Deep mutational scanning and machine learning uncover antimicrobial peptide features driving membrane selectivity.

Antimicrobial peptides commonly act by disrupting bacterial membranes, but also frequently damage mammalian membranes. Deciphering the rules governing membrane selectivity is critical to understanding their function and enabling their therapeutic use. Past attempts to decipher these rules have failed because they cannot interrogate adequate peptide sequence variation. To overcome this problem, we develop deep mutational surface localized antimicrobial display (dmSLAY), which reveals comprehensive positional residue importance and flexibility across an antimicrobial peptide sequence. We apply dmSLAY to Protegrin-1, a potent yet toxic antimicrobial peptide, and identify thousands of sequence variants that positively or negatively influence its antibacterial activity. Further analysis reveals that avoiding large aromatic residues and eliminating disulfide bound cysteine pairs while maintaining membrane bound secondary structure greatly improves Protegrin-1 bacterial specificity. Moreover, dmSLAY datasets enable machine learning to expand our analysis to include over 5.7 million sequence variants and reveal full Protegrin-1 mutational profiles driving either bacterial or mammalian membrane specificity. Our results describe an innovative, high-throughput approach for elucidating antimicrobial peptide sequence-structure-function relationships which can inform synthetic peptide-based drug design.

Deep mutational scanning and machine learning uncover antimicrobial peptide features driving membrane selectivity.

Antimicrobial peptides commonly act by disrupting bacterial membranes, but also frequently damage mammalian membranes. Deciphering the rules governing membrane selectivity is critical to understanding their function and enabling their therapeutic use. Past attempts to decipher these rules have failed because they cannot interrogate adequate peptide sequence variation. To overcome this problem, we develop deep mutational surface localized antimicrobial display (dmSLAY), which reveals comprehensive positional residue importance and flexibility across an antimicrobial peptide sequence. We apply dmSLAY to Protegrin-1, a potent yet toxic antimicrobial peptide, and identify thousands of sequence variants that positively or negatively influence its antibacterial activity. Further analysis reveals that avoiding large aromatic residues and eliminating disulfide bound cysteine pairs while maintaining membrane bound secondary structure greatly improves Protegrin-1 bacterial specificity. Moreover, dmSLAY datasets enable machine learning to expand our analysis to include over 5.7 million sequence variants and reveal full Protegrin-1 mutational profiles driving either bacterial or mammalian membrane specificity. Our results describe an innovative, high-throughput approach for elucidating antimicrobial peptide sequence-structure-function relationships which can inform synthetic peptide-based drug design.

An optimization method for stochastic reconstruction from empirical data - A limestone rock strain fields study-case using digital image correlation data.

Stochastic field reconstruction is a crucial technique to improve the accuracy of modern rock simulation. It allows explicit modelling of field conditions, often employed in uncertainty quantification analysis and upsampling and upscaling procedures. This paper presents a case-study of a framework for the stochastic reconstruction of rock's strain field using experimental data. The proposed framework is applied to a limestone outcrop in which the strain field is measured using Digital Image Correlation (DIC). Assuming that the strain fields of these rocks are well-represented by Gaussian random fields, we capitalize on the algorithms used for training Gaussian processes to estimate the correlation family and the parameters that best represent these fields. Although the spherical and exponential kernels often correspond to the best fit, our results depict that each field shall be analyzed separately and no general rule can be defined. We show that the method is versatile and can be employed in any measurable field reasonably represented by a Gaussian random field. Therefore, the present work aims to highlight the following topics:•A study-case of stochastic strain field reconstruction aims to contribute to uncertainty quantification of rock experimental procedures.•A stochastic minimization algorithm is presented to solve the maximum likelihood estimation to define the most suitable hyper-parameter: correlation length.•The calculated hyper-parameters of a set correlation functions are presented to best reproduce the strain fields of a rock sample.

Permeation of intrinsic water into ethanol- and water-saturated, monomer-infiltrated dentin bond interfaces.

OBJECTIVES: The aim of this study was to evaluate the formation of dentin bonding interfaces using the water-wet and the ethanol-wet techniques under simulated pulpal pressure, and to assess the effect of adhesive solvent and thermomechanical loading. METHODS: Flat dentin surfaces were restored under 20mm-simulated pulpal pressure following two bonding approaches (water-wet and ethanol-wet bonding) in combination with dental adhesives containing ethanol (Single Bond Plus and Scotchbond Multi-Purpose) or acetone (One-Step Plus and All-Bond 2) as solvent. Half of the restorations of each subgroup were subjected to thermocycling followed by cyclic loading (three teeth per group). Bond strength was measured using the microtensile bond strength test and fitted to a Weibull distribution (α=0.05). Ultrastructural analyses of the interface and leakage/nanoleakage evaluation were performed using confocal scanning microscopy (CLSM) and transmission electron microscopy (TEM). RESULTS: Water permeation through dentin tubules during adhesive application prevented adequate penetration of adhesive monomers into the demineralized collagen matrix in both bonding techniques, but more severely for water-wet bonding. Acetone-solvated adhesives showed worse bonding performance and hybridization than ethanol-based systems when applied in the ethanol-wet mode, both before and after thermomechanical challenge. SIGNIFICANCE: The ethanol-wet bonding technique helps to compensate for water permeation from dentin tubules during the bonding procedures to form more stable dentin bonds, especially when used in conjunction to ethanol-solvated systems.

Effect of dentin age and acid etching time on dentin bonding.

PURPOSE: To compare the bond strengths of young and old dentin using a single-bottle etch-and-rinse adhesive system with two acid-etching times (15 s and 30 s), and to examine the correlation between dentin hardness and bond strength. MATERIALS AND METHODS: Twenty-four molars from 18- to 22- or 55- to 60-year-old patients were prepared to expose the occlusal dentin, cut into two equal parts, and assigned to four groups (G), varying the etching time (15 s and 30 s) and dentin age (young [Y]or old [O]): G15Y, G30Y, G15O and G30O. After etching, AdperSingleBond (3M ESPE) adhesive was applied and the tooth was built up with a composite (Filtek Z250). The specimens were prepared for the microtensile bond strength test (µTBS) at a crosshead speed of 0.5 mm/min and the interfaces were observed under SEM. Also, the Knoop hardness (KHN) of young vs old dentin was measured. RESULTS: The mean (± SD) µTBS (MPa) were: G15Y = 45.9 (± 10.7)a, G15O = 34.1 (± 9.4)b, G30Y = 48.6 (± 14.3)a and G30O = 47.7 (± 11.0)a. Two-way ANOVA showed no difference in µTBS between young and old dentin. Old dentin acid etched for 15 s (G15O) had a lower µTBS than when acid etched for 30 s (G30O). Dentin hardness was higher for old dentin (67.0 ± 4.8KHN) than young dentin (63.7 ± 2.9KHN) (p < 0.004). No correlation between µTBS and dentin hardness was observed. Resin tags were larger and more numerous for young dentin. The hybrid layer formed in intertubular old dentin (G15O) was very thin. CONCLUSION: Bonding to old dentin with 30 s of etching time resulted in higher bond strength and more homogeneous hybrid layer formation than dentin acid etched for 15 s.

Clinical effectiveness and tooth sensitivity associated with different bleaching times for a 10 percent carbamide peroxide gel.

BACKGROUND: The daily application time for 10 percent carbamide peroxide (CP) typically is between four and eight hours. However, to the authors' knowledge, no investigators in clinical studies have compared different application times; this is the aim of this study. METHODS: The authors recruited 60 patients and categorized each of them into one of four groups. All participants used 10 percent CP in a bleaching tray. The daily application times were 15 minutes, 30 minutes, one hour or eight hours. Participants bleached their teeth for 16 days and those who were not satisfied with the results extended the bleaching time until they were satisfied. Patients recorded their tooth sensitivity on a 0 to 4 scale. The authors measured the shade changes by using a digital spectrophotometer and shade guide. They performed appropriate statistical analysis of the data (α = .05). RESULTS: Participants in the one- and eight-hour groups bleached their teeth for 18 and 16 days, respectively (P > .05), while statistically longer periods were required for participants in the other two groups (P < .001) to be satisfied with the results. Participants' tooth sensitivity ratings were similar for the 15-minute, 30-minute and one-hour application times (P > .05), and they were statistically lower than those for participants in the eight-hour group. CONCLUSIONS: The eight-hour bleaching protocol yielded faster bleaching; however, participants experienced higher sensitivity levels. The one-hour group most closely approached the eight-hour group with regard to bleaching speed, while those in the one-hour group experienced lower sensitivity levels. CLINICAL IMPLICATIONS: In this study, the difference in bleaching speed between the eight- and one-hour application times after 16 days was small, and the results showed less tooth sensitivity for patients in the one-hour group.