diaPASEF Proteomics and Feature Selection for the Description of Sputum Proteome Profiles in a Cohort of Different Subtypes of Lung Cancer Patients and Controls

The high mortality, the presence of an initial asymptomatic stage and the fact that diagnosis in early stages reduces mortality justify the implementation of screening programs in the populations at risk of lung cancer. It is imperative to develop less aggressive methods that can complement existing diagnosis technologies. In this study, we aimed to identify lung cancer protein biomarkers and pathways affected in sputum samples, using the recently developed diaPASEF mass spectrometry (MS) acquisition mode. The sputum proteome of lung cancer cases and controls was analyzed through nano-HPLC–MS using the diaPASEF mode. For functional analysis, the results from differential expression analysis were further analyzed in the STRING platform, and feature selection was performed using sparse partial least squares discriminant analysis (sPLS-DA). Our results showed an activation of inflammation, with an alteration of pathways and processes related to acute-phase, complement, and immune responses. The resulting sPLS-DA model separated between case and control groups with high levels of sensitivity and specificity. In conclusion, we showed how new-generation proteomics can be used to detect potential biomarkers in sputum samples, and ultimately to discriminate patients from controls and even to help to differentiate between different cancer subtypes.     

Flexible oligomeric silicon-containing poly(ether-azomethine)s obtained from epoxide derivatives. Synthesis and characterization

Three new diamines derived from epoxide compounds were synthesized. The preparation of diamine monomers implied the reaction between a phenoxyalkyloxirane (alkyl: H, methyl, isopropyl) and bisphenol A, obtaining the respective aliphatic diols, which produced the corresponding dinitro derivatives. Finally, these derivatives were reduced by using palladium/carbon activated as catalyst and hydrazine as a hydrogen source. Then, six oligomeric poly(ether-azomethine)s (PEAzMs) were obtained from a polycondensation reaction between the new diamines and bis(4-formylbiphenyl-4-yl)dialkylsilane (alkyl: methyl, phenyl) with 84–93% yields. The structural characterization of the diamines and PEAzMs was performed by elemental analysis, infrared spectroscopy, and nuclear magnetic resonance spectroscopy (¹H, ¹³C, and ²⁹Si). Furthermore, polymers were analyzed by solubility tests, gel permeation chromatography, ultraviolet–visible (UV–vis) spectroscopy, thermogravimetry, and differential scanning calorimetry analysis. The results showed PEAzMs with 2–11 repetitive units, where the design of the monomers allowed to obtain improved solution processability in comparison with previously reported silylated poly(azomethine)s and good thermal stability. Additionally, all samples showed high transparency in the UV–vis region. © 2019 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2019 , 136, 48055.     

Temporal and spatial Lagrangean decompositions in multi-site, multi-period production planning problems with sequence-dependent changeovers

We address in this paper the optimization of a multi-site, multi-period, and multi-product planning problem with sequence-dependent changeovers, which is modeled as a mixed-integer linear programming (MILP) problem. Industrial instances of this problem require the planning of a number of production and distribution sites over a time span of several months. Temporal and spatial Lagrangean decomposition schemes can be useful for solving these types of large-scale production planning problems. In this paper we present a theoretical result on the relative size of the duality gap of the two decomposition alternatives. We also propose a methodology for exploiting the economic interpretation of the Lagrange multipliers to speed the convergence of numerical algorithms for solving the temporal and spatial Lagrangean duals. The proposed methods are applied to the multi-site multi-period planning problem in order to illustrate their computational effectiveness.     

Energy, water and process technologies integration for the simultaneous production of ethanol and food from the entire corn plant

This paper presents simultaneous integration of different technologies such as the traditional dry-grind process to obtain ethanol from grain with the gasification of the corn stover followed by either syngas fermentation or catalytic mixed alcohols synthesis. The optimal integrated process when using the entire corn plant (18 kg/s of grain and 10.8 kg/s of stover) is the one in which the dry-grind technology to process corn grain is integrated with the catalytic path for the corn stover due to the improved integration of energy, requiring only 17 MW of energy, 50 MW of cooling and 1.56 gal/gal of freshwater, for an ethanol production cost of 1.22 $/gal. However, the production cost decreases as we only use stover to produce ethanol, while the grain is used for food due to the lower cost of the stover and the more favorable energy balance of the ethanol production process from gasification.     

A multiscale decomposition method for the optimal planning and scheduling of multi-site continuous multiproduct plants

This paper addresses the solution of simultaneous scheduling and planning problems in a production–distribution network of continuous multiproduct plants that involves different temporal and spatial scales. Production planning results in medium and long-term decisions, whereas production scheduling determines the timing and sequence of operations in the short-term. The production–distribution network is made up of several production sites distributing to different markets. The planning and scheduling model has to include spatial scales that go from a single production unit within a site, to a geographically distributed network. We propose to use two decomposition methods to solve this type of problems. One method corresponds to the extension of the bi-level decomposition of Erdirik-Dogan and Grossmann (2008) to multi-site, multi-market networks. A second method is a novel hybrid decomposition method that combines bi-level and spatial Lagrangean decomposition methods. We present four case studies to study the performance of the full space planning and scheduling model, the bi-level decomposition, and the bi-level Lagrangean method in profit maximization problems. Numerical results indicate that in large-scale problems, decomposition methods outperform the full space solution and that as problem size increases the hybrid decomposition method becomes faster than the bi-level decomposition alone.     

Global superstructure optimization for the design of integrated process water networks

We propose a general superstructure and a model for the global optimization for integrated process water networks. The superstructure consists of multiple sources of water, water‐using processes, wastewater treatment, and pre‐treatment operations. Unique features are that all feasible interconnections are considered between them and multiple sources of water can be used. The proposed model is formulated as a nonlinear programing (NLP) and as a mixed integer nonlinear programing (MINLP) problem for the case when 0–1 variables are included for the cost of piping and to establish optimal trade‐offs between cost and network complexity. To effectively solve the NLP and MINLP models to global optimality we propose tight bounds on the variables, which are expressed as general equations. We also incorporate the cut proposed by Karuppiah and Grossmann to significantly improve the strength of the lower bound for the global optimum. The proposed model is tested on several examples. © 2010 American Institute of Chemical Engineers AIChE J, 2011     

Stochastic inventory management for tactical process planning under uncertainties: MINLP models and algorithms

We address in this article the mid‐term planning of chemical complexes with integration of stochastic inventory management under supply and demand uncertainty. By using the guaranteed service approach to model time delays in the flows inside the network, we capture the stochastic nature of the supply and demand variations, and develop an equivalent deterministic optimization model to minimize the production, feedstock purchase, cycle inventory, and safety stock costs. The model determines the optimal purchases of the feedstocks, production levels of the processes, sales of final products, and safety stock levels of all the chemicals. We formulate the model as a mixed‐integer nonlinear program with a nonconvex objective function and nonconvex constraints. To solve the global optimization problem with modest computational times, we exploit some model properties and develop a tailored branch‐and‐refine algorithm based on successive piecewise linear approximation. Five industrial‐scale examples with up to 38 processes and 28 chemicals are presented to illustrate the application of the model and the performance of the proposed algorithm. © 2010 American Institute of Chemical Engineers AIChE J, 2011     

Mono‐Estolide Synthesis from trans‐8‐Hydroxy‐Fatty Acids by Lipases in Solvent‐Free Media and Their Physical Properties

Pseudomonas aeruginosa 42A2 is known to produce two hydroxy‐fatty acids, 10(S)‐hydroxy‐8(E)‐octadecenoic and 7,10(S,S)‐dihydroxy‐8(E)‐octadecenoic acids, when cultivated in a mineral medium using oleic acid as a single carbon source. These compounds were purified, 91 and 96 % respectively, to produce two new families of estolides: trans‐8‐estolides and saturated estolides from the monohydroxylated monomer. trans‐8‐estolides were produced by three different lipases (Novozym 435, Lipozyme RM IM and Lipozyme TL IM) with reaction yields between 68.4 ± 2.1 and 94.7 ± 2.4 % in a solvent‐free medium at 80 °C in 168 h under vacuum. Novozym 435 was found to be the most efficient biocatalyst for both hydroxy‐fatty acids with reaction yields of 71.7 ± 2.3 and 94.7 ± 2.4 %, respectively. Moreover, saturated estolides were also produced from a saturated 10(S)‐hydroxy‐8(E)‐octadecenoic. These estolides were chemically and enzymatically synthesized with Novozym 435, under the previous described reaction conditions with yields of 60.7 ± 2.1 and 71.2 ± 2.3 % respectively. Finally, viscosity, glass transition temperature, decomposition temperatures and enthalpies were determined to characterize both types of estolides. Thermal applications for both types of polyesters were improved since glass transition temperatures were lowered and decomposition temperatures were increased, with respect to their corresponding substrates.     

Numerical simulation of mass transport in a filter press type electrochemical reactor FM01-LC: Comparison of predicted and experimental mass transfer coefficient

This paper studies flow characteristics and their effect on local mass transfer rate to a flat plate electrode in a FM01-LC electrochemical reactor. 3D reactor simulations under limiting current and turbulent flow conditions were performed using potassium ferro-ferricyanide electrochemical system with sodium sulfate as supporting electrolyte. The model consists of mass-transport equations coupled to hydrodynamic solution obtained from Reynolds-averaged Navier–Stokes equations using standard k–? turbulence model, where the average velocity field, the turbulence level given by the eddy kinetic energy and the turbulent viscosity of the hydrodynamic calculation were used to evaluate the convection, turbulent diffusion and the concentration wall function. The turbulent mass diffusivity was evaluated by Kays–Crawford equation using heat and mass transfer analogies, while wall functions, for mass transport, were adapted from Launder–Spalding equations. Simulation results describe main flow properties, concentration profiles throughout the entire volume of the reactor and local diffusion flux over the electrode. Overall mass transfer coefficients estimated by simulation, without fitting parameters, agree closely with experimental coefficients determined from limiting current measurements (1.85% average error) for Re between 187 and 1407.