A practical and theoretical definition of very small field size for radiotherapy output factor measurements

Purpose This work introduces the concept of very small field size. Output factor (OPF) measurements at these field sizes require extremely careful experimental methodology including the measurement of dosimetric field size at the same time as each OPF measurement. Two quantifiable scientific definitions of the threshold of very small field size are presented. Methods A practical definition was established by quantifying the effect that a 1 mm error in field size or detector position had on OPFs, and setting acceptable uncertainties on OPF at 1%. Alternatively, for a theoretical definition of very small field size, the OPFs were separated into additional factors to investigate the specific effects of lateral electronic disequilibrium, photon scatter in the phantom and source occlusion. The dominant effect was established and formed the basis of a theoretical definition of very small fields. Each factor was obtained using Monte Carlo simulations of a Varian iX linear accelerator for various square field sizes of side length from 4 mm to 100 mm, using a nominal photon energy of 6 MV. Results According to the practical definition established in this project, field sizes < 15 mm were considered to be very small for 6 MV beams for maximal field size uncertainties of 1 mm. If the acceptable uncertainty in the OPF was increased from 1.0 % to 2.0 %, or field size uncertainties are 0.5 mm, field sizes < 12 mm were considered to be very small. Lateral electronic disequilibrium in the phantom was the dominant cause of change in OPF at very small field sizes. Thus the theoretical definition of very small field size coincided to the field size at which lateral electronic disequilibrium clearly caused a greater change in OPF than any other effects. This was found to occur at field sizes < 12 mm. Source occlusion also caused a large change in OPF for field sizes < 8 mm. Based on the results of this study, field sizes < 12 mm were considered to be theoretically very small for 6 MV beams. Conclusions Extremely careful experimental methodology including the measurement of dosimetric field size at the same time as output factor measurement for each field size setting and also very precise detector alignment is required at field sizes at least < 12 mm and more conservatively < 15 mm for 6 MV beams. These recommendations should be applied in addition to all the usual considerations for small field dosimetry, including careful detector selection.

Advances in mass spectrometry for lipidomics

Recent expansion in research in the field of lipidomics has been driven by the development of new mass spectrometric tools and protocols for the identification and quantification of molecular lipids in complex matrices. Although there are similarities between the field of lipidomics and the allied field of mass spectrometry (e.g., proteomics), lipids present some unique advantages and challenges for mass spectrometric analysis. The application of electrospray ionization to crude lipid extracts without prior fractionation-the so-called shotgun approach-is one such example, as it has perhaps been more successfully applied in lipidomics than in any other discipline. Conversely, the diverse molecular structure of lipids means that collision-induced dissociation alone may be limited in providing unique descriptions of complex lipid structures, and the development of additional, complementary tools for ion activation and analysis is required to overcome these challenges. In this article, we discuss the state of the art in lipid mass spectrometry and highlight several areas in which current approaches are deficient and further innovation is required.

Ultraviolet action spectroscopy of iodine labeled peptides and proteins in the gas phase

Structural investigations of large biomolecules in the gas phase are challenging. Herein, it is reported that action spectroscopy taking advantage of facile carbon-iodine bond dissociation can be used to examine the structures of large molecules, including whole proteins. Iodotyrosine serves as the active chromophore, which yields distinctive spectra depending on the solvation of the side chain by the remainder of the molecule. Isolation of the chromophore yields a double featured peak at ∼290 nm, which becomes a single peak with increasing solvation. Deprotonation of the side chain also leads to reduced apparent intensity and broadening of the action spectrum. The method can be successfully applied to both negatively and positively charged ions in various charge states, although electron detachment becomes a competitive channel for multiply charged anions. In all other cases, loss of iodine is by far the dominant channel which leads to high sensitivity and simple data analysis. The action spectra for iodotyrosine, the iodinated peptides KGYDAKA, DAYLDAG, and the small protein ubiquitin are reported in various charge states. © 2012 American Chemical Society.

Gas-Phase Transformation of Phosphatidylcholine Cations to Structurally Informative Anions via Ion/Ion Chemistry

Gas-phase transformation of synthetic phosphatidylcholine (PC) monocations to structurally informative anions is demonstrated via ion/ion reactions with doubly deprotonated 1,4-phenylenedipropionic acid (PDPA). Two synthetic PC isomers, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (PC16:0/18:1) and 1-oleoyl-2-palmitoyl-sn-glycero-3-phosphocholine (PC18:1/16:0), were subjected to this ion/ion chemistry. The product of the ion/ion reaction is a negatively charged complex, \[PC + PDPA - H](-). Collisional activation of the long-lived complex causes transfer of a proton and methyl cation to PDPA, generating \[PC - CH3](-). Subsequent collisional activation of the demethylated PC anions produces abundant fatty acid carboxylate anions and low-abundance acyl neutral losses as free acids and ketenes. Product ion spectra of \[PC - CH3](-) suggest favorable cleavage at the sn-2 position over the sn-1 due to distinct differences in the relative abundances. In contrast, collisional activation of PC cations is absent of abundant fatty acid chain-related product ions and typically indicates only the lipid class via formation of the phosphocholine cation. A solution phase method to produce the gas-phase adducted PC anion is also demonstrated. Product ion spectra derived from the solution phase method are similar to the results generated via ion/ion chemistry. This work demonstrates a gas-phase means to increase structural characterization of phosphatidylcholines via ion/ion chemistry. Grant Number ARC/CE0561607, ARC/DP120102922

Atomistic simulation of surface functionalization on the interfacial properties of graphene-polymer nanocomposites

Graphene has been increasingly used as nano sized fillers to create a broad range of nanocomposites with exceptional properties. The interfaces between fillers and matrix play a critical role in dictating the overall performance of a composite. However, the load transfer mechanism along graphene-polymer interface has not been well understood. In this study, we conducted molecular dynamics simulations to investigate the influence of surface functionalization and layer length on the interfacial load transfer in graphene polymer nanocomposites. The simulation results show that oxygen-functionalized graphene leads to larger interfacial shear force than hydrogen-functionalized and pristine ones during pull-out process. The increase of oxygen coverage and layer length enhances interfacial shear force. Further increase of oxygen coverage to about 7% leads to a saturated interfacial shear force. A model was also established to demonstrate that the mechanism of interfacial load transfer consists of two contributing parts, including the formation of new surface and relative sliding along the interface. These results are believed to be useful in development of new graphene-based nanocomposites with better interfacial properties.

Graph coloring applied to secure computation in non-Abelian groups

We study the natural problem of secure n-party computation (in the computationally unbounded attack model) of circuits over an arbitrary finite non-Abelian group (G,⋅), which we call G-circuits. Besides its intrinsic interest, this problem is also motivating by a completeness result of Barrington, stating that such protocols can be applied for general secure computation of arbitrary functions. For flexibility, we are interested in protocols which only require black-box access to the group G (i.e. the only computations performed by players in the protocol are a group operation, a group inverse, or sampling a uniformly random group element). Our investigations focus on the passive adversarial model, where up to t of the n participating parties are corrupted.

Characterising an ECG signal using statistical modelling : a feasibility study

For clinical use, in electrocardiogram (ECG) signal analysis it is important to detect not only the centre of the P wave, the QRS complex and the T wave, but also the time intervals, such as the ST segment. Much research focused entirely on qrs complex detection, via methods such as wavelet transforms, spline fitting and neural networks. However, drawbacks include the false classification of a severe noise spike as a QRS complex, possibly requiring manual editing, or the omission of information contained in other regions of the ECG signal. While some attempts were made to develop algorithms to detect additional signal characteristics, such as P and T waves, the reported success rates are subject to change from person-to-person and beat-to-beat. To address this variability we propose the use of Markov-chain Monte Carlo statistical modelling to extract the key features of an ECG signal and we report on a feasibility study to investigate the utility of the approach. The modelling approach is examined with reference to a realistic computer generated ECG signal, where details such as wave morphology and noise levels are variable.

Mechanical tension as a driver of connective tissue growth in vitro

We propose the progressive mechanical expansion of cell-derived tissue analogues as a novel, growth-based approach to in vitro tissue engineering. The prevailing approach to producing tissue in vitro is to culture cells in an exogenous “scaffold” that provides a basic structure and mechanical support. This necessarily pre-defines the final size of the implantable material, and specific signals must be provided to stimulate appropriate cell growth, differentiation and matrix formation. In contrast, surgical skin expansion, driven by increments of stretch, produces increasing quantities of tissue without trauma or inflammation. This suggests that connective tissue cells have the innate ability to produce growth in response to elevated tension. We posit that this capacity is maintained in vitro, and that order-of-magnitude growth may be similarly attained in self-assembling cultures of cells and their own extracellular matrix. The hypothesis that growth of connective tissue analogues can be induced by mechanical expansion in vitro may be divided into three components: (1) tension stimulates cell proliferation and extracellular matrix synthesis; (2) the corresponding volume increase will relax the tension imparted by a fixed displacement; (3) the repeated application of static stretch will produce sustained growth and a tissue structure adapted to the tensile loading. Connective tissues exist in a state of residual tension, which is actively maintained by resident cells such as fibroblasts. Studies in vitro and in vivo have demonstrated that cellular survival, reproduction, and matrix synthesis and degradation are regulated by the mechanical environment. Order-of-magnitude increases in both bone and skin volume have been achieved clinically through staged expansion protocols, demonstrating that tension-driven growth can be sustained over prolonged periods. Furthermore, cell-derived tissue analogues have demonstrated mechanically advantageous structural adaptation in response to applied loading. Together, these data suggest that a program of incremental stretch constitutes an appealing way to replicate tissue growth in cell culture, by harnessing the constituent cells’ innate mechanical responsiveness. In addition to offering a platform to study the growth and structural adaptation of connective tissues, tension-driven growth presents a novel approach to in vitro tissue engineering. Because the supporting structure is secreted and organised by the cells themselves, growth is not restricted by a “scaffold” of fixed size. This also minimises potential adverse reactions to exogenous materials upon implantation. Most importantly, we posit that the growth induced by progressive stretch will allow substantial volumes of connective tissue to be produced from relatively small initial cell numbers.

Differentiation of complex lipid isomers by radical-directed dissociation mass spectrometry

Contemporary lipidomics protocols are dependent on conventional tandem mass spectrometry for lipid identification. This approach is extremely powerful for determining lipid class and identifying the number of carbons and the degree of unsaturation of any acyl-chain substituents. Such analyses are however, blind to isomeric variants arising from different carbon carbon bonding motifs within these chains including double bond position, chain branching, and cyclic structures. This limitation arises from the fact that conventional, low energy collision-induced dissociation of even-electron lipid ions does not give rise to product ions from intrachain fragmentation of the fatty acyl moieties. To overcome this limitation, we have applied radical-directed dissociation (RDD) to the study of lipids for the first time. In this approach, bifunctional molecules that contain a photocaged radical initiator and a lipid-adducting group, such as 4-iodoaniline and 4-iodobenzoic acid, are used to form noncovalent complexes (i.e., adduct ions) with a lipid during electrospray ionization. Laser irradiation of these complexes at UV wavelengths (266 nm) cleaves the carbon iodine bond to liberate a highly reactive phenyl radical. Subsequent activation of the nascent radical ions results in RDD with significant intrachain fragmentation of acyl moieties. This approach provides diagnostic fragments that are associated with the double bond position and the positions of chain branching in glycerophospholipids, sphingomyelins and triacylglycerols and thus can be used to differentiate isomeric lipids differing only in such motifs. RDD is demonstrated for well-defined lipid standards and also reveals lipid structural diversity in olive oil and human very-low density lipoprotein.

Ozone-induced dissociation : Elucidation of double bond position within mass-selected lipid ions

Ions formed from lipids during electrospray ionization of crude lipid extracts have been mass-selected within a quadrupole linear ion trap mass spectrometer and allowed to react with ozone vapor. Gas-phase ion-molecule reactions between unsaturated lipid ions and ozone are found to yield two primary product ions for each carbon-carbon double bond within the molecule. The mass-to-charge ratios of these chemically induced fragments are diagnostic of the position of unsaturation within the precursor ion. This novel analytical technique, dubbed ozone-induced dissociation (OzID), can be applied both in series and in parallel with conventional collision-induced dissociation (CID) to provide near-complete structural assignment of unknown lipids within complex mixtures without prior fractionation or derivatization. In this study, OzID is applied to a suite of complex lipid extracts from sources including human lens, bovine kidney, and commercial olive oil, thus demonstrating the technique to be applicable to a broad range of lipid classes including both neutral and acidic glycerophospholipids, sphingomyelins, and triacylglycerols. Gas-phase ozonolysis reactions are also observed with different types of precursor ions including \[M + H](+), \[M + Li](+), \[M + Na](+), and \[M H](-): in each case yielding fragmentation data that allow double bond position to be unambiguously assigned. Within the human lens lipid extract, three sphingomyelin regioisomers, namely SM(d18:0/15Z-24:1), SM(d18:0/17Z-24:1), and SM(d18:0/19Z-24:1), and a novel phosphatidylethanolamine alkyl ether, GPEtn(11Z-18:1e/9Z18:1), are identified using a combination of CID and OzID. These discoveries demonstrate that lipid identification based on CID alone belies the natural structural diversity in lipid biochemistry and illustrate the potential of OzID as a complementary approach within automated, high-throughput lipid analysis protocols.

The Chemistry of Mycotoxins

Mycotoxins – from the Greek μύκης (mykes, mukos) “fungus” and the Latin (toxicum) “poison” – are a large and growing family of secondary metabolites and hence natural products produced by fungi, in particular by molds (1). It is estimated that well over 1,000 mycotoxins have been isolated and characterized so far, but this number will increase over the next few decades due the availability of more specialized analytical tools and the increasing number of fungi being isolated. However, the most important classes of fungi responsible for these compounds are Alternaria, Aspergillus (multiple forms), Penicillium, and Stachybotrys. The biological activity of mycotoxins ranges from weak and/or sometimes positive effects such as antibacterial activity (e.g. penicillin derivatives derived from Penicillium strains) to strong mutagenic (e.g. aflatoxins, patulin), carcinogenic (e.g. aflatoxins), teratogenic, neurotoxic (e.g. ochratoxins), nephrotoxic (e.g. fumonisins, citrinin), hepatotoxic, and immunotoxic (e.g. ochratoxins, diketopiperazines) activities (1, 2), which are discussed in detail in this volume.

Macromolecular engineering via RAFT chemistry : from sequential to modular design

Sequential Design Molecular Weight Range Functional Monomers: Possibilities, Limits, and Challenges Block Copolymers: Combinations, Block Lengths, and Purities Modular Design End-Group Chemistry Ligation Protocols Conclusions

A sub‒domain smoothed Galerkin method for solid mechanics problems

A sub‒domain smoothed Galerkin method is proposed to integrate the advantages of mesh‒free Galerkin method and FEM. Arbitrarily shaped sub‒domains are predefined in problems domain with mesh‒free nodes. In each sub‒domain, based on mesh‒free Galerkin weak formulation, the local discrete equation can be obtained by using the moving Kriging interpolation, which is similar to the discretization of the high‒order finite elements. Strain smoothing technique is subsequently applied to the nodal integration of sub‒domain by dividing the sub‒domain into several smoothing cells. Moreover, condensation of DOF can also be introduced into the local discrete equations to improve the computational efficiency. The global governing equations of present method are obtained on the basis of the scheme of FEM by assembling all local discrete equations of the sub‒domains. The mesh‒free properties of Galerkin method are retained in each sub‒domain. Several 2D elastic problems have been solved on the basis of this newly proposed method to validate its computational performance. These numerical examples proved that the newly proposed sub‒domain smoothed Galerkin method is a robust technique to solve solid mechanics problems based on its characteristics of high computational efficiency, good accuracy, and convergence.

Enhancement of 1,2-dehydration of alcohols by alkali cations and protons : a model for dehydration of carbohydrates

We have used electronic structure calculations to investigate the 1,2-dehydration of alcohols as a model for water loss during the pyrolysis of carbohydrates found in biomass. Reaction enthalpies and energy barriers have been calculated for neat alcohols, protonated alcohols and alcohols complexed to alkali metal ions (Li + and Na +). We have estimated pre-exponential A factors in order to obtain gas phase rate constants. For neat alcohols, the barrier to 1,2-dehydration is about 67 kcal mol -1, which is consistent with the limited experimental data. Protonation and metal complexation significantly reduce this activation barrier and thus, facilitate more rapid reaction. With the addition of alkali metals, the rate of dehydration can increase by a factor of 10 8 while addition of a proton can lead to an increase of a factor of 10 23.

Accessibility of pores in coal to methane and carbon dioxide

Fluid–solid interactions in natural and engineered porous solids underlie a variety of technological processes, including geological storage of anthropogenic greenhouse gases, enhanced coal bed methane recovery, membrane separation, and heterogeneous catalysis. The size, distribution and interconnectivity of pores, the chemical and physical properties of the solid and fluid phases collectively dictate how fluid molecules migrate into and through the micro- and meso-porous media, adsorb and ultimately react with the solid surfaces. Due to the high penetration power and relatively short wavelength of neutrons, smallangle neutron scattering (SANS) as well as ultra small-angle scattering (USANS) techniques are ideally suited for assessing the phase behavior of confined fluids under pressure as well as for evaluating the total porosity in engineered and natural porous systems including coal. Here we demonstrate that SANS and USANS can be also used for determining the fraction of the pore volume that is actually accessible to fluids as a function of pore sizes and study the fraction of inaccessible pores as a function of pore size in three coals from the Illinois Basin (USA) and Bowen Basin (Australia). Experiments were performed at CO2 and methane pressures up to 780 bar, including pressures corresponding to zero average contrast condition (ZAC), which is the pressure where no scattering from the accessible pores occurs. Scattering curves at the ZAC were compared with the scattering from same coals under vacuum and analysed using a newly developed approach that shows that the volume fraction of accessible pores in these coals varies between �90% in the macropore region to �30% in the mesopore region and the variation is distinctive for each of the examined coals. The developed methodology may be also applied for assessing the volume of accessible pores in other natural underground formations of interest for CO2 sequestration, such as saline aquifers as well as for estimating closed porosity in engineered porous solids of technological importance.