Peptide mimotopes of phomopsins: Identification, characterization and application in an immunoassay

Peptide mimotopes of plant-associated toxins offer the potential for improving analytical and diagnostic methodologies as well as providing candidates for potential protective vaccines against plant poisoning diseases. Monoclonal antibody (mAb) C₃C₁₁, which recognizes the antimicrotubule phomopsin mycotoxins, was used to isolate peptide mimics of phomopsin A from a random 15-mer phage display peptide library. A total of 46 clones were isolated that showed specific reactivity with the mAb. Amino acid sequence analysis revealed four different types of mimotope sequences, all of which contained a common motif V-A-L/V-C. Of the 46 clones isolated, 44 contained the motif V-A-L-C while 2 contained the V-A-V-C motif. All four types of phage clones inhibited the reactivity of the mAb with phomopsin A in a competition ELISA. The clone with the mimotope sequence CT VALCNMYFGAKLD demonstrated the strongest binding. It was further shown that synthetic peptides containing these mimotope amino acid sequences were able to inhibit the mAb-phomopsin A interaction, indicating that the peptide mimotopes were responsible for the specific binding, independent of the phage framework. The results also suggest that the mimotope peptides bind to mAb C₃C₁₁ at the same site as phomopsin A. The application of recombinant phage particles carrying phomopsin mimotopes in immunoassay was evaluated and the results demonstrated approximately 100-fold increase in sensitivity in comparison with a conventional immunoassay using a chemically linked phomopsin-horseradish peroxidase conjugate.     

Small-angle Coulomb collision model for particle-in-cell simulations

We construct and investigate a set of stochastic differential equations that incorporate the physics of velocity-dependent small-angle Coulomb collisions among the plasma particles in a particle-in-cell simulation. Each particle is scattered stochastically from all the other particles in a simulation cell modeled as one or more Maxwellians. Total energy and momentum are conserved by linear transformation of the velocity increments. In two test simulations the proposed “particle-moment” collision algorithm performs well with time steps as large as 10% of the relaxation time – far larger than a particle-pairing collision algorithm, in which pairs of particles are scattered from one another, requires to achieve the same accuracy.     

On the time-dependent moments of Markovian queues with reneging

We give an explicit representation for the time-dependent moments of a Markovian queueing system with reneging. Our expressions are comparable in form to the moment expressions for the M/M/1 queue found in Abate and Whitt (Queueing Syst. 2:41–65, 1987; Adv. Appl. Probab. 20:145–178, 1988). We also illustrate how to use these expressions to derive analogous moment expressions for a reflected Ornstein–Uhlenbeck process, with reflection at zero.     

The middleman as a panacea for supply chain coordination problems

The prevalence of intermediaries (middlemen) in supply chains is often seen as a dying remnant of less efficient times. Despite predictions that supply chains will rapidly “cut out the middleman” as technological advances have eased logistics, middlemen have continued to thrive. In this paper, we demonstrate a transaction role of middlemen that may help clarify their staying power. In a model with self-interested decision-making by both a manufacturer and a retailer, wherein incentive misalignment creates investment and production inefficiencies, we show that the integrated (first-best) outcome can be achieved with simple cost-based contracts if and only if a middleman is present. We further show that the approach of utilizing a middleman to fully coordinate the supply chain is robust in that it can be applied to a variety of circumstances discussed in the literature, including multilateral investment/effort choices, multiple product providers, and logistical investments made by the middleman.     

Direct cryopreservation of winter buds of nine cultivars of blackcurrant (Ribes nigrum L)

Direct cryopreservation of overwintering, dormant buds has been applied to nine blackcurrant cultivars, using a 7 day dehydration period at c.-20° C before plunging directly into liquid nitrogen. The buds on shoots thawed from -20° C showed normal development simply by standing them in water and all the cultivars could be successfully recovered (> 58%) by grafting. None of the shoots thawed from liquid nitrogen showed any development after standing in water and all of the grafts failed. Shoots thawed from liquid nitrogen showed significant damage to xylem transport, and the cortical tissues necessary fro successful grafting showed significant loss of membrane semipermeability. However, buds excised from shoots immediately after thawing from liquid nitrogen were viable and could be recovered using in vitro culture. Survival ranged from 88 to 55%, depending upon cultivar.     

Global stability in the 2D Ricker equation

We improve a previous result for the 2D Ricker equation by reducing an infinite number of topological conditions to a finite number. We also give sufficient conditions in terms of the parameters where many of these topological conditions are satisfied. We also discuss the various pathologies that occur for other parameter choices.     

MRICOM–MRI COntrast Modelling using 2D T1–T2 correlation spectra and relaxation signatures

Image contrast is calculated by inputting experimental 2D T₁–T₂ relaxation spectra into the ODIN software interface. The method involves characterising a magnetic resonance imaging pulse sequence with a “relaxation signature” which describes the sensitivity of the sequence to relaxation and is independent of sample parameters. Maximising (or minimising) the overlap between the experimental 2D T₁–T₂ relaxation spectra and the relaxation signature can then be used to maximise image contrast. The concept is illustrated using relaxation signatures for the echo planar imaging and Turbo spin-echo imaging sequences, together with in-vitro 2D T₁–T₂ spectra for liver and cartilage.     

The flipped longitudinal polarization sequence

By flipping the longitudinal magnetization with a chain of 180° pulses it is possible to effectively restore the effects of relaxation so that the same longitudinal magnetization is periodically recovered. The pulse sequence for achieving this, called Flipped LOngitudinal Polarization (FLOP), can be incorporated into any pulse sequence whenever it is desired to stop the attenuation in longitudinal magnetization caused by relaxation. We illustrate its use for fast, single-shot measurements of the longitudinal relaxation time and for three-dimensional T₁ mapping.     

Integrating 3D images using laboratory‐based micro X‐ray computed tomography and confocal X‐ray fluorescence techniques

The application of non‐destructive imaging to characterizing samples has become more important as the costs of samples increase. Imaging a sample via X‐ray techniques is preferable when altering or even touching the sample affects its properties, or when the sample is fielded after characterization. Two laboratory‐based X‐ray techniques used at Los Alamos include micro X‐ray computed tomography (MXCT) and confocal micro X‐ray fluorescence (confocal MXRF). Both methods create a 3D rendering of the sample non‐destructively. MXCT produces a high‐resolution (sub‐µm voxel) rendering of the sample based upon X‐ray absorption; the resulting model is a function of density and does not contain any elemental information. Confocal MXRF produces an elementally specific 3D rendering of the sample, but at a lower (30 × 30 × 65 µm) resolution. By combining data from these two techniques, scientists provided a more comprehensive method of analysis. We will describe a MATLAB routine written to render each of these data sets individually and/or within the same coordinate system. This approach is shown in the analysis of two samples: an integrated circuit surface mounted resistor and a machined piece of polystyrene foam. The samples chosen provide an opportunity to compare and contrast the two X‐ray techniques, identify their weaknesses and show how they are used in a complementary fashion. Copyright © 2010 John Wiley & Sons, Ltd.     

Perceptually based head-related transfer function database optimization

In the context of binaural audio rendering, choosing the best head-related transfer function (HRTF) for an individual from large databases poses several problems. This study proposes a method to reduce the size of a given HRTF database. Participants, 45 in total, were asked to rate the quality of binaural synthesis for 46 HRTFs. The lack of reciprocity in the ratings was noted. Results were used to create a perceptually optimized HRTF subset which satisfied all participants' judgments. The subset was validated using localization tests on a separate group of subjects with results showing reduced errors when subjects were given their best choice, rather than their worst choice HRTF.