Modeling, inference and optimization of regulatory networks based on time series data

In this survey paper, we present advances achieved during the last years in the development and use of OR, in particular, optimization methods in the new gene-environment and eco-finance networks, based on usually finite data series, with an emphasis on uncertainty in them and in the interactions of the model items. Indeed, our networks represent models in the form of time-continuous and time-discrete dynamics, whose unknown parameters we estimate under constraints on complexity and regularization by various kinds of optimization techniques, ranging from linear, mixed-integer, spline, semi-infinite and robust optimization to conic, e.g., semi-definite programming. We present different kinds of uncertainties and a new time-discretization technique, address aspects of data preprocessing and of stability, related aspects from game theory and financial mathematics, we work out structural frontiers and discuss chances for future research and OR application in our real world.     

Preliminary Structure–Activity Relationship Study of the MMV Pathogen Box Compound MMV675968 (2,4-Diaminoquinazoline) Unveils Novel Inhibitors of Trypanosoma brucei brucei

New drugs are urgently needed for the treatment of human African trypanosomiasis (HAT). In line with our quest for novel inhibitors of trypanosomes, a small library of analogs of the antitrypanosomal hit (MMV675968) available at MMV as solid materials was screened for antitrypanosomal activity. In silico exploration of two potent antitrypanosomal structural analogs (7-MMV1578647 and 10-MMV1578445) as inhibitors of dihydrofolate reductase (DHFR) was achieved, together with elucidation of other antitrypanosomal modes of action. In addition, they were assessed in vitro for tentative inhibition of DHFR in a crude trypanosome extract. Their ADMET properties were also predicted using dedicated software. Overall, the two diaminoquinazoline analogs displayed approximately 40-fold and 60-fold more potency and selectivity in vitro than the parent hit, respectively (MMV1578445 (10): IC₅₀ = 0.045 µM, SI = 1737; MMV1578467 (7): IC₅₀ = 0.06 µM; SI = 412). Analogs 7 and 10 were also strong binders of the DHFR enzyme in silico, in all their accessible protonation states, and interacted with key DHFR ligand recognition residues Val32, Asp54, and Ile160. They also exhibited significant activity against trypanosome protein isolate. MMV1578445 (10) portrayed fast and irreversible trypanosome growth arrest between 4–72 h at IC₉₉. Analogs 7 and 10 induced in vitro ferric iron reduction and DNA fragmentation or apoptosis induction, respectively. The two potent analogs endowed with predicted suitable physicochemical and ADMET properties are good candidates for further deciphering their potential as starting points for new drug development for HAT.     

Cytotoxicity of Silica Nanoparticles with Transcaucasian Nose-Horned Viper, <Emphasis Type="Italic">Vipera ammodytes transcaucasiana</Emphasis>, Venom on U87MG and SHSY5Y Neuronal Cancer Cells

Highly bioactive compounds of the snake venom make them particular sources for anticancer agent development. They contain very rich peptide-protein structures. Therefore, they are very susceptible to environmental conditions such as temperature, pH, and light. In this study, Vipera ammodytes transcaucasiana venom was encapsulated in PAMAM-G4 dendrimer by sol-gel method in order to prevent degradation of venom contents from the environmental conditions. For this purpose, nanoparticles were prepared by sol-gel methodology and SEM analyses were performed. U87MG and SHSY5Y neuronal cancer cell lines were treated with different concentrations of venom-containing nanoparticles and cytotoxicity was determined by MTT assay. IC₅₀ values of nanoparticles with snake venom were calculated as 37.24 and 44.64 μg/ml for U87MG and SHSY5Y cells, respectively. The IC₅₀ values of nanoparticles with snake venom were calculated as 10.07 and 7.9 μg/ml for U87MG and SHSY5Y cells, respectively. As a result, nanoparticles with V. a. transcaucasiana venom showed remarkably high cytotoxicity. Encapsulation efficiency of nanoparticles with 1 mg/ml snake venom was determined as %67 via BCA? protein analysis. In conclusion, this method is found to be convenient and useful for encapsulating snake venom as well as being suitable for drug delivery systems.     

Electrochemical Detection of Epinephrine Based on a Screen-printed Electrode Modified with NiO−ERGO Nanocomposite Film

This study presents a new electrochemical sensor (NiO−ERGO/SPE) for sensitive and selective detection of epinephrine (EPI) on the screen-printed electrode (SPE) which is modified with a nanocomposite film consisting of electrochemically reduced graphene oxide and NiO nanoparticles. After surface functionalization, structural and electrochemical characterization of NiO−ERGO film, DPV signals of NiO−ERGO/SPE towards the oxidation of EPI exhibited a linear correlation in the concentration range of 0.025 μM to 175 μM with a detection limit of 0.015 μM, which reveals NiO−ERGO film is manifested a good electrocatalytic activity for EPI detection compared with the previous reports. The selectivity of NiO−ERGO film was also tested on a very wide scale of possible interferents (ascorbic acid, uric acid, dopamine, lactic acid, phenylalanine, tyrosine, tryptophan, Li⁺, Na⁺, K⁺, Ca²⁺, and Zn²⁺). Moreover, to evaluate the applicability of the proposed sensor for real sample analysis, NiO−ERGO/SPE was successfully utilized for the determination of EPI in pharmaceutical samples.     

Preparation and characterization of W/O/W type double emulsion containing PGPR–lecithin mixture as lipophilic surfactant

The objective of this study is to produce double emulsion by combining polyglycerol polyricinoleate (PGPR) with lecithin as lipophilic surfactant. Although lecithin alone produced only oil-in-water type emulsion, the mixture of lecithin and PGPR could produce water-in-oil type emulsion as well. Moreover, different emulsification treatments were applied to study the influence of homogenization methods on the physicochemical characteristics. The obtained double emulsions were compared in terms of stability and droplet size. It was found that the homogenization method influenced the physiochemical characteristics of the double emulsion and the most stable double emulsion with the smallest droplet size was obtained by high-speed homogenization method.     

Relaxation and Miscibility of the Blends of a Poly (Ether Imide) (Ultem™) and a Phenol-A-Based Copolyester (Ardel™) by Inverse Gas Chromatography

Inverse gas chromatography (IGC) was used to analyze the secondary transition temperatures and the miscibility of binary mixtures of poly (ether imide) (Ultem™) and a copolyester of bisphenol-A with terephthalic and isophthalic acids (50/50) (Ardel™) in three compositions (25/50, 50/50 and 75/25). Retention diagrams of the mixtures of Ultem™ and Ardel™ for n-nonane, n-decane, n-butyl acetate and isoamyl acetate were obtained at temperatures between 60 and 285 °C. Second-order transition temperatures of the mixtures were determined according to the slope change in retention diagrams of the solvents. The glass transition temperatures of the mixtures suggested the miscibility of the polymers. Polymer–polymer interaction parameters of binary mixtures of the polymers were determined at temperatures between 260 and 285 °C by Flory–Huggins theory. The polymer–polymer interaction parameters were dependent on the solvent used. The small values of polymer–polymer interaction parameters close to zero suggest some weak interactions between the polymers in the mixture. It was concluded that it was possible to obtain more meaningful information related to the interactions of polymers in a mixture from IGC measurements, if binary polymer–solvent interaction parameters of the used solvent probes were around 0.5.

     

Modeling company failure: a longitudinal study of Turkish banks

Determining the factors related to the financial failure of a company is important. In this paper, we extend literature on bank failure prediction by modelling bank failures in Turkey from 1998 to 2000 using three statistical models combined with a principal component analysis on financial ratios. The three statistical models employed are a logistic regression, a logistic regression that takes serial correlation into account via generalized estimating equations and a marginalized transition model (MTM). Time and financial ratios that are related with capital adequacy and profitability, risk, non-interest income and Fx assets to Fx liabilities are found to be significant in classifying failed banks. Each of our methods achieves a correct classification rate of 93.3%. Among the three models, MTM, which is the soundest model in terms of statistical assumptions, shows slightly better model fit properties.     

Synthesis of boron carbon nitride layers for the adsorption of hazardous basic dye from aqueous solutions

Research on Chemical Intermediates - Many researchers have investigated the usage of carbonaceous materials as adsorbents. In this study, boron carbon nitride (BCN) was synthesized using boric acid...     

Isolation and Structural Elucidation of Compounds from Pleiocarpa bicarpellata and Their In Vitro Antiprotozoal Activity

Species of the genus Pleiocarpa are used in traditional medicine against fever and malaria. The present study focuses on the isolation and identification of bioactive compounds from P. bicarpellata extracts, and the evaluation of their antiprotozoal activity. Fractionation and isolation combined to LC-HRMS/MS-based dereplication provided 16 compounds: seven indole alkaloids, four indoline alkaloids, two secoiridoid glycosides, two iridoid glycosides, and one phenolic glucoside. One of the quaternary indole alkaloids (7) and one indoline alkaloid (15) have never been reported before. Their structures were elucidated by analysis of spectroscopic data, including 1D and 2D NMR experiments, UV, IR, and HRESIMS data. The absolute configurations were determined by comparison of the experimental and calculated ECD data. The extracts and isolated compounds were evaluated for their antiprotozoal activity towards Trypanosoma brucei rhodesiense, Trypanosoma cruzi, Leishmania donovani, and Plasmodium falciparum, as well as for their cytotoxicity against rat skeletal myoblast L6 cells. The dichloromethane/methanol (1:1) root extract showed strong activity against P. falciparum (IC₅₀ value of 3.5 µg/mL). Among the compounds isolated, tubotaiwine (13) displayed the most significant antiplasmodial activity with an IC₅₀ value of 8.5 µM and a selectivity index of 23.4. Therefore, P. bicarpallata extract can be considered as a source of indole alkaloids with antiplasmodial activity.     

An investigation of frequently consumed edible oils in Turkey in terms of omega fatty acids

The fatty acid profiles of frequently consumed oils and crops cultivated in Turkey were investigated in regard to omega fatty acids. Analyses were carried out on commercially sold oils, sunflower, olive, and fish oils, and oils extracted from fatty seeds of hazelnut, walnut, olive, sunflower, poppy, sesame, and pumpkin, and butter produced in Turkey. Hazelnut and olive oils were found to be rich in omega-9 (oleic acid 18:1), walnut, poppy seed, sesame, and pumpkin seed were rich in omega-6 (linoleic acid 18:2), and butter was rich in short chain fatty acids and omega-9. Fish oil, from mackerel, was the richest in omega-3 fatty acids and fatty acid diversity. There were some alterations between commercially sold oils and oils extracted from seeds in regard to fatty acid percentages and variety.