Continuous-flow fast atom bombardment mass spectrometry of oligonucleotides

Although frit-fast atom bombardment (frit-FAB) and continuous-flow FAB mass spectrometry have become standard methods for the analysis of peptides and peptide mixtures, these techniques have not been applied previously to the analysis of oligonucleotides. Mobilephase composition, flow rate, and sample size were optimized for the analysis of oligonucleotides by negative ion frit-FAB mass spectrometry (a type of continuous-flow FAB mass spectrometry). With a mobile phase consisting of methanol/water/triethanolamine (80:20:0.5, v/v/w), flow injection frit-FAB analysis of oligonucleotides showed lower limits of detection compared to standard probe FAB mass spectrometry. For example, in order to obtain a signal-to-noise ratio of 3:1, 38 prnol of d(GTIAAC) were required for frit-FAB mass spectrometry and 62 pmol were required for standard probe FAB mass spectrometry. The largest difference between frit-FAB and standard probe FAB was observed for d(pC)₅, for which the limit of detection by frit-FAB was approximately 11-fold lower than by standard FAB mass spectrometry. Adjustment of the mobile phase to pH 7 with trifluoroacetic acid increased the limit of detection (reduced sensitivity) a minimum of sixfold. Equimolar mixtures of two or three oligonucleotides produced deprotonated molecules in identical relative abundances whether analyzed by frit-FAB or standard probe FAB mass spectrometry. Finally, frit-FAB liquid chromatography mass spectrometry was demonstrated by separating mixtures of oligonucleotides on a β -cyclodextrin high-performance liquid chromatography column with a mobile phase containing methanol, water, and triethanolamine.     

Fast Field Echo imaging: an overview and contrast calculations

Current fast imaging techniques are based on gradient echo sequences with reduced flip angle excitation pulses and very short repetition times TR. Practical T2 values may be of the order of TR or longer. In this situation, a different image contrast can be obtained, depending on details of the sequence. Four essentially different versions of the basic Fast Field Echo (FFE) sequence can be distinguished and are described systematically in this article. For these sequences, image contrast formulas are presented. Practical imaging should tolerate small field inhomogeneities. This requirement can be satisfied by only three of the four versions. Numerical simulations are used to study the influence of a modified phase alternation scheme on image contrasts of two of the remaining sequences. The results of the calculations are verified by phantom studies on a 1.5-T whole-body imager. Implications for contrast in clinical images are discussed in relation to head images obtained on the same machine.     

EPR investigations of solid solutions of TSCC and TSCB doped with Mn2+

EPR investigations of Mn²⁺-doped solid solutions of TSCC and TSCB were performed between 4.2 K and 300 K. The Curie temperature vs. molar fraction of bromide x is nonlinear, for x ≧ 0,75 no ferroelectric EPR-line splitting occurs. The relation between the line widths and the molar fraction of bromide is discussed by means of a simple statistical model.     

A 15N labelling,FD and FAB study of ammonia loss from protonated arginine molecules

The positive ion field desorption (FD) spectrum of arginine taken at the best anode temperature only contains a peak due to [M+H]⁺ ions. At higher emitter temperatures a considerable amount of fragmentation is induced and the [M+H NH₃]⁺ ions become most abundant. Specific ¹⁵N labelling reveals that the eliminated ammonia molecule, exclusively, contains one of the terminal nitrogen atoms of the guanidyl group. This also applies to the ammonia loss from metastably decomposing [M+H]⁺ ions. The positive ion fast atom bombardment (FAB) spectrum shows more fragmentation than the FD spectrum. In contrast with the FD results, the [M+H]⁺ ions generated upon FAB with ion lifetimes <10⁻⁶ s eliminate both ammonia containing one of the terminal nitrogen atoms of the guanidyl group and ammonia containing the α-amino group in the ratio of 1.35, as found by ¹⁵N labelling. The metastably decomposing [M+H]⁺ ions, however, eliminate only the former ammonia molecule. In the negative ion FD and FAB spectra no other peak than that corresponding to the [M H]⁻ ion is observed. Some attention has been paid to the thermal degradation of arginine on the basis of a few Curie-point pyrolysis experiments.     

Observation of concentration boundary layers around growing or dissolving KH2PO4 crystals in stagnant solutions

The solute concentration profiles around KH₂PO₄ crystals growing or dissoloving in stagnant aqueous solutions were studied by the schlieren method after Toepler. By this technique the thicknesses of concentration boundary layers around the crystals, formed by free convection of solution, were measured in dependence of crystal size and super (under) saturation. In the case of dissolution, theoretical estimation of the boundary layer thickness yielded a fair agreement with the observed value. For growth, the process is dominantly limited by surface kinetics, whereas volume diffusion plays a minor role.     

Optimal dispatching in a tandem queue

Motivated by a capacity allocation problem within a finite planning period, we conduct a transient analysis of a single-server queue with Lévy input. From a cost minimization perspective, we investigate the error induced by using stationary congestion measures as opposed to time-dependent measures. Invoking recent results from fluctuation theory of Lévy processes, we derive a refined cost function, that accounts for transient effects. This leads to a corrected capacity allocation rule for the transient single-server queue. Extensive numerical experiments indicate that the cost reductions achieved by this correction can be significant.     

A feedback fluid queue with two congestion control thresholds

Feedback fluid queues play an important role in modeling congestion control mechanisms for packet networks. In this paper we present and analyze a fluid queue with a feedback-based traffic rate adaptation scheme which uses two thresholds. The higher threshold B ₁ is used to signal the beginning of congestion while the lower threshold B ₂ signals the end of congestion. These two parameters together allow to make the trade-off between maximizing throughput performance and minimizing delay. The difference between the two thresholds helps to control the amount of feedback signals sent to the traffic source. In our model the input source can behave like either of two Markov fluid processes. The first applies as long as the upper threshold B ₁ has not been hit from below. As soon as that happens, the traffic source adapts and switches to the second process, until B ₂ (smaller than B ₁) is hit from above. We analyze the model by setting up the Kolmogorov forward equations, then solving the corresponding balance equations using a spectral expansion, and finally identifying sufficient constraints to solve for the unknowns in the solution. In particular, our analysis yields expressions for the stationary distribution of the buffer occupancy, the buffer delay distribution, and the throughput.     

A minimization version of a directed subgraph homeomorphism problem

We consider a special case of the directed subgraph homeomorphism or topological minor problem, where the host graph has a specific regular structure. Given an acyclic directed pattern graph, we are looking for a host graph of minimal height which still allows for an embedding. This problem has applications in compiler design for certain coarse-grain reconfigurable architectures. In this application domain, the task is to simultaneously schedule, bind and route a so-called data-flow graph, where vertices represent operations and arcs stand for data dependencies between the operations, given an orthogonal grid structure of reconfigurable processing elements (PEs) that have restricted communication abilities. We show that the problem of simultaneously scheduling, binding and routing is NP-complete by describing a logic engine reduction from NAE-3-SAT. This result holds even when the input graph is a directed tree with maximum indegree two. We also give a |V|^3/2-approximation algorithm. J. A. Brenner’s research supported by the DFG Research Center Matheon “Mathematics for key technologies”. J. C. van der Veen’s research supported by DFG Focus Program 1148, “Reconfigurable Architectures”, Grants FE 407/8-1 and FE 407/8-2.