Mass spectrometry imaging as a tool for surgical decision‐making

Despite significant advances in image‐guided therapy, surgeons are still too often left with uncertainty when deciding to remove tissue. This binary decision between removing and leaving tissue during surgery implies that the surgeon should be able to distinguish tumor from healthy tissue. In neurosurgery, current image‐guidance approaches such as magnetic resonance imaging (MRI) combined with neuronavigation offer a map as to where the tumor should be, but the only definitive method to characterize the tissue at stake is histopathology. Although extremely valuable information is derived from this gold standard approach, it is limited to very few samples during surgery and is not practically used for the delineation of tumor margins. The development and implementation of faster, comprehensive, and complementary approaches for tissue characterization are required to support surgical decision‐making – an incremental and iterative process with tumor removed in multiple and often minute biopsies. The development of atmospheric pressure ionization sources makes it possible to analyze tissue specimens with little to no sample preparation. Here, we highlight the value of desorption electrospray ionization as one of many available approaches for the analysis of surgical tissue. Twelve surgical samples resected from a patient during surgery were analyzed and diagnosed as glioblastoma tumor or necrotic tissue by standard histopathology, and mass spectrometry results were further correlated to histopathology for critical validation of the approach. The use of a robust statistical approach reiterated results from the qualitative detection of potential biomarkers of these tissue types. The correlation of the mass spectrometry and histopathology results to MRI brings significant insight into tumor presentation that could not only serve to guide tumor resection, but that is also worthy of more detailed studies on our understanding of tumor presentation on MRI. Copyright © 2013 John Wiley & Sons, Ltd.     

Two new zinc(II) and mercury(II) complexes based on N,N′‐(cyclohexane‐1,2‐diylidene)bis(4‐fluorobenzohydrazide): synthesis,crystal structures and antibacterial activities

Reaction of N,N′‐(cyclohexane‐1,2‐diylidene)bis(4‐fluorobenzohydrazide), C₂₀H₁₈F₂N₄O₂, ( L^F ), with zinc chloride and mercury(II) chloride produced different types and shapes of neutral coordination complexes, namely, dichlorido[N,N′‐(cyclohexane‐1,2‐diylidene)bis(4‐fluorobenzohydrazide)‐κ²N,O]zinc(II), [ZnCl₂(C₂₀H₁₈F₂N₄O₂)], ( 1 ), and dichlorido[N,N′‐(cyclohexane‐1,2‐diylidene)bis(4‐fluorobenzohydrazide)‐κ⁴O,N,N′,O′]mercury(II), [HgCl₂(C₂₀H₁₈F₂N₄O₂)], ( 2 ). The organic ligand and its metal complexes are characterized using various techniques: IR, UV–Vis and nuclear magnetic resonance (NMR) spectroscopies, in addition to powder X‐ray diffraction (PXRD), single‐crystal X‐ray crystallography and microelemental analysis. Depending upon the data from these analyses and measurements, a typical tetrahedral geometry was confirmed for zinc complex ( 1 ), in which the Zn^II atom is located outside the bis(benzhydrazone) core. The Hg^II atom in ( 2 ) is found within the core and has a common octahedral structure. The in vitro antibacterial activities of the prepared compounds were evaluated against two different bacterial strains, i.e. gram positive Bacillus subtilis and gram negative Pseudomonas aeruginosa bacteria. The prepared compounds exhibited differentiated growth‐inhibitory activities against these two bacterial strains based on the difference in their lipophilic nature and structural features.     

Structural characterization of intact proteins is enhanced by prevalent fragmentation pathways rarely observed for peptides

While collisionally activated dissociation (CAD) pathways for peptides are well characterized, those of intact proteins are not. We systematically assigned CAD product ions of ubiquitin, myoglobin, and bovine serum albumin generated using high-yield, in-source fragmentation. Assignment of >98% of hundreds of product ions implies that the fragmentation pathways described are representative of the major pathways. Protein dissociation mechanisms were found to be modulated by both source declustering potential and precursor ion charge state. Like peptides, higher charge states of proteins fragmented at lower energies next to Pro, via mobile protons, while lower charge states fragmented at higher energies after Asp and Glu, via localized protons. Unlike peptides, however, predominant fragmentation channels of proteins occurred at intermediate charge states via non-canonical mechanisms and produced extensive internal fragmentation. The non-canonical mechanisms include prominent cleavages C-terminal to Pro and Asn, and N-terminal to Ile, Leu, and Ser; these cleavages, along with internal fragments, led to a 45% increase in sequence coverage, improving the specificity of top-down protein identification. Three applications take advantage of the different mechanisms of protein fragmentation. First, modulation of declustering potential selectively fragments different charge states, allowing the source region to be used as the first stage of a low-resolution tandem mass spectrometer, facilitating pseudo-MS3 of product ions with known parent charge states. Second, development and integration of automated modulation of ion funnel declustering potential allows users access to a particular fragmentation mechanism, yielding facile cleavage on a liquid chromatography timescale. Third, augmentation of a top-down search engine improved protein characterization.     

Memory‐efficient calculation of the isotopic mass states of a molecule

Our previous work postulated a transition concept among different isotopic mass states (i.e., isotopic species) of a molecule, and developed a hierarchical algorithm for accurately calculating their masses and abundances. A theoretical mass spectrum can be generated by convoluting a peak shape function to these discrete mass states. This approach suffers from limited memory if a level in the hierarchical structure has too many mass states. Here we present a memory efficient divide‐and‐recursively‐combine algorithm to do the calculation, which also improves the truncation method used in the previous hierarchical algorithm. Instead of treating all of the elements in a molecule as a whole, the new algorithm first ‘strips’ each element one by one. For the mass states of each element, a hierarchical structure is established and kept in the memory. This process reduces the memory usage by orders of magnitude (e.g., for bovine insulin, memory can be reduced from gigabytes to kilobytes). Next, a recursive algorithm is applied to combine mass states of elements to mass states of the whole molecule. The algorithm described above has been implemented as a computer program called Isotope Calculator, which was written in C++. It is freely available under the GNU Lesser General Public License from http://www.cs.brandeis.edu/～hong/software.html or http://people.brandeis.edu/～agar . Copyright © 2010 John Wiley & Sons, Ltd.     

Comparison of Flow and Transport Experiments on 3D Printed Micromodels with Direct Numerical Simulations

Understanding pore-scale flow and transport processes is important for understanding flow and transport within rocks on a larger scale. Flow experiments on small-scale micromodels can be used to experimentally investigate pore-scale flow. Current manufacturing methods of micromodels are costly and time consuming. 3D printing is an alternative method for the production of micromodels. We have been able to visualise small-scale, single-phase flow and transport processes within a 3D printed micromodel using a custom-built visualisation cell. Results have been compared with the same experiments run on a micromodel with the same geometry made from polymethyl methacrylate (PMMA, also known as Perspex). Numerical simulations of the experiments indicate that differences in experimental results between the 3D printed micromodel and the Perspex micromodel may be due to variability in print geometry and surface properties between the samples. 3D printing technology looks promising as a micromodel manufacturing method; however, further work is needed to improve the accuracy and quality of 3D printed models in terms of geometry and surface roughness.

     

Drugmart: Heroin epidemics as complex adaptive systems

Illicit drug epidemics are infamous for their unexpected arrival and their speed of onset. Based on ethnographic work with youthful heroin experimenters in the Baltimore metropolitan area, an explanation was constructed based on circulating stories of drug reputation. An agent‐based model was built in SWARM to evaluate the explanation with good and bad stories about the drug passed among agents, which changed their initial attitudes. On repeated runs with different initial attitudes the model shows wide variation in outcomes and a dampening effect of increased social connections, contrary to epidemiologic expectations. The conclusion spells out implications for drug intervention and social research that relies on single case studies. © 2002 Wiley Periodicals, Inc.