Statistical model for large-scale peptide identification in databases from tandem mass spectra using SEQUEST

Recent technological advances have made multidimensional peptide separation techniques coupled with tandem mass spectrometry the method of choice for high-throughput identification of proteins. Due to these advances, the development of software tools for large-scale, fully automated, unambiguous peptide identification is highly necessary. In this work, we have used as a model the nuclear proteome from Jurkat cells and present a processing algorithm that allows accurate predictions of random matching distributions, based on the two SEQUEST scores Xcorr and DeltaCn. Our method permits a very simple and precise calculation of the probabilities associated with individual peptide assignments, as well as of the false discovery rate among the peptides identified in any experiment. A further mathematical analysis demonstrates that the score distributions are highly dependent on database size and precursor mass window and suggests that the probability associated with SEQUEST scores depends on the number of candidate peptide sequences available for the search. Our results highlight the importance of adjusting the filtering criteria to discriminate between correct and incorrect peptide sequences according to the circumstances of each particular experiment.     

Accurate spatio-temporal reconstruction of missing data in dynamic scenes

In this paper, the accurate method for texture reconstruction with non-desirable moving objects into dynamic scenes is proposed. This task is concerned to editor off-line functions, and the main criteria are the accuracy and visibility of the reconstructed results. The method is based on a spatio-temporal analysis and includes two stages. The first stage uses a feature points tracking to locate the rigid objects accurately under the assumption of their affine motion model. The second stage involves the accurate reconstruction of video sequence based on texture maps of smoothness, structural properties, and isotropy. These parameters are estimated by three separate neural networks of a back propagation. The background reconstruction is realized by a tile method using a single texton, a line, or a field of textons. The proposed technique was tested into reconstructed regions with a frame area up to 8–20%. The experimental results demonstrate more accurate inpainting owing to the improved motion estimations and the modified texture parameters.     

Localized Densification during the Compaction of Alumina Granules: The Stage I—II Transition

Tungsten marker layers and X-ray computed tomography were used to monitor the compaction of spray-dried alumina. Local density changes and compaction curves show that the well-known Stage I—II transition indicates an alteration in the direction of transmitted pressure through the uppermost layer. Stage I pressure is dispersed in local agglomerate contacts until "pockets" of low density are eliminated. In Stage II, these deformed/fragmented agglomerates behave as a continuous body and interact with wall friction to transmit pressure nonuniformly into the bulk. Discrete element simulations reproduced the compaction curves and provided clear explanation of the density distribution development.     

Effect of temperature on structural properties of Aloe vera (Aloe barbadensis Miller) gel and Weibull distribution for modelling drying process

Aloe vera (Aloe barbadensis Miller) gel was dried at five inlet temperatures 50, 60, 70, 80 and 90 °C, in a convective dryer with a constant air flow of 2.0 ± 0.2 m/s. Rehydration ratio, water holding capacity, texture, microstructure and total polysaccharide content were evaluated. Drying kinetics was estimated using the Weibull distribution (r² > 0.97 and Chi-square < 0.0009). Values of scale and shape parameters ranged from 90.94 to 341.06 (min) and 1.43 to 1.49, respectively. Furthermore, the influence of temperature on the model parameters as well as on the quality attributes was analysed using a least significant difference test (p-value < 0.05). These effects were more evident for the long drying period (e.g. 810 min at 50 °C). However, minor alterations in the structural properties and total polysaccharide content were produced at drying temperatures of 60–70 °C, resulting in a high quality gel.     

Time-varying Volterra-series analysis of spectral regrowth andnoise power ratio in FET mixers

This paper presents a direct and robust analysis technique for evaluating nonlinear distortion phenomena in FET mixers excited by multitone signals. Time-varying Volterra-series analysis has previously been proven to be appropriate for small-signal intermodulation-distortion calculations in mixers excited by simple RF signals. Spectral convolutions of the suitably mapped control voltages are introduced in this paper in order to solve the nonlinear current source calculations for narrow-band modulated or broad-band multicarrier RF signals. Simulations and measurements of a properly characterized resistive mixer validate the accuracy of this direct and noniterative analysis tool for spectral regrowth and noise-power-ratio prediction in such applications     

Antimicrobial properties of grape seed extracts and their effectiveness after incorporation into pea starch films

Chemical analysis and antimicrobial nature of grape seed extracts (GSE) and their Reisling Vitis vinifera L. application as fortificants for edible starch films were investigated. GSE possessed an antioxidant activity of 17.18 ± 1.29 mmol TROLOX equivalents g_extract⁻¹ and total phenolic content of 327.58 ± 7.24 mmol gallic acid equivalents g_extract⁻¹ mainly attributed to their flavonoid and phenolic acid composition determined by high-performance liquid chromatography accomplished to a diode array detector and a electrospray ionisation mass spectrometer in negative mode (HPLC-DAD/ESI-MS). GSE inhibited the growth of Gram-positive food-borne pathogens while Gram-negatives were not inhibited. After GSE were incorporated into pea starch films, thickness of enriched films increased and the puncture and tensile strength decreased compared to control films. Furthermore, migration of phenolic compounds from the films to different food simulants, aqueous, acidic and alcoholic solution was determined according to 89\109\EEC directive. A higher particle migration in acidic simulants was found. Finally, the effect of GSE incorporated pea starch films was tested in vitro with pork loins infected with Brochothrix thermosphacta. GSE films reduced the bacterial growth in 1.3 log colony forming units mL⁻¹ after 4 days incubation at 4 °C.     

N-Stearoyl-phosphatidylserine: Synthesis and role in divalent-cation-induced aggregation and fusion

N-Acylphosphatidylserines have been isolated from intact and injured tissues, but the participation of such acidic phospholipids in membrane aggregation and fusion has not been demonstrated. We have synthesized N-stearoylphosphatidylserine (NSPS) and examined divalent-cation-induced aggregation of NSPS-liposomes, which leads to membrane destabilization and fusion. The purified lipid was characterized by its chromatographic and spectroscopic (infrared and ¹H nuclear magnetic resonance) properties and by its chemical degradation pattern. Aggregation of unilamellar NSPS-liposomes was studied as a function of calcium and magnesium concentration. The ability of calcium and magnesium to induce vesicle aggregation is higher for phosphatidylserine (PS)-liposomes (threshold concentration 1.5 mM for calcium and 4.6 mM for magnesium) than for NSPS-liposomes (threshold concentration 2.8 mM for calcium and 6.6 mM for magnesium). The irreversibility of the aggregation reactions after adding EDTA suggests that vesicle fusion might occur in the presence of calcium and magnesium. Preliminary studies, based on mixing of both lipid and internal aqueous contents, show that fusion rather than aggregation of NSPS-liposomes occurs in the presence of calcium ions. The tendency of NSPS-liposomes to aggregate at higher cation concentrations than PS-liposomes suggests that N-acylation of phosphatidylserine protects the membrane against degenerative damage caused by aggregation and fusion.     

Prenylated Flavonoids with Potential Antimicrobial Activity: Synthesis,Biological Activity,and In Silico Study

Prenylated flavonoids are an important class of naturally occurring flavonoids with important biological activity, but their low abundance in nature limits their application in medicines. Here, we showed the hemisynthesis and the determination of various biological activities of seven prenylated flavonoids, named 7–13, with an emphasis on antimicrobial ones. Compounds 9, 11, and 12 showed inhibitory activity against human pathogenic fungi. Compounds 11, 12 (flavanones) and 13 (isoflavone) were the most active against clinical isolated Staphylococcus aureus MRSA, showing that structural requirements as prenylation at position C-6 or C-8 and OH at positions C-5, 7, and 4′ are key to the antibacterial activity. The combination of 11 or 12 with commercial antibiotics synergistically enhanced the antibacterial activity of vancomycin, ciprofloxacin, and methicillin in a factor of 10 to 100 times against drug-resistant bacteria. Compound 11 combined with ciprofloxacin was able to decrease the levels of ROS generated by ciprofloxacin. According to docking results of S enantiomer of 11 with ATP-binding cassette transporter showed the most favorable binding energy; however, more studies are needed to support this result.     

Thermodynamics of the process of adsorption of aliphatic amidpolyamine on cellulose

The subject of this research is the thermodynamics of the adsorption equilibrium of three types of bleached pulp in water solutions of aliphatic amidpolyamine—Lamid-1, (L-1) in concentrations from 0.03 to 0.50 g/L in a temperature interval of 0–60°C and the influence of pH of the environment on the adsorption process. It was established that with the increase of temperature the quantity of adsorbed L-1 decreases. The values of the heat of adsorption are negative, do not depend on the quantity of adsorbed L-1, and are of the order 111.7–14.7 kJ/mol. The values of the entropy of the entropy of adsorption are also negative and are of the order of 76.8 ÷ 84.5 J/mol?K. Adsorption equilibrium is described by ther adsorption isotherm of Langmuir. Optimum pH for lower concentrations of the solution is from 5 to 7. When the concentrations of the solution are higher (C ≧ 0.15 g/L) the process can also take place very satisfactorily in an alkaline environment.