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Molecules, Vol. 26, Pages 7254: Parsimonious Optimization of Multitask Neural Network Hyperparameters
In this study, we compared four of the most widely used approaches for tuning hyperparameters, namely, grid search, random search, tree-structured Parzen estimator, and genetic algorithms on three multitask QSAR datasets. We mainly focused on parsimonious optimization and thus not only on the performance of neural networks, but also the computational time that was taken into account. Furthermore, since the optimization approaches do not directly provide information about the influence of hyperparameters, we applied experimental design strategies to determine their effects on the neural network performance. We found that ge...
Source: Molecules - November 30, 2021 Category: Chemistry Authors: Cecile Valsecchi Viviana Consonni Roberto Todeschini Marco Emilio Orlandi Fabio Gosetti Davide Ballabio Tags: Article Source Type: research

Molecules, Vol. 25, Pages 2859: Pomegranate Peel as Suitable Source of High-Added Value Bioactives: Tailored Functionalized Meat Products
orenzo In the last few years, the consumer’s concern with the relationship between health and diet has led to the search of foods with functional properties beyond the nutritional. In this framework, the consumption of pomegranate has increased due to their sensorial attributes and remarkable amounts of bioactive compounds, which generate, at the same time, huge amounts of by-products. A search in the Scopus database for the last 10 years has revealed the rising interest in pomegranate peel (PP), the main residue from this fruit. The meat industry is a food sector that has had to search for new alternativ...
Source: Molecules - June 20, 2020 Category: Chemistry Authors: Patricia Gull ón Gonzalo Astray Beatriz Gull ón Igor Tomasevic Jos é M. Lorenzo Tags: Review Source Type: research

Molecules, Vol. 26, Pages 1134: Establishing an Analogue Based in Silico Pipeline in the Pursuit of Novel Inhibitory Scaffolds against the SARS Coronavirus 2 Papain-Like Protease
ahman The ongoing coronavirus pandemic has been a burden on the worldwide population, with mass fatalities and devastating socioeconomic consequences. It has particularly drawn attention to the lack of approved small-molecule drugs to inhibit SARS coronaviruses. Importantly, lessons learned from the SARS outbreak of 2002-2004, caused by severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1), can be applied to current drug discovery ventures. SARS-CoV-1 and SARS-CoV-2 both possess two cysteine proteases, the main protease (Mpro) and the papain-like protease (PLpro), which play a significant role in facilitating vi...
Source: Molecules - February 20, 2021 Category: Chemistry Authors: Roxanna Hajbabaie Matthew T. Harper Taufiq Rahman Tags: Article Source Type: research

Molecules, Vol. 26, Pages 2027: Discovery of Post-Translational Modifications in Emiliania huxleyi
okeun Lee Emiliania huxleyi is a cosmopolitan coccolithophore that plays an essential role in global carbon and sulfur cycling, and contributes to marine cloud formation and climate regulation. Previously, the proteomic profile of Emiliania huxleyi was investigated using a three-dimensional separation strategy combined with liquid chromatography-tandem mass spectrometry (LC-MS/MS). The current study reuses the MS/MS spectra obtained, for the global discovery of post-translational modifications (PTMs) in this species without specific enrichment methods. Twenty-five different PTM types were examined using Trans-Proteomic...
Source: Molecules - April 2, 2021 Category: Chemistry Authors: Van-An Duong Onyou Nam EonSeon Jin Jong-Moon Park Hookeun Lee Tags: Communication Source Type: research

Molecules, Vol. 26, Pages 2431: Prospects for the Personalized Multimodal Therapy Approach to Pain Management via Action on NO and NOS
edev Regina F. Nasyrova Chronic pain syndromes are an important medical problem generated by various molecular, genetic, and pathophysiologic mechanisms. Back pain, neuropathic pain, and posttraumatic pain are the most important pathological processes associated with chronic pain in adults. Standard approaches to the treatment of them do not solve the problem of pain chronicity. This is the reason for the search for new personalized strategies for the prevention and treatment of chronic pain. The nitric oxide (NO) system can play one of the key roles in the development of peripheral pain and its chronicity. The purpo...
Source: Molecules - April 22, 2021 Category: Chemistry Authors: Natalia A. Shnayder Marina M. Petrova Tatiana E. Popova Tatiana K. Davidova Olga P. Bobrova Vera V. Trefilova Polina S. Goncharova Olga V. Balberova Kirill V. Petrov Oksana A. Gavrilyuk Irina A. Soloveva German V. Medvedev Regina F. Nasyrova Tags: Review Source Type: research

Molecules, Vol. 27, Pages 1699: Revolution of Current Dental Zirconia: A Comprehensive Review
Sohail Zafar The aim of this article is to comprehensively review the revolution of dental zirconia (Zir), including its types, properties, applications, and cementation procedures. A comprehensive search of PubMed and Embase was conducted. The search was limited to manuscripts published in English. The final search was conducted in October 2021. Newly developed monolithic Zir ceramics have substantially enhanced esthetics and translucency. However, this material must be further studied in vitro and in vivo to determine its long-term ability to maintain its exceptional properties. According to the literature, monolith...
Source: Molecules - March 4, 2022 Category: Chemistry Authors: Ahmed Yaseen Alqutaibi Omar Ghulam Majid Krsoum Suhail Binmahmoud Hasan Taher Wael Elmalky Muhammad Sohail Zafar Tags: Review Source Type: research

Molecules, Vol. 27, Pages 2155: Discovery of Cinnamylidene Derivative of Rhodanine with High Anthelmintic Activity against Rhabditis sp.
Żesławska The treatment of parasitic infections requires the application of chemotherapy. In view of increasing resistance to currently in-use drugs, there is a constant need to search for new compounds with anthelmintic activity. A series of 16 cinnamylidene derivatives of rhodanine, including newly synthesized methoxy derivatives (1–11) and previously obtained chloro, nitro, and diethylamine derivatives (12–16), was investigated towards anthelmintic activity. Compounds (1–16) were evaluated against free-living nematodes of the genus Rhabditis sp. In the tested group of rhod...
Source: Molecules - March 27, 2022 Category: Chemistry Authors: Waldemar Tejchman Przemys ław Kołodziej Justyna Kalinowska-T łuścik Wojciech Nitek Grzegorz Żuchowski Anna Bogucka-Kocka Ewa Żesławska Tags: Article Source Type: research

Molecules, Vol. 19, Pages 17872-17896: RNA/aTNA Chimeras: RNAi Effects and Nucleases Resistance of Single and Double Stranded RNAs
The RNA interference pathway (RNAi) is a specific and powerful biological process, triggered by small non-coding RNA molecules and involved in gene expression regulation. In this work, we explored the possibility of increasing the biological stability of these RNA molecules by replacing their natural ribose ring with an acyclic L-threoninol backbone. In particular, this modification has been incorporated at certain positions of the oligonucleotide strands and its effects on the biological properties of the siRNA have been evaluated. In vitro cellular RNAi assays have demonstrated that the L-threoninol backbone is well tole...
Source: Molecules - November 4, 2014 Category: Chemistry Authors: Adele AlagiaMontserrat TerrazasRamon Eritja Tags: Article Source Type: research

Molecules, Vol. 20, Pages 4020-4041: Hybridisation Potential of 1',3'-Di-O-methylaltropyranoside Nucleic Acids
In further study of our series of six-membered ring-containing nucleic acids, different 1',3'-di-O-methyl altropyranoside nucleoside analogs (DMANA) were synthesized comprising all four base moieties, adenine, cytosine, uracil and guanine. Following assembly into oligonucleotides (ONs), their affinity for natural oligonucleotides was evaluated by thermal denaturation of the respective duplexes. Data were compared with results obtained previously for both anhydrohexitol (HNAs) and 3'-O-methylated altrohexitol modified ONs (MANAs). We hereby demonstrate that ONs modified with DMANA monomers, unlike some of our previously des...
Source: Molecules - March 3, 2015 Category: Chemistry Authors: Akkaladevi VenkateshamDhuldeo KachareGuy SchepersJef RozenskiMathy FroeyenArthur Van Aerschot Tags: Article Source Type: research

Molecules, Vol. 20, Pages 13055-13070: Cell-Type Specific Penetrating Peptides: Therapeutic Promises and Challenges
Cell penetrating peptides (CPP), also known as protein transduction domains (PTD), are small peptides able to carry peptides, proteins, nucleic acid, and nanoparticles, including viral particles, across the cellular membranes into cells, resulting in internalization of the intact cargo. In general, CPPs can be broadly classified into tissue-specific and non-tissue specific peptides, with the latter further sub-divided into three types: (1) cationic peptides of 6–12 amino acids in length comprised predominantly of arginine, lysine and/or ornithine residues; (2) hydrophobic peptides such as leader sequences of secreted gro...
Source: Molecules - July 20, 2015 Category: Chemistry Authors: Maliha ZahidPaul Robbins Tags: Review Source Type: research

Molecules, Vol. 20, Pages 17944-17975: Therapeutic Oligonucleotides Targeting Liver Disease: TTR Amyloidosis
The liver has become an increasingly interesting target for oligonucleotide therapy. Mutations of the gene encoding transthyretin (TTR), expressed in vast amounts by the liver, result in a complex degenerative disease, termed familial amyloid polyneuropathy (FAP). Misfolded variants of TTR are linked to the establishment of extracellular protein deposition in various tissues, including the heart and the peripheral nervous system. Recent progress in the chemistry and formulation of antisense (ASO) and small interfering RNA (siRNA) designed for a knockdown of TTR mRNA in the liver has allowed to address the issue of gene-spe...
Source: Molecules - September 30, 2015 Category: Chemistry Authors: Christoph NiemietzGursimran ChandhokHartmut Schmidt Tags: Review Source Type: research

Molecules, Vol. 21, Pages 952: Protective Effect of the Total Flavonoids from Rosa laevigata Michx Fruit on Renal Ischemia-Reperfusion Injury through Suppression of Oxidative Stress and Inflammation
Renal ischemia-reperfusion injury (IRI) is a major cause of acute kidney injury (AKI). Our previous studies have shown that the total flavonoids (TFs) from Rosa laevigata Michx fruit has various activities, however, there were no papers reporting the role of the TFs against renal IRI. In the present work, a hypoxia/reoxygenation (H/R) model in NRK-52E cells and ischemia-reperfusion model in rats were used. The results showed that the TFs significantly attenuated cell injury and markedly decreased serum creatinine (Cr) and blood urea nitrogen (BUN) levels in rats. Further investigation revealed that the TFs markedly decreas...
Source: Molecules - July 20, 2016 Category: Chemistry Authors: Lisha Zhao Lina Xu Xufeng Tao Xu Han Lianhong Yin Yan Qi Jinyong Peng Tags: Article Source Type: research

Molecules, Vol. 21, Pages 1033: Salidroside Suppresses HUVECs Cell Injury Induced by Oxidative Stress through Activating the Nrf2 Signaling Pathway
This study is the first to demonstrate that SAL suppresses HUVECs cell injury induced by oxidative stress through activating the Nrf2 signaling pathway.
Source: Molecules - August 8, 2016 Category: Chemistry Authors: Yao Zhu Ya-Jie Zhang Wei-Wei Liu Ai-Wu Shi Ning Gu Tags: Article Source Type: research

Molecules, Vol. 21, Pages 1613: Multivalent Aptamers: Versatile Tools for Diagnostic and Therapeutic Applications
Nucleic acid aptamers generated through an in vitro selection are currently extensively applied as very valuable biomolecular tools thanks to their prominent advantages. Diversity of spatial structures, ease of production through chemical synthesis and a large variety of chemical modifications make aptamers convenient building blocks for the generation of multifunctional constructs. An opportunity to combine different aptamer functionalities with other molecules of interest such as reporter groups, nanoparticles, chemotherapeutic agents, siRNA or antisense oligonucleotides provides a widest range of applications of multiva...
Source: Molecules - November 24, 2016 Category: Chemistry Authors: Mariya Vorobyeva Pavel Vorobjev Alya Venyaminova Tags: Review Source Type: research

Molecules, Vol. 22, Pages 41: The Effects of Destruxin A on Relish and Rel Gene Regulation to the Suspected Immune-Related Genes of Silkworm
Destruxin A (DA), a cyclodepsipeptidic mycotoxin of entomopathogenic fungus, Metarhizium anisopliae, has anti-immunity activity against insects, but the mechanism of immune regulation is not clear yet. In our previous experiment, the significant expression changes of Bm_nscaf2838_045, Bm_nscaf2674_066, and Bm_nscaf2767_133 genes in a silkworm ’s hemocytes were found, which suggested that these genes might be involved in insect’s innate immunity. In the current experiment, the silkworm cell line Bm12 was used to survey the expression levels of these genes after the cells were treated with DA and the transcription factor...
Source: Molecules - December 28, 2016 Category: Chemistry Authors: Weina Hu Guangwei He Jingjing Wang Qiongbo Hu Tags: Article Source Type: research