metabolomic data analysis

Background: Metabolomic and lipidomic studies generate vast quantities of data that are often analysed in a closed software environment with little to no access to the underlying algorithms. As a result, data processed via different software pipelines yield different results thus leading to a widespread problem of low reproducibility within these fields. To address this problem, we are developing LipidAnalyst; an R based lipidomics software pipeline. As a part of this project, we are creating a simple statistical analysis and graphing module in R to generate accurate, reproducible, high-resolution figures. Methods: R scripts were developed under version 3.5.3 with the capability to undertake statistical analyses (e.g. ANOVA) and post-hoc tests (e.g. Tukey). Additional code plotted resultant information as high resolution violin and box plots that depicted statistical significance. Thereafter, lipidomic and metabolomic data were analysed by this code and compared against commercial software and Metaboanalyst, a primary software used in metabolomic and lipidomic research. Results: Code generated in house demonstrated the same results as those generated using commercial software (e.g. JMP 14.0 Pro) but were different from results obtained by using the MetaboAnalyst pipeline. Conclusions: This study demonstrated the prevalent danger of using closed-source software pipelines for the analysis of lipidomic and metabolomic data without validating the analysis outcomes via open-source software. Open source software such as LipidAnalyst, that has also been independently validated using multiple data sets, can then be published with the results to enable transparency of data analysis and improve the replicability of results across different labs.https://scholarscompass.vcu.edu/gradposters/1092/thumbnail.jp

Correlated Quantum Transport of Density Wave Electrons

Recently observed Aharonov-Bohm quantum interference of period h/2e in charge density wave rings strongly suggest that correlated density wave electron transport is a cooperative quantum phenomenon. The picture discussed here posits that quantum solitons nucleate and transport current above a Coulomb blockade threshold field. We propose a field-dependent tunneling matrix element and use the Schrodinger equation, viewed as an emergent classical equation as in Feynman's treatment of Josephson tunneling, to compute the evolving macrostate amplitudes, finding excellent quantitative agreement with voltage oscillations and current-voltage characteristics in NbSe3. A proposed phase diagram shows the conditions favoring soliton nucleation versus classical depinning. (Published in Phys. Rev. Lett. 108, 036404 (2012).)Comment: 9 pages, 4 figures, (5 pages & 3 figures for main article), includes Supplemental Material with 1 figure. Published version: Physical Review Letters, vol. 108, p. 036404 (2012

Non-invasive detection of animal nerve impulses with an atomic magnetometer operating near quantum limited sensitivity

Magnetic fields generated by human and animal organs, such as the heart, brain and nervous system carry information useful for biological and medical purposes. These magnetic fields are most commonly detected using cryogenically-cooled superconducting magnetometers. Here we present the frst detection of action potentials from an animal nerve using an optical atomic magnetometer. Using an optimal design we are able to achieve the sensitivity dominated by the quantum shot noise of light and quantum projection noise of atomic spins. Such sensitivity allows us to measure the nerve impulse with a miniature room-temperature sensor which is a critical advantage for biomedical applications. Positioning the sensor at a distance of a few millimeters from the nerve, corresponding to the distance between the skin and nerves in biological studies, we detect the magnetic field generated by an action potential of a frog sciatic nerve. From the magnetic field measurements we determine the activity of the nerve and the temporal shape of the nerve impulse. This work opens new ways towards implementing optical magnetometers as practical devices for medical diagnostics.Comment: Main text with figures, and methods and supplementary informatio

The Role of Geography in Management: A Timely Matter of Concern in Education and Knowledge Management in Sri Lanka

AbstractAccording to Hartshorne (1939) geography is the science that provides accurate, orderly and rational description of the variable character of the earth surface. This definition emphasizes that everything on this earth has a geographic dimension as everything is place specific and changing from place to place. Thus, management is also a geographic phenomenon, as managerial methods, practices and decisions also change from place to place. They are time and place specific and acting as processes changing over time and space which are emphasized as identities in geography.At present, geographical concepts are significantly applied in management. Particularly in environmental, real estate, human resource and marketing management its application is salient. Internationally, geography is taught as a subject in different faculties of commerce and management. In UK and USA universities even degrees on geography and management are offered.Unfortunately the management faculties in Sri Lanka have neglected its importance particularly in the recent past. Nearly two decades ago economic and commercial geography was taught as a subject of the commerce degree programme but that has also been excluded after the revision of curricular. However, geographical concepts are still significantly applied in management but it seems that academics and practitioners in the field of education and knowledge management are not well aware of geography behind management. Therefore, the objective of this paper is to emphasize the importance of the role of geography for creative and innovative business management practices in Sri Lanka.Methodologically this is a conceptual and thought raising paper by emphasizing the significance of various concepts in geography to the field of management. This is done through a literature survey by following purposive sampling technique for the selection of literature. To emphasize its significance many theoretical and practical aspects particularly accepted internationally are cited. As the outcome, it is expected that the expertise in the field of education and knowledge management will understand the importance of this subject for creative business management practices in Sri Lanka as the paper emphasizes its importance through the geographical identity and the concepts applied in management, decision making in management, world practices in different universities and the text books published in the field of geography and management.Keywords: Education and knowledge management, Geography, Place specific, Process, Time

DEVELOPMENT OF A PROTOTYPE IN-SITU FATIGUE SENSOR FOR STRUCTURAL HEALTH MONITORING OF HIGHWAY BRIDGES

Fatigue damage to bridges has been identified as a threat to bridge safety. Fatigue cracks usually occur at stresses lower than the anticipated design stress levels. Unlike yielding or corrosion, fatigue cracks are seldom visible enough to be detected by visual inspection and therefore can be easily overlooked. Since a larger portion of the life of a structure is spent on crack initiation (as opposed to crack propagation), it is vital to develop methods to detect fatigue crack initiation.Unfortunately, most of the methods that are developed to detect fatigue cracks do not accommodate crack initiation and are not sensitive enough to detect fatigue nucleation. A prototype in-situ fatigue senor has been developed to detect nucleation of fatigue damage in steel highway bridges.The in-situ fatigue sensor is designed to be bonded to the base structure and is based on the strain-life fatigue analysis method. Sensors are constructed of electrically conductive material with notched sensor arms producing varying stress concentration factors. The sensor operates on the principle of predictable progressive failure of the parallel arms as fatigue damage is accumulated in the base structure. Experimental results of the behavior of the fatigue sensor under constant amplitude loading and variable amplitude loading of a base structure-mimicking carrier specimen are compared with the simulation results obtained by the finite element analysis method and show reasonable agreement

Metabolic Modulation Predicts Heart Failure Tests Performance

The metabolic changes that accompany changes in Cardiopulmonary testing (CPET) and heart failure biomarkers (HFbio) are not well known. We undertook metabolomic and lipidomic phenotyping of a cohort of heart failure (HF) patients and utilized Multiple Regression Analysis (MRA) to identify associations to CPET and HFBio test performance (peak oxygen consumption (Peak VO2), oxygen uptake efficiency slope (OUES), exercise duration, and minute ventilation-carbon dioxide production slope (VE/VCO2 slope), as well as the established HF biomarkers of inflammation C-reactive protein (CRP), beta-galactoside-binding protein (galectin-3), and N-terminal prohormone of brain natriuretic peptide (NT-proBNP)). A cohort of 49 patients with a left ventricular ejection fraction \u3c 50%, predominantly males African American, presenting a high frequency of diabetes, hyperlipidemia, and hypertension were used in the study. MRA revealed that metabolic models for VE/VCO2 and Peak VO2 were the most fitted models, and the highest predictors’ coefficients were from Acylcarnitine C18:2, palmitic acid, citric acid, asparagine, and 3-hydroxybutiric acid. Metabolic Pathway Analysis (MetPA) used predictors to identify the most relevant metabolic pathways associated to the study, aminoacyl-tRNA and amino acid biosynthesis, amino acid metabolism, nitrogen metabolism, pantothenate and CoA biosynthesis, sphingolipid and glycerolipid metabolism, fatty acid biosynthesis, glutathione metabolism, and pentose phosphate pathway (PPP). Metabolite Set Enrichment Analysis (MSEA) found associations of our findings with pre-existing biological knowledge from studies of human plasma metabolism as brain dysfunction and enzyme deficiencies associated with lactic acidosis. Our results indicate a profile of oxidative stress, lactic acidosis, and metabolic syndrome coupled with mitochondria dysfunction in patients with HF tests poor performance. The insights resulting from this study coincides with what has previously been discussed in existing literature thereby supporting the validity of our findings while at the same time characterizing the metabolic underpinning of CPET and HFBio

Optical palpation for the visualization of tumor in human breast tissue

Australian Research Council; Cancer Council Western Australia; Department of Health, Government of Western Australia; OncoResMedical; William and Marlene Schrader Trust of The University of Western AustraliaAccurate and effective removal of tumor in one operation is an important goal of breast-conserving surgery. However, it is not always achieved. Surgeons often utilize manual palpation to assess the surgical margin and/or the breast cavity. Manual palpation, however, is subjective and has relatively low resolution. Here, we investigate a tactile imaging technique, optical palpation, for the visualization of tumor. Optical palpation generates maps of the stress at the surface of tissue under static preload compression. Stress is evaluated by measuring the deformation of a contacting thin compliant layer with known mechanical properties using optical coherence tomography. In this study, optical palpation is performed on 34 freshly excised human breast specimens. Wide field-of-view (up to ~46 × 46 mm) stress images, optical palpograms, are presented from four representative specimens, demonstrating the capability of optical palpation to visualize tumor. Median stress reported for adipose tissue, 4 kPa, and benign dense tissue, 8 kPa, is significantly lower than for invasive tumor, 60 kPa. In addition, we demonstrate that optical palpation provides contrast consistent with a related optical technique, quantitative micro-elastography. This study demonstrates that optical palpation holds promise for visualization of tumor in breast-conserving surgery.PostprintPeer reviewe

Conversion of Parameters Among Variants of Scatchard's Neutral-Electrolyte Model for Electrolyte Mixtures that Have Different Numbers of Mixing Terms

Various model equations are available for representing the excess Gibbs energy properties (osmotic and activity coefficients) of aqueous and other liquid mixed-electrolyte solutions. Scatchard's neutral-electrolyte model is among the simplest of these equations for ternary systems and contains terms that represent both symmetrical and asymmetric deviations from ideal mixing behavior when two single-electrolyte solutions are mixed in different proportions at constant ionic strengths. The usual form of this model allows from zero to six mixing parameters. In this report we present an analytical method for transforming the mixing parameters of neutral-electrolyte-type models with larger numbers of mixing parameters directly to those of models with fewer mixing parameters, without recourse to the source data used for evaluation of the original model parameters. The equations for this parameter conversion are based on an extension to ternary systems of the methodology of Rard and Wijesinghe [J. Chem. Thermodyn. 35, 439-473 (2003)] and Wijesinghe and Rard [J. Chem. Thermodyn. 37, 1196-1218 (2005)] that was applied by them to binary systems. It was found that the use of this approach with a constant ionic-strength cutoff of I {le} 6.2 mol {center_dot} kg{sup -1} (the NaCl solubility limit) yielded parameters for the NaCl + SrCl{sub 2} + H{sub 2}O and NaCl + MgCl{sub 2} + H{sub 2}O systems that predicted osmotic coefficients {phi} in excellent agreement with those calculated using the same sets of parameters whose values were evaluated directly from the source data by least-squares, with root mean square differences of RMSE({phi}) = 0.00006 to 0.00062 for the first system and RMSE({phi}) = 0.00014 to 0.00042 for the second. If, however, the directly evaluated parameters were based on experimental data where the ionic strength cutoff varied with the ionic-strength fraction, i.e. because they were constrained by isopiestic ionic strengths (MgCl{sub 2} + MgSO{sub 4} + H{sub 2}O) or solubility/oversaturation ionic strengths (NaCl + SrCl{sub 2} + H{sub 2}O and NaCl + MgCl{sub 2} + H{sub 2}O), then parameters converted by this approach assuming a constant ionic-strength cutoff yield RMSE({phi}) differences about an order of magnitude larger than the previous case. This indicates that for an accurate conversion of model parameters when the source model is constrained with variable ionic strength cutoffs, an extension of the parameter conversion method described herein will be required. However, when the source model parameters are evaluated at a constant ionic strength cutoff, such as when source isopiestic data are constrained to ionic strengths at or below the solubility limit of the less soluble component, or are Emf measurements that are commonly made at constant ionic strengths, then our method yields accurate converted models