Data-driven spatial branch-and-bound algorithms for box-constrained simulation-based optimization

Journal of Global Optimization - The ability to use complex computer simulations in quantitative analysis and decision-making is highly desired in science and engineering, at the same rate as...     

Characterization of the volatile profile of Antarctic bacteria by using solid-phase microextraction-gas chromatography-mass spectrometry

Bacteria belonging to the Burkholderia cepacia complex (Bcc) are significant pathogens in Cystic Fibrosis (CF) patients and are resistant to a plethora of antibiotics. In this context, microorganisms from Antarctica are interesting because they produce antimicrobial compounds inhibiting the growth of other bacteria. This is particularly true for bacteria isolated from Antarctic sponges. The aim of this work was to characterize a set of Antarctic bacteria for their ability to produce new natural drugs that could be exploited in the control of infections in CF patients by Bcc bacteria. Hence, 11 bacterial strains allocated to different genera (e.g., Pseudoalteromonas, Arthrobacter and Psychrobacter) were tested for their ability to inhibit the growth of 21 Bcc strains and some other human pathogens. All these bacteria completely inhibited the growth of most, if not all, Bcc strains, suggesting a highly specific activity toward Bcc strains. Experimental evidences showed that the antimicrobial compounds are small volatile organic compounds, and are constitutively produced via an unknown pathway. The microbial volatile profile was obtained by SPME-GC-MS within the m/z interval of 40-450. Solid phase micro extraction technique affords the possibility to extract the volatile compounds in head space with a minimal sample perturbation. Principal component analysis and successive cluster discriminant analysis was applied to evaluate the relationships among the volatile organic compounds with the aim of classifying the microorganisms by their volatile profile. These data highlight the potentiality of Antarctic bacteria as novel sources of antibacterial substances to face Bcc infections in CF patients.     

Histidine affinity chromatography-based methodology for the simultaneous isolation of Escherichia coli small and ribosomal RNA

Research on RNA has led to many important biological discoveries and the improvement of therapeutic technologies. In particular, there is a great focus on small RNA and ribosomal RNA owing to their key functions in the cell, which make them excellent therapeutic targets. Although the study of these RNA classes is progressing, some limitations have been found regarding the use of suitable techniques that are able to produce and isolate biologically competent and chemically stable RNA. To address this, we have developed a novel histidine affinity chromatography-based isolation methodology for small and ribosomal RNA molecules. The new procedure involves three main steps: (1) cell lysis with guanidinium buffer, (2) RNA primary isolation with ammonium sulfate precipitation and (3) histidine affinity chromatography to specifically purify small RNA and ribosomal RNA from other Escherichia coli impurities (genomic DNA and proteins). The RNA quality assessment revealed that both RNA species were obtained with a high recovery, integrity and purity. The potential of this method to achieve a reproducible RNA isolation with appropriate quality has been demonstrated and it should have broad application in the structural, biophysical and biomedical investigation of systems involving RNA components.     

Numerical simulation of ultrasonic wave propagation for the evaluation of dental implant biomechanical stability

Osseointegration of dental implants remains poorly understood. The objective of this numerical study is to understand the propagation phenomena of ultrasonic waves in prototypes cylindrically shaped implants and to investigate the sensitivity of their ultrasonic response to the surrounding bone biomechanical properties. The 10 MHz ultrasonic response of the implant was calculated using a finite difference numerical simulation tool and was compared to rf signals taken from a recent experimental study by Mathieu et al. [Ultrasound Med. Biol. 37, 262-270 (2011a)]. Reflection and mode conversion phenomena were analyzed to understand the origin of the different echoes and the importance of lateral wave propagation was evidenced. The sensitivity of the ultrasonic response of the implant to changes of (i) amount of bone in contact with the implant, (ii) cortical bone thickness, and (iii) surrounding bone material properties, was compared to the reproducibility of the measurements. The results show that, either a change of 1 mm of bone in contact with the implant, or 1.1 mm of cortical thickness or 12% of trabecular bone mass density should be detectable. This study paves the way for the investigation of the use of quantitative ultrasound techniques for the evaluation of bone-implant interface properties and implant stability.     

Effect of chromatographic conditions and plasmid DNA size on the dynamic binding capacity of a monolithic support

DNA therapies are becoming recognized alternatives for the treatment and prevention of severe pathologies. Although most current trials have used plasmids <10 kbp, in the future larger plasmids would be required. The purpose of this work was to study the chromatographic behavior of nongrafted carbonyldiimidazole monolithic disks using plasmids with different sizes under hydrophobic conditions. Thereunto, the purification of several plasmids was performed. Higher size plasmids needed lower ammonium sulfate concentration, due to the greater number of interactions between the plasmids and monolith. The dynamic binding capacity experiments for the different plasmids revealed a lower capacity for bigger plasmids. It was also verified that the increase of salt concentration from 2.5 to 3 M of ammonium sulfate increased the capacity. At the highest salt concentration, a slight improvement in the capacity using lower flow rate was observed, possibly due to compaction of plasmid molecules and its better organization on the monolith channels. Finally, a low pH also had a positive effect on the capacity. So, this monolithic support proved to be appropriate to purify the supercoiled isoform of different plasmids with different sizes, providing a valuable instrument as a purification technique.     

Chromatographic Analysis of Adsorption: Chemisorption and/or Physisorption

Eight systems namely the C₆H₆ /Fe₂O₃, C₆H₆/NO₂/Fe₂O₃, C₆H₅CH₃/Fe₂O_3, C₆H₅CH₃/NO₂/Fe₂O₃, C₆H₆/ZnO, C₆H₆/NO₂/ZnO, C₆H₅CH₃/ZnO, C₆H₅CH₃/NO₂/ZnO are examined through a version of inverse gas chromatography and six physicochemical adsorption quantities are determined for each heterogeneous system. Thus, the reversed flow—(inverse) gas chromatography is used for the investigation and study of adsorption phenomena taking place on these heterogeneous solid surfaces. In the case of iron oxide the presence of nitrogen dioxide facilitates the chemisorption. This is not obvious in the case of zinc oxide. However, nitrogen dioxide facilitates the adsorption of benzene and toluene through van der Waals forces in both oxides. Through the experimental local quantities determined and the detailed time-resolved analysis, useful information for the nature and the strength of the adsorbate–adsorbent as well as the adsorbate–adsorbate interactions have been extracted giving an insight into the topography of the active sites and the nature of the surface bonds.     

Controlling morphology,adhesion, and electrochromic behavior of PEDOT films through molecular design and processing

Poly(3,4-ethylenedioxythiophene) ( PEDOT ) is a well-known semiconducting polymer with favorable properties which find it often applied as the active material in biological sensors and electrochromic devices. However, PEDOT has several drawbacks which can prohibit its effective or long-term use, including weak adhesion to substrates such as ITO-coated glass, poorly controlled surface morphology, and reduced electrochemical stability over time. While a diverse range of approaches have been explored to overcome these issues, most involve additives or substrate modification, while solutions based on direct covalent adaptation are relatively lacking. We present a novel polymer based on covalently modified EDOT ( PEDOT-Crown ), featuring polar motifs and a 15-crown-5 moiety. Compared to PEDOT , PEDOT-Crown demonstrates a wealth of advantageous properties including: superior adhesion to ITO under physical and electrochemical duress; a more uniform surface morphology; and electrochemical properties including a higher contrast ratio, red-shifted polaron and bipolaron absorption features, bleaching of the neutral absorption band across a narrower voltage range, and more Faradaic rather than capacitive behavior. Additionally, we note that in the presence of Na⁺, PEDOT-Crown appears to show modified behavior in long-term electrochemical experiments. These features make PEDOT-Crown a material with improved suitability for application in biological sensing and electrochromic devices, compared to PEDOT .     

A preface to the special issue in memory of Professor Christodoulos A. Floudas

Optimization Letters -     

Computational and experimental study on the interaction of three novel rare earth complexes containing 2,9-dimethyl-1,10-phenanthroline with human serum albumin

In this paper, several rare earth [terbium(III), ytterbium(III) and yttrium(III)] complexes containing 2,9-dimethyl-1,10-phenanthroline (Me₂Phen) were successfully synthesized and characterized by means of elemental analysis (CHN), infrared spectroscopy (FT-IR), UV–vis absorption spectroscopy and ¹HNMR. To explore the potential medicinal value of these complexes (MMe₂Phen), their binding interactions with human serum albumin (HSA) were investigated through UV–vis and fluorescence spectroscopies and also molecular docking examinations. The thermodynamic parameters, binding forces and Förster resonance distance between these complexes and Trp-214 of HSA were estimated from the analysis of fluorescence measurements. The values of estimated binding constants (K_b) ranging for the formation of MMe₂Phen:HSA complex were in the order of 10⁵ M^?1. The thermodynamic parameters determined by van’t Hoff analysis of K_b (ΔH°?<?0 and ΔS°?<?0) clearly indicate the major rules of hydrogen bonds and van der Waals interactions in the formation process of MMe₂Phen:HSA. The values of Stern–Volmer constant and the evaluation of dynamic quenching constant at various temperatures provided good evidences for static quenching mechanism. Furthermore, the results of molecular docking calculation and competitive binding experiments represent the binding of these complexes to site 3 of HSA located in subdomain IB, containing both polar and apolar residues. The consistency of computational and experimental results, according to the binding sites and the order of binding affinities (TbMe₂Phen?>?YbMe₂Phen?>?YMe₂Phen), supports the accuracy of docking calculation.     

Characterization of polyplexes involving small RNA

The purpose of the present study is to provide a tool for an efficient design and synthesis of non-viral vectors for small RNA delivery. The effects of properties of the polycation, such as molecular weight, charge density and backbone structure, to polyplex structure and physicochemical behavior were systematically evaluated. The condensing agents, polyethylenimine (PEI), chitosan (CS) and poly(allylamine) (PAA) were added to sRNA molecules at different N/P ratio. The efficiency of encapsulation and protection of sRNA, as well as polyplex size, zeta potential and morphology were followed and compared. The results show that PEI/sRNA polyplexes display a small size and positive zeta potential. However, for low molecular weights, this polycation is unable to protect sRNA in the presence of a decompacting agent. With chitosan, sRNA is efficiently compacted at high N/P ratios. The CS/sRNA complexes display small sizes, ca. 200 nm, positive surface charge and also good stability. Finally, the PAA/sRNA polyplexes were found to be the smallest at low N/P ratios, displaying a good encapsulation efficiency and high stability. A rationale for the experimental observations is provided using Monte Carlo simulation for systems with polycations of different length and charge density. The simulations showed that there is an interplay between the size of polycation chains and its charge density that define the degree of condensation for sRNA.