Expanding Lipidome Coverage Using LC-MS/MS Data-Dependent Acquisition with Automated Exclusion List Generation

Untargeted omics analyses aim to comprehensively characterize biomolecules within a biological system. Changes in the presence or quantity of these biomolecules can indicate important biological perturbations, such as those caused by disease. With current technological advancements, the entire genome can now be sequenced; however, in the burgeoning fields of lipidomics, only a subset of lipids can be identified. The recent emergence of high resolution tandem mass spectrometry (HR-MS/MS), in combination with ultra-high performance liquid chromatography, has resulted in an increased coverage of the lipidome. Nevertheless, identifications from MS/MS are generally limited by the number of precursors that can be selected for fragmentation during chromatographic elution. Therefore, we developed the software IE-Omics to automate iterative exclusion (IE), where selected precursors using data-dependent topN analyses are excluded in sequential injections. In each sequential injection, unique precursors are fragmented until HR-MS/MS spectra of all ions above a user-defined intensity threshold are acquired. IE-Omics was applied to lipidomic analyses in Red Cross plasma and substantia nigra tissue. Coverage of the lipidome was drastically improved using IE. When applying IE-Omics to Red Cross plasma and substantia nigra lipid extracts in positive ion mode, 69% and 40% more molecular identifications were obtained, respectively. In addition, applying IE-Omics to a lipidomics workflow increased the coverage of trace species, including odd-chained and short-chained diacylglycerides and oxidized lipid species. By increasing the coverage of the lipidome, applying IE to a lipidomics workflow increases the probability of finding biomarkers and provides additional information for determining etiology of disease.

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Understanding Behavior of Polycaprolactone–Gelatin Blends under High Pressure CO<Subscript>2</Subscript>

Polycaprolactone (PCL) is widely used in biomedical applications as electrospun fibers or porous foams. As PCL is synthetic polymer, many researchers have explored blends of PCL–gelatin to combine mechanical and bioactive properties of individual components. High pressure carbon dioxide (CO2) has been studied to foam and impregnate many biocompatible polymers. In case of PCL–gelatin blends, certain compositions can be swelled reversibly under high pressure CO₂ without permanent deformation. This allows successful impregnation of PCL–gelatin blends under CO₂. This study summarizes effect of different treatments adopted during impregnation process including high pressure CO2 on several blend compositions of PCL–gelatin blends. Stress relaxation, polymer melting and dissolution were observed during several treatments which affects porosity and scaffold structure significantly. Results summarized in this study will aid in optimum selection of PCL–gelatin blend composition for biomedical applications. Furthermore, CO₂ solubility in polymers is restricted due to thermodynamic limitations but can be altered in the presence of a co-solvent to produce better foams. PCL can be foamed using supercritical CO₂. However, CO₂ foaming of PCL–gelatin blend becomes challenging to simultaneous swelling of PCL and compression of gelatin providing blend structural stability. This study has demonstrated ability of supercritical CO₂ to foam PCL–gelatin blends in presence of water to create porous structure. These foams were subjected post-fabrication crosslinking and supercritical CO₂ without losing porosity of foams. Thus, creating a strategy to use environmentally benign processes to fabricate, crosslink and impregnate porous scaffolds for biomedical applications.     

Imminent fracture detection in graphite/epoxy using acoustic emission

An experiment designed to detect incipient failure in graphite/epoxy tensile specimens is described. Tests using eighteen samples of six different graphite/epoxy compositions in six-ply balanced [0/+45/?45], laminates indicate that a failure precursor does exist. This precursor takes the form of a sudden reduction in the acoustic-emission output at 99 percent of the ultimate tensile load, and evidence indicates that the reduction is the result of a change in the fundamental failure mechanism. The shape of the acoustic-emission countrate curve is analyzed and found to correlate well with micro-mechanical fracture activity.     

A Method for Determining Model‐Structure Errors and for Locating Damage in Vibrating Systems

A method is proposed for the determination of natural frequencies and mode shapes of a system which is constrained so that unknown stiffnesses are replaced by rigid connections. The constraint is not imposed physically but only in mathematics so that the behaviour of the constrained system is inferred from the unconstrained measurements. Since stiffnesses which are made rigid cannot experience any elastic strain they can have no effect on the inferred measurements. A procedure for comparing the inferred measurements with similarly constrained finite element predictions can be used to determine modelstructure errors. Damage, such as a crack in a beam, can be located by comparing the inferred measurements from the structure in its undamaged and current states. It is demonstrated how unmeasured rotations may be constrained by using rigidbody modes and a reduction/expansion transformation from a finite element model.Sommario. Viene proposto un metodo per la determinazione delle frequenze proprie e dei modi di vibrazione di un sistema vincolato in modo tale che alcuni elementi elastici siano sostituiti da collegamenti rigidi. Il vincolo non viene imposto fisicamente, ma solo matematicamente, e pertanto il comportamento del sistema vincolato viene dedotto dalle misure sul sistema non vincolato. Poiché gli elementi che sono resi rigidi non possono subire alcuna deformazione elastica, essi non hanno certamente alcun effetto sulle misure dedotte per il sistema vincolato. Una procedura che mette a confronto le misure dedotte per il sistema vincolato con le previsioni fornite da un modello ad elementi finiti con analoghi vincoli, può essere utilizzata per determinare errori nella struttura del modello. Danni del tipo di una cricca su una trave possono essere localizzati confrontando le misure dedotte – per sistemi analogamente vincolati – da quelle effettuate sulla struttura non danneggiata e sulla struttura danneggiata. Si dimostra come si possono imporre vincoli sulle rotazioni (non misurate) utilizzando i modi di corpo rigido dell'elemento e una tecnica di riduzione/espansione dei gradi di libertà di un modello ad elementi finiti.     

Strain gages in cryogenic environment

The increasing use of cryogenics in all fields of endeavor necessitates the use of strain gages for stress analysis of structures under extreme temperatures. This has been a continuing program at the McDonnell Douglas Astronautics Co.'s Strain Gage Engineering Laboratory (Huntington Beach facility). Many characteristics of strain gages were investigated, and a majority of the commercial strain gage types were evaluated. Tests results are presented, as well as composite curves, showing the comparison between various types of strain gages.     

Orientability and Energy Minimization in Liquid Crystal Models

Uniaxial nematic liquid crystals are modelled in the Oseen–Frank theory through a unit vector field n. This theory has the apparent drawback that it does not respect the head-to-tail symmetry in which n should be equivalent to ?n. This symmetry is preserved in the constrained Landau–de Gennes theory that works with the tensor \({Q=s \left(n\otimes n-\frac{1}{3} Id\right)}\). We study the differences and the overlaps between the two theories. These depend on the regularity class used as well as on the topology of the underlying domain. We show that for simply-connected domains and in the natural energy class W^1,2 the two theories coincide, but otherwise there can be differences between the two theories, which we identify. In the case of planar domains with holes and various boundary conditions, for the simplest form of the energy functional, we completely characterise the instances in which the predictions of the constrained Landau–de Gennes theory differ from those of the Oseen–Frank theory.     

Poroelasticity-I: Governing Equations of the Mechanics of Fluid-Saturated Porous Materials

We present here the approach to the theory of fluid-filled poroelastics based on consideration of poroelastics as a continuum of “macropoints” (representative elementary volumes), which “internal” states can be described by as a set of internal parameters, such as local relative velocity of fluid and solid, density of fluid, internal strain tensor, specific area, and position of the center of mass of porous space. We use the generalized Cauchy–Born hypothesis and suggest that there is a system of (structural) relationships between external parameters, describing the deformation of the continuum and internal parameters, characterizing the state of representative elementary volumes. We show that in nonhomogenous (and, particularly, nonlinear) poroelastics, an interaction force between solid and fluid appears. Because this force is proportional to the gradient of porosity, absent in homogeneous poroelastics, and one can neglect with dynamics of internal degrees of freedom, this force is equivalent to the interaction force, introduced earlier by Nikolaevskiy from phenomenological reasons. At last, we show that developed theory naturally incorporates three mechanisms of energy absorption: visco-inertial Darcy mechanism, “squirt flow” attenuation, and skeleton attenuation.     

Nonlinear stability analysis of miscible displacements

A simulator for three-dimensional horizontal miscible displacements in porous media is developed. Using this simulator, we examine the initiation and development of instabilities, viscous fingers and gravity tongues.With the only perturbations to the system being truncation and round-off errors, a density ratio (the ratio of the density of the displacing fluid to that of the displaced fluid) different from one is responsible for the initiation of the instabilities, and an unfavorable mobility ratio (the ratio of the viscosity of the displaced fluid to that of the displacing fluid) is responsible for the growth of the instabilities.     

Blast wave measurements close to explosive charges

The paper reports the results of experimental measurements of the reflection pressures close to spherical charges of TNT. These measurements were made using a pressure bar technique. Charge weights of up to 3.6 kg were used, with the reflecting plane in the range 25 to 300 mm from the charge surface.A possible wave interaction model is discussed, to account for the observed pressure profiles, and its qualitative correctness checked by means of numerical simulation.This article was processed using Springer-Verlag T_EX Shock Waves macro package 1.0 and the AMS fonts, developed by the American Mathematical Society.