Ensemble learning from ensemble docking: revisiting the optimum ensemble size problem.

Despite considerable advances obtained by applying machine learning approaches in protein-ligand affinity predictions, the incorporation of receptor flexibility has remained an important bottleneck. While ensemble docking has been used widely as a solution to this problem, the optimum choice of receptor conformations is still an open question considering the issues related to the computational cost and false positive pose predictions. Here, a combination of ensemble learning and ensemble docking is suggested to rank different conformations of the target protein in light of their importance for the final accuracy of the model.

Online Solid-Phase Extraction of Prometon and Prometryne Using MIL-101(Cr) as Sorbent before Gas Chromatographic Analysis: A Computational and Experimental Study and Comparison between Splitless and PTV Inlets.

In this study, prometryne and prometon were extracted and preconcentrated from aqueous media using an online solid-phase extraction-thermal desorption method coupled with gas chromatography-flame ionization detector (GC-FID), equipped with two different inlets: split and programmable temperature vaporizer (PTV). For this purpose, the applicability of Tenax and a metal-organic framework were investigated as solid-phase sorbents. Several effective parameters on the extraction efficiency, such as the amount of sorbent, sample volume, sample pH and thermal desorption procedure were optimized.

The Potential Role of Curcumin in Modulating the Master Antioxidant Pathway in Diabetic Hypoxia-Induced Complications.

Oxidative stress is the leading player in the onset and development of various diseases. The Keap1-Nrf2 pathway is a pivotal antioxidant system that preserves the cells' redox balance. It decreases inflammation in which the nuclear trans-localization of Nrf2 as a transcription factor promotes various antioxidant responses in cells.

On-Site Detection of Carcinoembryonic Antigen in Human Serum.

Real-time connectivity and employment of sustainable materials empowers point-of-care diagnostics with the capability to send clinically relevant data to health care providers even in low-resource settings. In this study, we developed an advantageous kit for the on-site detection of carcinoembryonic antigen (CEA) in human serum. CEA sensing was performed using cellulose-based lateral flow strips, and colorimetric signals were read, processed, and measured using a smartphone-based system.

An Overview of the Challenges and Progress of Synthesis, Characterization and Applications of Plugged SBA-15 Materials for Heterogeneous Catalysis.

A new generation of SBA-15, plugged SBA-15, was initially synthesized in 2002 using extra silica precursors (Si/organic template molar ratios ≈ 80-140) in the gel mixture. The plugged SBA-15 materials possess short cylinders (length ≈ 20-100 nm), which are connected to neighbors by constricted entrances (windows) through the central axis. The gas adsorption-desorption isotherms of plugged SBA-15 materials present unique hysteresis loop Type H5 classification identified by IUPAC in 2015, which is related to certain pore structures containing open and plugged mesopores.

Preparation and characterization of nano MnO-CaLs as a green catalyst for oxidation of styrene.

Hydrophilic nano MnO is shown to have significant stability in aqueous media for oxidation of styrene. Different catalysts have been used to synthesis styrene oxide, but MnO-CaL is considered the efficient and selective catalyst to produce styrene oxide. In general, this paper reported especial strategy for synthesis of novel nano MnO that stabilized with oleic acid in chloroform and changing nature of its stabilizer by exchanging oleic acid with lignosulfunate and displays its catalytic activity towards selective oxidation of styrene.

Identification of key stabilizing interactions of amyloid-β oligomers based on fragment molecular orbital calculations on macrocyclic β-hairpin peptides.

Analyzing the electronic states and inter-/intra-molecular interactions of amyloid oligomers expand our understanding of the molecular basis of Alzheimer's disease and other amyloid diseases. In the current study, several high-resolution crystal structures of oligomeric assemblies of Aβ-derived peptides have been studied by the ab initio fragment molecular orbital (FMO) method. The FMO method provides comprehensive details of the molecular interactions between the residues of the amyloid oligomers at the quantum mechanical level.

Toward Smart Diagnostics in a Pandemic Scenario: COVID-19.

The incredible spread rate of coronavirus disease 2019 (COVID-19) outbreak has shocked the world. More than ever before, this dramatic scenario proved the significance of diagnostics as a cornerstone to make life-saving decisions. In this context, novel diagnostics that generates smart data leading to superior strategies for treatment, control, surveillance, prediction, prevention, and management of pandemic diseases is vital.

(Nano)tag-antibody conjugates in rapid tests.

Antibodies (Abs) are naturally derived materials with favorable affinity, selectivity, and fast binding kinetics to the respective antigens, which enables their application as promising recognition elements in the development of various types of biosensors/bioassays, especially in rapid tests. These tests are low-cost and easy-to-use biosensing devices with broad applications including medical or veterinary diagnostics, environmental monitoring and industrial usages such as safety and quality analysis in food, providing on-site quick monitoring of various analytes, making it possible to save analysis costs and time. To reach such features, the conjugation of Abs with various nanomaterials (NMs) as tags is necessary, which range from conventional gold nanoparticles to other nanoparticles recently introduced, where magnetic, plasmonic, photoluminescent, or multi-modal properties play a critical role in the overall performance of the analytical device.

Preparation of two amide-bonded stationary phases and comparative evaluation under mixed-mode chromatography.

In this work, the conventional reactions were used to functionalize the silica surface with amide and hydrocarbon chain groups affording two different mixed-mode stationary phases (Sil-amide-C11 and Sil-C12-amide). The prepared stationary phases were analyzed by elemental analysis and thermogravimetric analysis. The retention of benzene, phenol, pyridine, and aniline was investigated and compared with synthesized and commercial columns, and this led to prove the existence of different interactions on the synthesized stationary phases.

ET-score: Improving Protein-ligand Binding Affinity Prediction Based on Distance-weighted Interatomic Contact Features Using Extremely Randomized Trees Algorithm.

The molecular docking simulation is a key computational tool in modern drug discovery research that its predictive performance strongly depends on the employed scoring functions. Many recent studies have shown that the application of machine learning algorithms in the development of scoring functions has led to a significant improvement in docking performance. In this work, we introduce a new machine learning (ML) based scoring function called ET-Score, which employs the distance-weighted interatomic contacts between atom type pairs of the ligand and the protein for featurizing protein-ligand complexes and Extremely Randomized Trees algorithm for the training process.

Treatment of nano-oil polluted wastewater in an expanded bed adsorption column based on carboxymethyl cellulose-cellulose-nickel composite beads.

In the present work, spherical carboxymethyl cellulose-cellulose-nickel (CMC-C-Ni) composite beads as novel adsorbent was synthesized to make a stable expanded bed adsorption (EBA) column for the treatment of the oily wastewater collected from the downstream of rapeseed industry. The morphology and structure of the CMC-C-Ni composite beads were studied by scanning electron microscopy (SEM) and optical microscope. The SEM images revealed that the synthesized composite beads were spherical with porous structure.

Investigation of simultaneous multiple UV filters degradation efficiency of plasmonic AgAgCl photocatalyst in the aquatic environment under sunlight irradiation.

UV filters as an important class of emerging organic pollutants are continuously released into and transported between the aquatic environments. So, the removal of these compounds from aquatic environments is of great importance. This study was conducted to evaluate the simultaneous photodegradation of three widely used UV filter compounds (4-methylbenzylidene camphor, 2-ethylhexyl 4-(dimethylamino) benzoate, ethylhexyl methoxycinnamate), in an aqueous environment under sunlight and Ag@AgCl photocatalyst integrated with plasmonic effect.

Fluorescence resonance energy transfer-thermal lens spectrometry (FRET-TLS) as molecular counting of methamphetamine.

A novel and sensitive approach has been presented for the determination of methamphetamine (METH) based on fluorescence resonance energy transfer-thermal lens spectrometry (FRET-TLS). Due to the affinity of fluorescein molecules to the surface of AuNPs through the electrostatic interaction and thereby caused reduction of the distance between fluorescein and AuNPs, the best way for de-excitation of excited fluorescein is FRET. The energy absorbed by fluorescein transferred to AuNPs causes enhancement of the thermal lens effect.

Photophysical Properties and Kinetic Studies of 2-Vinylpyridine-Based Cycloplatinated(II) Complexes Containing Various Phosphine Ligands.

A series of cycloplatinated(II) complexes with general formula of [PtMe(Vpy)(PR)], Vpy = 2-vinylpyridine and PR = PPh (); PPhMe (); PPhMe (), were synthesized and characterized by means of spectroscopic methods. These cycloplatinated(II) complexes were luminescent at room temperature in the yellow-orange region's structured bands. The PPhMe derivative was the strongest emissive among the complexes, and the complex with PPh was the weakest one.

Superadsorbent FeO-coated carbon black nanocomposite for separation of light rare earth elements from aqueous solution: GMDH-based Neural Network and sensitivity analysis.

A series of nanocomposites adsorbents with different magnetite/carbon black ratios were synthesized by using the co-precipitation method and used for separation of LREEs (Ce, La, and Nd) from aqueous solution. The adsorption efficiency of nanocomposites is strongly dependent on both pH and the loading carbon on nanocomposite. The maximum adsorption capacity (370 mg/g) was reported by nanocomposite with 20% Fe3O4 and 80% carbon in pH 7 for LREE initial concentration of 250 ppm.

Application of [PVI-SOH]NO as a novel polymeric nitrating agent with ionic tags in preparation of high-energetic materials.

In this paper, poly(vinyl imidazole) sulfonic acid nitrate [PVI-SOH]NO was synthesized and fully characterized. Then, [PVI-SOH]NO was applied for the preparation of energetic materials such as 1,1-diamino-2,2-dinitroethene (FOX-7), pentaerythritol tetranitrate (PETN), 1,3,5-trinitro-1,3,5-triazinane (RDX) and trinitrotoluene (TNT). The major advantages of the presented methodology are mild, facile workup, high yields and short reaction times.

Recovery of Persipeptides from Fermentation Broth by Enhanced Adsorption.

Background: Drug discovery process is growing considerably due to the noteworthy resource of natural products. Persipeptides A and B are cyclopeptide antibiotics, which are produced by UTMC 1154. Although extraction of culture broth with the help of solvent has been optimized previously, no effort for extraction of persipeptides has been done yet.

Enhancmentation of Photo-Thermal Lens of Fluorescence Molecules by Fluorescence Resonance Energy Transfer Mechanism.

The photo-thermal lens technique is based on the measurement of the gradient temperature that is produced in an illuminated sample by laser beam as a result of non-radiative relaxation. The sensitivity of photo-thermal lens is higher than conventional absorption techniques, due to the direct measurement of absorbed energy. However, the main drawback of the photo-thermal lens technique is the inability to measure molecules that release their excess energy of absorption in the form of radiation relaxation.

Potential effective inhibitory compounds against Prostate Specific Membrane Antigen (PSMA): A molecular docking and molecular dynamics study.

One of the most prevalent cancers in men is prostate cancer and could be managed with immunotoxins or antibody treatment. Because of the substantial rise of the Prostate-Specific Antigen and the Prostate-Specific Membrane Antigen (PSMA), cancer vaccination should be rendered with these antigens. Through pharmacodynamic experiments in a library of natural compounds from ZINC database, the current research sought to identify compounds that could suppress PSMA protein.

Phytochemicals toward Green (Bio)sensing.

Because of numerous inherent and unique characteristics of phytochemicals as bioactive compounds derived from plants, they have been widely used as one of the most interesting nature-based compounds in a myriad of fields. Moreover, a wide variety of phytochemicals offer a plethora of fascinating optical and electrochemical features that pave the way toward their development as optical and electrochemical (bio)sensors for clinical/health diagnostics, environmental monitoring, food quality control, and bioimaging. In the current review, we highlight how phytochemicals have been tailored and used for a wide variety of optical and electrochemical (bio)sensing and bioimaging applications, after classifying and introducing them according to their chemical structures.

Nanopaper-based screen-printed electrodes: a hybrid sensing bioplatform for dual opto-electrochemical sensing applications.

Given the importance of developing easy-to-use, disposable, affordable, and portable hybrid opto-electrochemical sensing devices, for the first time, we have developed a nanopaper-based screen-printed electrode (SPE) by taking advantage of the high optical transparency, affordability, biocompatibility, printability, flexibility, and other unrivaled physicochemical properties of bacterial cellulose (BC) nanopaper in screen printing technology. To fabricate the BC-SPE platform, a screen-printed three-electrode system was transferred onto the dried film of a pre-printed BC nanopaper-based substrate. Because of the optical transparency of the BC nanopaper, the fabricated BC-SPE platform can be used as a hybrid sensing platform for simultaneous optical and electrochemical (bio)sensing applications.

Recent advancements in the production of rhamnolipid biosurfactants by .

Rhamnolipid (RL) biosurfactant which is produced by species is one of the most effective surface-active agents investigated in the literature. Over the years, many efforts have been made and an array of techniques has been developed for the isolation of RL produced strains as well as RL homolog characterization. Reports show that RL productivity by the best-known producer, , is very diverse, from less than 1 gr/l to more than 200 g L.

Carbon dots doped by nitrogen and sulfur for dual-mode colorimetric and fluorometric determination of Fe and histidine and intracellular imaging of Fe in living cells.

The first dual-modality highly intensive fluorescent and colorimetric nanoprobe for Fe ions and histidine is reported. The carbon dots doped by nitrogen and sulfur (N,S-CDs) prepared by the one-pot hydrothermal method have an excitation/emission wavelength of 320/420 nm with 56% quantum yield. N,S-CDs exhibit strong visible fluorescence with high stability at pH ~ 7.

Recent progress to construct calixarene-based polymers using covalent bonds: synthesis and applications.

The combination of supramolecular chemistry and polymer sciences creates a great possibility to afford calixarene-based polymers offering unique features and applications. The enhancement of calixarene's versatility in this manner has made chemists better able to achieve different objectives in host-guest chemistry. The calixarene-based polymers can be divided into covalent polymers and supramolecular polymers regarding the interactions.