Stochastic molecular descriptors for polymers. 4. Study of complex mixtures with topological indices of mass spectra spiral and star networks: The blood proteome case

The Quantitative Structure-Property Relationships (QSPRs) based on Graph or Network Theory are important for predicting the properties of polymeric systems. In the three previous papers of this series (Polymer 45 (2004) 3845-3853; Polymer 46 (2005) 2791-2798; and Polymer 46 (2005) 6461-6473) we focused on the uses of molecular graph parameters called topological indices (TIs) to link the structure of polymers with their biological properties. However, there has been little effort to extend these TIs to the study of complex mixtures of artificial polymers or biopolymers such as nucleic acids and proteins. In this sense, Blood Proteome (BP) is one of the most important and complex mixtures containing protein polymers. For instance, outcomes obtained by Mass Spectrometry (MS) analysis of BP are very useful for the early detection of diseases and drug-induced toxicities. Here, we use two Spiral and Star Network representations of the MS outcomes and defined a new type of TIs. The new TIs introduced here are the spectral moments (π_k) of the stochastic matrix associated to the Spiral graph and describe non-linear relationships between the different regions of the MS characteristic of BP. We used the MARCH-INSIDE approach to calculate the π_k(SN) of different BP samples and S2SNet to determine several Star graph TIs. In the second step, we develop the corresponding Quantitative Proteome-Property Relationship (QPPR) models using the Linear Discriminant Analysis (LDA). QPPRs are the analogues of QSPRs in the case of complex biopolymer mixtures. Specifically, the new QPPRs derived here may be used to detect drug-induced cardiac toxicities from BP samples. Different Machine Learning classification algorithms were used to fit the QPPRs based on π_k(SN), showing J48 decision tree classifier to have the best performance. These results suggest that the present approach captures important features of the complex biopolymers mixtures and opens new opportunities to the application of the idea supporting classic QSPRs in polymer sciences.     

Color and COD retention by nanofiltration membranes

In the present study the application of the nanofiltration process was investigated mainly in the retention ofcolor and chemical oxygen demand (COD) present in textile industry wastewater. Nanofiltration experiments were carried out in a pilot unit, operating in crossflow. Three different types of spiral wound membranes, DK 1073, NF 45 and MPS 31 were used simultaneously in the same unit. The results of the tests showed that for color retention, the values were around 99% for the DK 1073 and NF 45 membranes and the 87% for COD retention for the DK 1073. The permeate flux for the different wastewaters varied from 30.5 to 70 L/h.m². Fouling was observed in all membranes due to the accumulation of molecular species close to the filtering surface. The process was efficient and promising for the reuse of wastewater from this type of industry.     

A modified consensus approach to mutagenesis inverts the cofactor specificity of Bacillus stearothermophilus lactate dehydrogenase

Lactate dehydrogenase from Bacillus stearothermophilus is specific for NAD+. There have been several attempts to alter the cofactor specificity of this enzyme, but these have yielded enzymes with relatively low activities that still largely prefer NAD+. A modified consensus approach was used to create a library of phylogenetically preferred amino acids situated near the cofactor binding site, and variants were screened for their ability to utilize NMN+. A triple mutant (Mut31) was discovered that proved to be more catalytically efficient than wild-type. Mut31 was also better at utilizing NAD+ than the wild-type enzyme and was weakly active with NADP+ and NMN+. An analysis of single amino acid substitutions suggested that all three mutations worked in a concerted fashion to yield robust cofactor utilization. When two previously identified amino acid substitutions were introduced into the Mut31 background, the resultant quintuply substituted enzyme not only utilized NADP+ far better than the wild-type enzyme, it actually inverted its preference for NAD+ and NADP+.     

Thermal dehydrochlorination of pure PVC polymer: Part I—thermal degradation kinetics by thermogravimetric analysis

Thermal degradation of PVC occurs in two stages, with each stage subdivided into two substages. The first refers to the dehydrochlorination, where hydrochloric acid is formed, and giving polyene structures. Hitherto, the degradation mechanism and action of hydrochloric acid as a catalyst during the dehydrochlorination stage are poorly known. Recently, the importance of the tacticity has gained attention for its influence on the dehydrochlorination mechanism. The present work focused on the dehydrochlorination stage, studying the molecular structure by FTIR analysis and the kinetic parameters by TGA analysis in Nitrogen atmosphere, based on three mathematical methods: Friedman, Kissinger, and Flynn-Wall-Ozawa. The sample was a pure homopolymer obtained by suspension polymerization. The dehydrochlorination kinetics follows a first order reaction model and occurs by nucleation and growth. The dehydrochlorination begins with the loss of very labile chlorine atoms present in defective and isotactic molecular segments. The formed HCl acts as a catalyst in the degradation. Following 40% conversion, a drop in Ea is observed. After that, chlorine atoms present in syndiotactic and atactic sequences, are released and, added to the large number of polyene chain sequences, and an increase in Ea is observed up to 60% conversion, where the dehydrochlorination stage is concluded.     

Estimating vulnerability to risks: an application in a biofuel supply chain

In the present work, we propose a theoretical model to identify and prioritize risks involved in a biofuel supply chain. We adopt a set of indicators associated with determinant factors of the supply chain to identify risks that are characterized through a risk matrix. We consider the five largest world biodiesel producers and included China due to its global market importance and potential impacts of its growth on the environment and society. To determine the impacts and the probability of occurrence of risks, we use the Canberra distance, as metrics. To facilitate the analysis and interpretation, a convenient manner is to express the results in terms of matrices. To exemplify the potentiality of the scheme and for the sake of simplicity, a more comprehensive discussion is focused on the Brazilian case, restricted to the Technology and Innovation, and Integration, Logistics and Infrastructure determining factors (dimensions) of the biodiesel supply chain. Concerning these determining factors, the Brazilian biodiesel chain shows strong vulnerability when compared with developed and developing countries, despite that the evolution of the data over recent years indicates small improvements in Integration, Logistics and Infrastructure dimension. Although in this work the calculations are restricted to the Canberra distance, the present approach may be applied to other distances to compare or validate the results. This work presents a contribution to model vulnerability to risks, providing to policy makers and stakeholders a tool to design, analyze and improve sustainability system by measuring its risks. The study of the contribution of each indicator suggests corrections to be taken and which indicators should be prioritized.     

A class of aggregation functions encompassing two-dimensional OWA operators

In this paper we prove that, under suitable conditions, Atanassov’s K_α operators, which act on intervals, provide the same numerical results as OWA operators of dimension two. On one hand, this allows us to recover OWA operators from K_α operators. On the other hand, by analyzing the properties of Atanassov’s operators, we can generalize them. In this way, we introduce a class of aggregation functions - the generalized Atanassov operators - that, in particular, include two-dimensional OWA operators. We investigate under which conditions these generalized Atanassov operators satisfy some properties usually required for aggregation functions, such as bisymmetry, strictness, monotonicity, etc. We also show that if we apply these aggregation functions to interval-valued fuzzy sets, we obtain an ordered family of fuzzy sets.     

A novel induction motor control scheme using IDA-PBC

A new control scheme for induction motors is proposed in the present paper, applying the interconnection and damping assignment-passivity based control （IDA-PBC） method. The scheme is based exclusively on passivity based control, without restricting the input frequency as it is done in field oriented control （FOC）. A port-controlled Hamiltonian （PCH） model of the induction motor is deduced to make the interconnection and damping of energy explicit on the scheme. The proposed controller is validated under computational simulations and experimental tests using an inverter prototype.     

The Stress Response of the Holothurian Central Nervous System: A Transcriptomic Analysis

Injury to the central nervous system (CNS) results in permanent damage and lack of function in most vertebrate animals, due to their limited regenerative capacities. In contrast, echinoderms can fully regenerate their radial nerve cord (RNC) following transection, with little to no scarring. Investigators have associated the regenerative capacity of some organisms to the stress response and inflammation produced by the injury. Here, we explore the gene activation profile of the stressed holothurian CNS. To do this, we performed RNA sequencing on isolated RNC explants submitted to the stress of transection and enzyme dissection and compared them with explants kept in culture for 3 days following dissection. We describe stress-associated genes, including members of heat-shock families, ubiquitin-related pathways, transposons, and apoptosis that were differentially expressed. Surprisingly, the stress response does not induce apoptosis in this system. Other genes associated with stress in other animal models, such as hero proteins and those associated with the integrated stress response, were not found to be differentially expressed either. Our results provide a new viewpoint on the stress response in the nervous system of an organism with amazing regenerative capacities. This is the first step in deciphering the molecular processes that allow echinoderms to undergo fully functional CNS regeneration, and also provides a comparative view of the stress response in other organisms.     

Identification of Potential New Aedes aegypti Juvenile Hormone Inhibitors from N-Acyl Piperidine Derivatives: A Bioinformatics Approach

Aedes aegypti mosquitoes transmit several human pathogens that cause millions of deaths worldwide, mainly in Latin America. The indiscriminate use of insecticides has resulted in the development of species resistance to some such compounds. Piperidine, a natural alkaloid isolated from Piper nigrum, has been used as a hit compound due to its larvicidal activity against Aedes aegypti. In the present study, piperidine derivatives were studied through in silico methods: pharmacophoric evaluation (PharmaGist), pharmacophoric virtual screening (Pharmit), ADME/Tox prediction (Preadmet/Derek 10.0^®), docking calculations (AutoDock 4.2) and molecular dynamics (MD) simulation on GROMACS-5.1.4. MP-416 and MP-073 molecules exhibiting ΔG binding (MMPBSA −265.95 ± 1.32 kJ/mol and −124.412 ± 1.08 kJ/mol, respectively) and comparable to holo (ΔG binding = −216.21 ± 0.97) and pyriproxyfen (a well-known larvicidal, ΔG binding= −435.95 ± 2.06 kJ/mol). Considering future in vivo assays, we elaborated the theoretical synthetic route and made predictions of the synthetic accessibility (SA) (SwissADME), lipophilicity and water solubility (SwissADME) of the promising compounds identified in the present study. Our in silico results show that MP-416 and MP-073 molecules could be potent insecticides against the Aedes aegypti mosquitoes.