Diversity of phage-displayed libraries of peptides during panning and amplification

The amplification of phage-displayed libraries is an essential step in the selection of ligands from these libraries. The amplification of libraries, however, decreases their diversity and limits the number of binding clones that a screen can identify. While this decrease might not be a problem for screens against targets with a single binding site (e.g., proteins), it can severely hinder the identification of useful ligands for targets with multiple binding sites (e.g., cells). This review aims to characterize the loss in the diversity of libraries during amplification. Analysis of the peptide sequences obtained in several hundred screens of peptide libraries shows explicitly that there is a significant decrease in library diversity that occurs during the amplification of phage in bacteria. This loss during amplification is not unique to specific libraries: it is observed in many of the phage display systems we have surveyed. The loss in library diversity originates from competition among phage clones in a common pool of bacteria. Based on growth data from the literature and models of phage growth, we show that this competition originates from growth rate differences of only a few percent for different phage clones. We summarize the findings using a simple two-dimensional "phage phase diagram", which describes how the collapse of libraries, due to panning and amplification, leads to the identification of only a subset of the available ligands. This review also highlights techniques that allow elimination of amplification-induced losses of diversity, and how these techniques can be used to improve phage-display selection and enable the identification of novel ligands.     

Buckling analysis of stringer-stiffened laminated cylindrical shells with nonuniform eccentricity

In this study, the influence of nonuniformity of eccentricity of stringers on the general axial buckling load of stiffened laminated cylindrical shells with simply supported end conditions is investigated. The critical loads are calculated using Love’s First-order Shear Deformation Theory and solved using the Rayleigh-Ritz procedure. The effects of the shell length-to-radius ratio, shell thickness-to-radius ratio, number of stringers, and stringers depth-to-width ratio on the buckling load of nonuniformly eccentric shells, are examined. The research demonstrates that an appropriate nonuniform distribution of eccentricity of stringers leads the buckling load to increase significantly.     

A Langevin equation for the rates of currency exchange based on the Markov analysis

We propose a method for analyzing the data for the rates of exchange of various currencies versus the U.S. dollar. The method analyzes the return time series of the data as a Markov process, and develops an effective equation which reconstructs it. We find that the Markov time scale, i.e., the time scale over which the data are Markov-correlated, is one day for the majority of the daily exchange rates that we analyze. We derive an effective Langevin equation to describe the fluctuations in the rates. The equation contains two quantities, D⁽¹⁾ and D⁽²⁾, representing the drift and diffusion coefficients, respectively. We demonstrate how the two coefficients are estimated directly from the data, without using any assumptions or models for the underlying stochastic time series that represent the daily rates of exchange of various currencies versus the U.S. dollar.     

Interactive effects of local smoothing window size and fundamental frequency on shimmer calculation

Slow amplitude modulation of human voice was approximated by a sinusoidal wave. The theoretical effects of smoothing window size, F₀, and modulation frequency on window amplitude average as well as calculated shimmer were mathematically derived. Subsequently, the theoretical predictions were tested using idealized and real voice signals from normal speakers. The theoretical and experimental results suggest that shimmer (when calculated using a smoothing window) is a function of window duration and modulation frequency. Window duration when defined as a constant number of pitch periods varies from speaker to speaker depending on their F₀. It may not be desirable to use local smoothing windows with a constant number of cycles for shimmer computation, especially if voices with known low-frequency amplitude modulations but notably different fundamental frequencies are compared.     

Bounding the performance of tandem queues with finite buffer spaces

We consider a queueing system with three single servers in tandem with two intermediate buffer storages of finite capacity. The processing times are exponentially distributed and the first server has unlimited number of customers in front of it. Using a negative dependence property between the number of customers at the first and second buffer storages we show that a popular form of decomposition approach applied to this model, indeed, provides a lower bound for its performance. The approach used here to establish the bound is new and could be extended to establish bounds for other types of tandem queues with finite buffer spaces.     

On the Apéry sets of monomial curves

In this paper, we use the Apéry table of the numerical semigroup associated to an affine monomial curve in order to characterize arithmetic properties and invariants of its tangent cone. In particular, we precise the shape of the Apéry table of a numerical semigroup of embedding dimension 3, when the tangent cone of its monomial curve is Buchsbaum or 2-Buchsbaum, and give new proofs for two conjectures raised by Sapko (Commun. Algebra 29:4759–4773, 2001) and Shen (Commun. Algebra 39:1922–1940, 2001). We also provide a new simple proof in the case of monomial curves for Sally’s conjecture (Numbers of Generators of Ideals in Local Rings, 1978) that the Hilbert function of a one-dimensional Cohen-Macaulay ring with embedding dimension three is non-decreasing. Finally, we obtain that monomial curves of embedding dimension 4 whose tangent cones are Buchsbaum, and also monomial curves of any embedding dimensions whose numerical semigroups are balanced, have non-decreasing Hilbert functions. Numerous examples are provided to illustrate the results, most of them computed by using the NumericalSgps package of GAP (Delgado et al., NumericalSgps-a GAP package, 2006).     

Homotopy analysis method for solving Abel differential equation of fractional order

In this study, the homotopy analysis method is used for solving the Abel differential equation with fractional order within the Caputo sense. Stabilityand convergence of the proposed approach is investigated. The numerical results demonstrate that the homotopy analysis method is accurate and readily implemented.     

Differentiation of hepatic cavernous hemangioma from metastases by rare sequence MR imaging.

In this study, in order to differentiate cavernous hemangioma and hepatic metastases, rapid acquisition relaxation enhanced (RARE) sequence was used. First, in vivo measurements of T1, T2 relaxation times and proton density were obtained using T1, T2 calculation protocol (TOMIKON S50, 0.5T) and multipoint techniques. These measurements were made from regions of interest placed over the liver, spleen (because of similarity of relaxation time values between hepatic metastases and spleen) and cavernous hemangioma (HCH). Based on these intrinsic parameters, T2 curves signal intensity of three different tissues were constructed. At TE = 500 ms, the signal intensity of the liver and spleen has been near zero whereas in HCH, the signal intensity remained. As RARE sequence is very similar to spin echo (SE), by replacing effective TE(ETE) = 500 ms in the RARE equation, two dimensional contrast-to-noise ratio (CNR) contour plots were constructed demonstrating signal intensity contrast between liver-spleen, liver-Hemangioma for two different scan times (3 min, 7.5 s) and pulse timing. Then, optimal RARE factor and inter echo times were obtained in order to have maximum CNR between liver-Hemangioma and minimum CNR between liver-spleen. These optimal parameters were performed on ten normal and five persons with known HCH. Images showed that in both scan times (3 min, 7.5 s); the liver and spleen were suppressed whereas the HCH was enhanced. The image quality in the scan time of 3 min was better than the scan time of 7.5 s. Moreover, in this study, two different sequences were compared: i) Multi-slice single echo (MSSE) for T1 weighted image ii) RARE (ETE = 80 ms) for T2-weighted image. This comparison was done to show maximum CNR between liver-spleen (metastases) and to choose a better sequence for detecting metastases. CNR in the RARE sequence was more than in the MSSE sequence.     

Analysis and evaluation of the antimicrobial and anticancer activities of the essential oil isolated from Foeniculum vulgare from Hamedan,Iran

In this study, biological properties of the essential oil isolated from seeds of Foeniculum vulgare (F. vulgare) were evaluated. GC-MS analysis revealed Trans-Anethole (80.63%), L-Fenchone (11.57%), Estragole (3.67%) and Limonene (2.68%) were the major compounds of the essential oil. Antibacterial activity of the essential oil against nine Gram-positive and Gram-negative strains was studied using disc diffusion and micro-well dilution assays. Essential oil exhibited the antibacterial activity against three Gram-negative strains of Pseudomonas aeruginosa, Escherichia coli, and Shigella dysenteriae. The preliminary study on toxicity of seed oil was performed using Brine Shrimp lethality test (BSLT). Results indicated the high toxicity effect of essential oil (LC50 = 10 μg/mL). In vitro anticancer activity of seed oil was investigated against human breast cancer (MDA-Mb) and cervical epithelioid carcinoma (Hela) cell lines by MTT assay. Results showed the seed oil behave as a very potent anticancer agent with IC50 of lower than 10 μg/mL in both cases.