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Preprint ARTICLE | doi:10.20944/preprints202404.1039.v1

Supramolecular Assemblies in Mn(II) and Zn(II) Metal-Organic Compounds Involving Phenanthroline and Benzoate: Experimental and Theoretical Studies

Mridul Boro, Subham Banik, Rosa M. Gomila, Antonio Frontera, Miquel Barceló-Oliver, Manjit K. Bhattacharyya

Subject: Chemistry And Materials Science, Inorganic And Nuclear Chemistry Keywords: metal-organic compounds; supramolecular dimer; self-association; DFT; QTAIM; MEP

Online: 16 April 2024 (10:54:52 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202312.1843.v1

Preparative and Catalytic Properties of MoVI Mononuclear and Metallosupramolecular Coordination Assemblies Bearing Hydrazonato Ligands

Mirna Mandarić, Edi Topić, Dominique Agustin, Jana Pisk, Višnja Vrdoljak

Subject: Chemistry And Materials Science, Other Keywords: molybdenum; hydrazone; metallosupramolecular; dinuclear; metallacycles; polymers; epoxidation; cyclooctene; catalysis; DFT

Online: 25 December 2023 (11:24:35 CET)

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Preprint ARTICLE | doi:10.20944/preprints202310.0516.v1

The Synthesis of Trans-enediones From Furan Derivatives Using Pyridinium Chlorochromate. An Explanation

Maurizio D’Auria, Fausto Langerame

Subject: Chemistry And Materials Science, Organic Chemistry Keywords: Pyridinium chlorochromate; furan oxidation; enediones synthesis; XRD; XPS; DFT calculations

Online: 10 October 2023 (03:01:11 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202307.1662.v1

Structural Studies of Monounsaturated and ω-3 Polyunsaturated Free Fatty Acids in Solution with the Combined Use οf NMR and DFT calculations -Comparison with the Liquid State

Ioannis P. Gerothanassis, Michael G. Siskos, Georgios Papamokos, Themistoklis Venianakis

Subject: Chemistry And Materials Science, Organic Chemistry Keywords: 1D 1H NOE; 1H chemical shift; ALA; EPA; DHA; DFT

Online: 25 July 2023 (07:33:59 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202306.0276.v1

Strain Modulation of Electronic Properties in Monolayer SnP2S6 and GeP2S6

Junlei Zhou, Yuzhou Gu, Yue-E Xie, Fen Qiao, Jiaren Yuan, JingJing He, Sake Wang, Yangsheng Li, Yangbo Zhou

Subject: Physical Sciences, Condensed Matter Physics Keywords: Monolayer semiconductor; Band gap; Electronic structure; Biaxial strain; DFT calculations

Online: 5 June 2023 (09:58:45 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202212.0225.v1

Charge Transport in Organic Semiconducting Crystals Exhibiting TADF: Insight from Quantum-Chemical Calculations

Andrey Yu. Sosorev, Dmitry I. Dominskiy, Nikita O. Dubinets

Subject: Physical Sciences, Atomic And Molecular Physics Keywords: OLED; charge mobility; DFT; hopping transport; transfer integrals; reorganization energy

Online: 13 December 2022 (03:25:26 CET)

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Preprint ARTICLE | doi:10.20944/preprints202201.0095.v2

Theoretical DFT Study of the Antioxidant Activity of Five Plant Food Benzoic Acid Derivatives: Dearomatization and Stability of H Abstraction Radicals

Bienfait Kabuyaya Isamura, Issofa Patouossa, Isaac Kaba Elaka, Aristote Matondo, Pius Tshimankinda Mpiana

Subject: Chemistry And Materials Science, Theoretical Chemistry Keywords: antioxidant activity; eearomatization; frontier molecular orbital; fukui function f0; DFT

Online: 3 February 2022 (15:19:51 CET)

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Preprint ARTICLE | doi:10.20944/preprints202003.0008.v1

Tunable Photodetectors via in Situ Thermal Conversion of TiS₃ to TiO₂

Foad Ghasemi, Riccardo Frinsenda, Eduardo Flores, Nikos Papadopoulos, Robert Biele, David Perez de Lara, Herre S. J. van der Zant, Kenji Watanabe, Takashi Taniguchi, Roberto D’Agosta, Jose R. Ares, Carlos Sanchez, Isabel J. Ferrer, Andres Castellanos-Gomez

Subject: Chemistry And Materials Science, Nanotechnology Keywords: 2D materials; photodetectors; oxidation; TiS3; TiO2; Raman spectroscopy; DFT GW

Online: 1 March 2020 (03:43:01 CET)

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Preprint ARTICLE | doi:10.20944/preprints201909.0286.v1

Using Pd Doped γ-Graphyne to Detect Dissolved Gases in Transformer Oil: A Density Functional Theory Investigation

Xiaoxing Zhang, Rongxing Fang, Dachang Chen, Guozhi Zhang

Subject: Chemistry And Materials Science, Surfaces, Coatings And Films Keywords: pd doped graphyne; dissolved gases; adsorption; density functional theory (dft)

Online: 25 September 2019 (16:01:58 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201812.0020.v1

Steric Effects of Alkyl Substituents at N-Donor Bidentate Amines Direct the Nuclearity, Bonding and Bridging Modes in Thiocyanato-Copper(II) Complexes

Franz A. Mautner, Roland C. Fischer, Ana Torvisco, Maher M. Henary, Andrew Milner, Hunter DeVillier, Tolga N. V. Karsili, Febee R. Louka, Salah S. Massoud

Subject: Chemistry And Materials Science, Inorganic And Nuclear Chemistry Keywords: coordination compounds; coordination polymers; copper; thiocyanate; crystal Structure; DFT calculations

Online: 3 December 2018 (10:02:16 CET)

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Preprint ARTICLE | doi:10.20944/preprints201806.0423.v1

Multi-Scale Computational Simulation of Amorphous Silicates. Structural, Dielectric and Vibrational Spectroscopic Properties

José Ángel Martínez-González, Javier Navarro-Ruiz, Albert Rimola

Subject: Physical Sciences, Atomic And Molecular Physics Keywords: DFT; periodic simulations; amorphous minerals; physico-chemical properties; super-cell

Online: 26 June 2018 (13:10:49 CEST)

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Silicates are among the most abundant and important inorganic materials, not only in the Earth’s crust but also in the interstellar medium in the form of micro-/nano-particles or embedded in the matrices of comets, meteorites and other asteroidal bodies. Although the crystalline phases of silicates are indeed present in Nature, amorphous forms are also highly abundant. Here we report a theoretical investigation of the structural, dielectric and vibrational properties of the amorphous bulk for forsterite (Mg₂SiO₄) as a silicate test case by a combined approach of classical molecular dynamics (MD) simulations for structure evolution, and periodic quantum mechanical DFT calculations for electronic structure analysis. Using classical MD based on an empirical partial charge rigid ionic model within a melt-quenching scheme at different temperatures performed with the GULP 4.0 code amorphous bulk structures for Mg₂SiO₄ were generated using as initial guess the crystalline phase. This has been done for bulks with three different unit cell sizes adopting a super-cell approach; i.e., 1×1×2, 2×1×2 and 2×2×2. The radial distribution functions indicated a good degree of amorphisation of the structures. Periodic B3LYP-geometry optimizations performed with the CRYSTAL14 code on the generated amorphous systems were used to analyze their structure, to calculate their high frequency dielectric constants (ε_∞), and to simulate the IR, Raman and reflectance spectra, which were compared with the experimental and theoretical crystalline Mg₂SiO₄. The most significant changes of the physico-chemical properties of the amorphous systems compared to the crystalline ones are presented and discussed (e.g., larger deviations in the bond distances and angles, broadening of the IR bands, etc.), which are consistent with their disordered nature. It is also shown that by increasing the unit cell size the bulk structures present larger degree of amorphisation.

Preprint ARTICLE | doi:10.20944/preprints201806.0418.v1

DFT simulations of the vibrational spectrum and hydrogen bonds of ice XIV

Kai Zhang, Peng Zhang, Ze-Ren Wang, Xu-Liang Zhu, Ying-Bo Lu, Cheng-Bo Guan, Yan-Hui Li

Subject: Chemistry And Materials Science, Physical Chemistry Keywords: ice XIV; vibrational spectrum; hydrogen bond; CASTEP, first-principles; DFT

Online: 26 June 2018 (12:44:03 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202401.0732.v1

Expression Profiling Uncovers Novel Genes Associated with Plant Hormone Signal Transduction Involved in Regulation of Anthocyanin Biosynthesis in Red-Fleshed Apple Cultivars

Sylwia Keller-Przybylkowicz, Michal Oskiera, Xueqing Liu, Laiquing Song, Lingling Zhao, Xiaoyun Du, Dorota E. Kruczyńska, Agnieszka Walencik, Norbert Jakub Kowara, Grzegorz Bartoszewski

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: apple; expression profiling; KEGG; red-flesh fruits; RNA-seq; RT-qPCR; transcriptome

Online: 10 January 2024 (04:33:22 CET)

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Preprint ARTICLE | doi:10.20944/preprints202312.0316.v1

Temporal Trend of the SARS-CoV-2 Omicron Variant and Res-Piratory Syncytial Virus in the Nasal Cavity and Accuracy of the Newly Developed Antigen-Detecting Rapid Diagnostic Test

Daisuke Tamura, Yuji Morisawa, Takashi Mato, Shin Nunomiya, Masaki Yoshihiro, Yuta Maehara, Shizuka Ito, Yasushi Ochiai, Hirokazu Yamagishi, Toshihiro Tajima, Takanori Yamagata, Hitoshi Osaka

Subject: Medicine And Pharmacology, Clinical Medicine Keywords: Omicron; rapid diagnostic test; RT-PCR; RSV; SARS-CoV-2; viral antigens

Online: 6 December 2023 (07:38:00 CET)

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Preprint ARTICLE | doi:10.20944/preprints202308.1098.v1

A Shortcut From Genome to Drug: The Employment of Bioinformatic Tools to Find New Targets for Gastric Cancer Treatment

Daiane M.S. Brito, Odnan G. Lima, Felipe P. Mesquita, Emerson L. da Silva, Maria E. A. de Moraes, Rommel M. R. Burbano, Raquel C. Montenegro, Pedro F.N. Souza

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Transcriptional meta-analysis; molecular docking; RT-qPCR; Bioinformatics; Structural-based virtual screening

Online: 15 August 2023 (11:47:28 CEST)

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Gastric cancer (GC) is a highly heterogeneous, complex disease and the fifth most common cancer worldwide (about one million cases and 784 000 deaths worldwide in 2018). CG is lately diagnosed and guarantees a poor prognosis for GC (the 5-year survival rate is less than 20%, but in early detection can reach 90%). This study evaluated the transcriptional profile in tumor gastric samples to find genes highly expressed during tumor establishment and use the related proteins as targets to find new anticancer molecules. Data was collected at Gene Expression Omnibus (GEO) bank to obtain 3 dataset matrices that analyze gastric tumor tissue versus normal gastric tissue, performed microarray using GPL570 platform, and from different sources. The genes found in silico analysis were confirmed in several lines of GC cells by RT-qPCR. The protein data bank was used to find the correspondent proteins. Then a structural-based virtual screening was done to find molecules, and docking analysis was done using the DockThor server. Our results of transcriptomic analysis, together with RT-qPCR, confirm the high expression of the genes AJUBA, FBXL13, CCDC69, CD80 and NOLC1 in GC lines. Based on that, the correspondent proteins were used in SBVS analysis. Five molecules, one each target, MCULE-2386589557-0-6, MCULE-7343047040-0-1, MCULE-5230409338-0-3, MCULE-9178344200-0-1 and MCULE -5881513100-0-29. All molecules have favorable pharmacokinetic, pharmacodynamic and toxicological properties. Molecular docking analysis revealed that the molecules interact with proteins in critical sites for their activity. Using a virtual screening approach, a molecular docking study was performed for proteins encoded by genes that play important roles in cellular functions for carcinogenesis. Combining a systematic collection of public microarray data with a comparative meta-profiling, RT-qPCR, SBVS, and molecular docking analysis provided a suitable approach to find genes involved in GC and work the correspondent protein to strive for new molecules with anticancer properties.

Preprint ARTICLE | doi:10.20944/preprints202107.0548.v1

Transfer Learning for the Detection and Diagnosis of Types of Pneumonia Including Pneumonia Induced by the COVID-19 from Chest X-Ray Images

Yusuf Brima, Marcellin Atemkeng, Stive Tankio Djiokap, Jaures Ebiele, Franklin Tchakounté

Subject: Engineering, Automotive Engineering Keywords: ANN; COVID-19; CT; mRNA; MRI; RT-PCR; SARS-CoV-2; XCR

Online: 23 July 2021 (15:02:40 CEST)

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Preprint REVIEW | doi:10.20944/preprints202106.0320.v1

Inherent Bias of SARS-CoV-2 RNA Quantification for Wastewater Surveillance Due to Variable RT-qPCR Assay Parameters

Aaron Bivins, Devrim Kaya, Kyle Bibby, Stuart Simpson, Stephen Bustin, Orin Shanks, Warish Ahmed

Subject: Environmental And Earth Sciences, Water Science And Technology Keywords: RT-qPCR; assay validity; standard curve; quality assurance; quality control; wastewater surveillance

Online: 11 June 2021 (14:10:51 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202003.0413.v1

Ontological and Bioinformatic Analysis of Anti-Coronavirus Drugs and Their Implication for Drug Repurposing against COVID-19

Yingtong Liu, Wallace K.B. Chan, Zhigang Wang, Junguk Hur, Jiangan Xie, Hong Yu, Yongqun He

Subject: Medicine And Pharmacology, Pharmacology And Toxicology Keywords: coronavirus; drug; COVID-19; SARS; MERS; ontology; ChEBI; NDF-RT; DrON; bioinformatics

Online: 29 March 2020 (01:58:40 CET)

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Coronavirus-infected diseases have posed great threats to human health. In past years, highly infectious coronavirus-induced diseases, including COVID-19, SARS, and MERS, have resulted in world-wide severe infections. Our literature annotations identified 110 chemical drugs and 26 antibodies effective against at least one human coronavirus infection in vitro or in vivo. Many of these drugs inhibit viral entry to cells and viral replication inside cells or modulate host immune responses. Many antimicrobial drugs, including antimalarial (e.g., chloroquine and mefloquine) and antifungal (e.g., terconazole and rapamycin) drugs as well as antibiotics (e.g., teicoplanin and azithromycin) were associated with anti-coronavirus activity. A few drugs, including remdesivir, chloroquine, favipiravir, and tocilizumab, have already been reported to be effective against SARS-CoV-2 infection in vitro or in vivo. After mapping our identified drugs to three ontologies ChEBI, NDF-RT, and DrON, many features such as roles and mechanisms of action (MoAs) of these drugs were identified and categorized. For example, out of 57 drugs with MoA annotations in NDF-RT, 47 have MoAs of different types of inhibitors and antagonists. A total of 29 anticoronaviral drugs are anticancer drugs with the antineoplastic role. Two clustering analyses, one based on ChEBI-based semantic similarity, the other based on drug chemical similarity, were performed to cluster 110 drugs to new categories. Moreover, differences in physicochemical properties among the drugs were found between those inhibiting viral entry and viral replication. A total of 163 host genes were identified as the known targets of 68 anti-coronavirus drugs, resulting in a network of 428 interactions among these drugs and targets. Chlorpromazine, dasatinib, and anisomycin are the hubs of the drug-target network with the highest number of connected target proteins. Many enriched pathways such as calcium signaling and neuroactive ligand-receptor interaction pathways were identified. These findings may be used to facilitate drug repurposing against COVID-19.

Preprint ARTICLE | doi:10.20944/preprints201909.0142.v1

Chronic Kidney Disease–Associated Pruritus is Caused by Dysregulated Ion Channels in Sensory Neurons

Akishi Momose, Michihiko Yabe, Shigetoshi Chiba, Kenjirou Kumakawa, Yasuo Shiraiwa, Hiroki Mizukami

Subject: Medicine And Pharmacology, Urology And Nephrology Keywords: uremic pruritus; ion channels; cell signaling; Cav3.2 calcium channel; RT-PCR; skin

Online: 14 September 2019 (19:00:34 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202310.0477.v1

Modeling Field Electron Emission From a Flat Au (100) Surface With Density-Functional Theory

Yiming Li, Joshua Mann, James Rosenzweig

Subject: Physical Sciences, Other Keywords: field electron emission; DFT; Au (100); Fowler-Nordheim; laser field emission

Online: 10 October 2023 (03:20:46 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202207.0310.v1

Ab-initio Molecular Dynamics Simulation of the Changes in the Optical Properties of 2D MoS₂ When Doped with Pt at 300 K

Juan Manuel Ramírez-de-Arellano, Ali Fransuani Jiménez-González, Mónica Canales, Luis Fernando Magaña

Subject: Physical Sciences, Condensed Matter Physics Keywords: ab-initio; DFT calculations; 2D materials; MoS2; optical properties; platinum; FPMD

Online: 21 July 2022 (03:24:52 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202206.0399.v1

Theoretical Perspectives on the Gas-phase Oxidation Mechanism and Kinetics of Carbazole Initiated by OH Radical in the Atmosphere

Zhuochao Teng, Xiaotong Wang, Mohammad Hassan Hadizadeh, Yanan Han, Xianwei Zhao, Qi Zhang, Hetong Wang, Ying Li, Fei Xu, Yanhui Sun

Subject: Environmental And Earth Sciences, Atmospheric Science And Meteorology Keywords: carbazole; OH radical; rate constants; oxidation mechanism; density functional theory (DFT)

Online: 29 June 2022 (08:19:43 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202204.0064.v1

First-Principles Study of the Electronic Structure of LLM-105 Crystal and (101) Plane Under High Pressure

Gang He, Wen Kun Zhu, Zhi Qiang Qiao, Zheng Guo Chen, Jun Wen

Subject: Chemistry And Materials Science, Materials Science And Technology Keywords: low-Miller-index; High pressure; (101) plane; DFT calculation; LLM-105

Online: 7 April 2022 (14:27:56 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202012.0364.v1

Unveiling the Unexpected Reactivity of Electrophilic Diazoalkanes in [3+2] Cycloaddition Reactions within Molecular Electron Density Theory

Luis R. Domingo, Mar Ríos-Gutiérrez, Nivedita Acharjee

Subject: Chemistry And Materials Science, Analytical Chemistry Keywords: Molecular Electron Density Theory; Norbornadiene; Diazoalkanes; Conceptual DFT; Electron Localization Function.

Online: 15 December 2020 (10:04:22 CET)

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Working Paper ARTICLE

Bioactive Coating on Titanium Dental Implants for Improved Anticorrosion Protection: A Combined Experimental and Theoretical Study

Jozefina Katić, Ankica Šarić, Ines Despotović, Nives Matijaković, Marin Petković, Željka Petrović

Subject: Chemistry And Materials Science, Electrochemistry Keywords: titanium dental implant; vitamin D3; bioactive coating; anticorrosion protection; EIS; DFT

Online: 10 September 2019 (11:35:26 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201809.0547.v1

Exotic spectra and lattice vibrations of ice X using the DFT method

Lu Jiang, Shu-Kai Yao, Kai Zhang, Ze-Ren Wang, Hui-Wen Luo, Xu-Liang Zhu, Yue Gu, Peng Zhang

Subject: Chemistry And Materials Science, Physical Chemistry Keywords: ice X; vibrational spectrum; first-principles DFT; Raman scattering; IR absorption

Online: 27 September 2018 (13:25:06 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202404.1845.v1

Determination Mitochondria's Quality Control of Parkinsonism Using Real-Time Reverse-Transcription Polymerase Chain Reaction

Al-Baraa Akram

Subject: Neuroscience And Neurology, Biology And Life Sciences Keywords: RT: real time, PCR: polymerase chain reaction, WT: wild type, dNTP: deoxynucleotide triphosphate

Online: 28 April 2024 (10:36:25 CEST)

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Nuclear DNA mutations, mitochondrial DNA mutations, combined nuclear and mitochondrial DNA defects, and random occurrences are the main causes of mitochondrial disease. Black pigmentation loss is a major sign of Parkinsonism. Because of the loss of dopaminergic neurons in the substantia nigra, it drops to less than 80%. The degree of motor impairment was correlated with the amount of black pigmentation loss. After RNA extraction, reverse transcription is carried out because reverse transcriptase was used to create cDNA. One microliter of total RNA supplemented with IORT Buffer, dNTPs, random hexamers, Multi-Scribe Reverse Transcriptase, and nuclease-free was used to create cDNA. The following was how the reaction was carried out in a thermal cycler: 10 minutes at 25°C, 120 minutes at 37°C, 5 seconds at 85°C, and lastly 4°C. The data was expressed as a v-value, which shows how much the target gene is enriched in comparison to the reference gene. Earlier research using mice injected with functional HtrA2/Omi protease activity revealed similar outcomes, including induced up-regulation of CHOP, decreased mitochondrial function, and early brain cell aging because of an increase in mtDNA deletions. The cell viability of the genotypes exhibits a dmg concentration-dependent effect in these results, suggesting that high content ratios of drug treatment with 6-OHDA may be the cause of cellular content depletion. After 6-OHDA neurotoxin treatment, CHOP is up-regulated. Prior in vitro research has shown that treatment with a model based on 6-OHDA neurotoxin causes the activation of mitochondrial stress pathways, which in turn promotes the death of neurons. 6-OHDA reversibly inhibited complexes I and IV's activities in rat brain cells, which led to dopaminergic neurodegeneration, a defining feature of PD pathogens. As a result, the number of living cells will directly correlate with the dmg concentration, supporting the results of the current study. Real-time PCR can generally demonstrate that the removal of HtrA 2 results in a significant up-regulation of Hsp60 expression when compared to WT cells. This could be linked to a decreased threshold for mitochondrial stress in HtrA2 KO cells, which would explain why, following ADEP4 and ACP5 treatment, Hsp60 is significantly up-regulated in HtrA2 KO cells compared to WT cells.

Preprint ARTICLE | doi:10.20944/preprints202404.0301.v1

Evaluation of Safety and Efficacy of Repeated Mesenchymal Stem Cell Transplantation in Patients with ALS by Investigating Patient's Specific MicroRNAs as Novel Biomarkers: A Retrospective Study

Zahraa Alkhazaali, Sajad Sahab-Negah, Amir Reza Boroumand, Najmeh Kaffash Farkhad, Mohammad Ali Khodadoust, Rashin Ganjali, Jalil Tavakol-Afshari

Subject: Medicine And Pharmacology, Neuroscience And Neurology Keywords: bone marrow-derived mesenchymal stem cells; ALS; microRNA; Mir206; Mir338-3p; RT -PCR.

Online: 3 April 2024 (14:25:24 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202403.0205.v1

The Probiotic Paradox: Thriving in High-Hopped Sour Beer Bitter

Marcos Edgar Herkenhoff

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: craft beer; probiotic; gene expression; PMA-qPCR; RT-qPCR; microbiological resistance to hops.

Online: 5 March 2024 (12:25:02 CET)

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Preprint ARTICLE | doi:10.20944/preprints202307.1362.v1

The Rise and Fall of Omicron BA.1 Variant as Seen in Wastewater Supports Epidemiological Model Predictions

Michal Liddor Naim, Yu Fu, Marilou Shagan, Itay Bar-Or, Robert Marks, Qun Sun, Rony Granek, Ariel Kushmaro

Subject: Public Health And Healthcare, Health Policy And Services Keywords: SARS-CoV-2; Omicron; Wastewater-based epidemiology; RT-qPCR; SIR model; SIRS model

Online: 20 July 2023 (11:44:24 CEST)

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Preprint REVIEW | doi:10.20944/preprints202104.0481.v1

Minimizing Errors in RT-PCR Detection and Quantification of SARS-CoV-2 RNA for Wastewater Surveillance

Warish Ahmed, Stuart Simpson, Paul Bertsch, Kyle Bibby, Aaron Bivins, Linda Blackall, Silvia Bofill-Mas, Albert Bosch, Joao Brandao, Phil Choi, Mark Ciesielski, Erica Donner, Nishita D'Souza, Andreas Farnleitner, Daniel Gerrity, Raul Gonzalez, John Griffith, Pradip Gyawali, Charles Haas, Kerry Hamilton, Chanditha Hapuarachchi, Valerie Harwood, Rehnuma Haque, Greg Jackson, Stuart Khan, Wesaal Khan, Masaaki Kitajima, Asja Korajkic, Giuseppina La Rosa, Blythe Layton, Erin Lipp, Sandra McLellan, Brian McMinn, Gertjan Medema, Suzanne Metcalfe, Wim Meijer, Jochen Mueller, Heather Murphy, Colleen Naughton, Rachel Noble, Sudhi Payyappat, Susan Petterson, Tarja Pitkanen, Veronica Rajal, Brandon Reyneke, Fernando Roman, Joan Rose, Marta Rusinol, Michael Sadowsky, Laura Sala-Comorera, Yin Xiang Setoh, Samendra Sherchan, Kwanrawee Sirikanchana, Wendy Smith, Joshua Steele, Rosalie Sabburg, Erin Symonds, Phong Thai, Kevin Thomas, Josh Tynan, Simon Toze, Janelle Thompson, Andy Whiteley, Judith Wong, Daisuke Sano, Stefan Wuertz, Irene Xagoraraki, Qian Zhang, Amity Zimmer-Faust, Orin Shanks

Subject: Environmental And Earth Sciences, Waste Management And Disposal Keywords: COVID-19; SARS-CoV-2; Wastewater; Surveillance; False-positive; False-negative; RT-PCR

Online: 19 April 2021 (13:08:13 CEST)

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Wastewater surveillance for pathogens using the reverse transcription-polymerase chain reaction (RT-PCR) is an effective, resource-efficient tool for gathering additional community-level public health information, including the incidence and/or prevalence and trends of coronavirus disease-19 (COVID-19). Surveillance of SARS-CoV-2 in wastewater may provide an early-warning signal of COVID-19 infections in a community. The capacity of the world’s environmental microbiology and virology laboratories for SARS-CoV-2 RNA characterization in wastewater is rapidly increasing. However, there are no standardized protocols nor harmonized quality assurance and quality control (QA/QC) procedures for SARS-CoV-2 wastewater surveillance. This paper is a technical review of factors that can lead to false-positive and -negative errors in the surveillance of SARS-CoV-2, culminating in recommendations and strategies that can be implemented to identify and mitigate these errors. Recommendations include, stringent QA/QC measures, representative sampling approaches, effective virus concentration and efficient RNA extraction, amplification inhibition assessment, inclusion of sample processing controls, and considerations for RT-PCR assay selection and data interpretation. Clear data interpretation guidelines (e.g., determination of positive and negative samples) are critical, particularly during a low incidence of SARS-CoV-2 in wastewater. Corrective and confirmatory actions must be in place for inconclusive and/or potentially significant results (e.g., initial onset or reemergence of COVID-19 in a community). It will also be prudent to perform inter-laboratory comparisons to ensure results are reliable and interpretable for ongoing and retrospective analyses. The strategies that are recommended in this review aim to improve SARS-CoV-2 characterization for wastewater surveillance applications. A silver lining of the COVID-19 pandemic is that the efficacy of wastewater surveillance was demonstrated during this global crisis. In the future, wastewater will play an important role in the surveillance of a range of other communicable diseases.

Preprint ARTICLE | doi:10.20944/preprints201912.0093.v1

Genome-Wide Association Study for Resistance to the Meloidogyne javanica Causing Root-Knot Nematode in Soybean

Jean Carlos Alekcevetch, André Luiz de Lima Passianotto, Everton Geraldo Capote Ferreira, Adriana Brombini dos Santos, Danielle Cristina Gregório da Silva, Waldir Pereira Dias, François Belzile, Ricardo Vilela Abdelnoor, Francismar Corrêa Marcelino-Guimarães

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: mixed linear model; genotyping-by-sequencing; functional validation; RT-qPCR; resistance genes; GWAS

Online: 7 December 2019 (12:41:39 CET)

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Preprint ARTICLE | doi:10.20944/preprints202403.1821.v1

Oxygen Defects Containing TiN Films for the Hydrogen Evolution Reaction: A Robust Thin Film Electrocatalyst With Outstanding Performance

Ayoub Laghrissi, Mohammed Es-Souni

Subject: Chemistry And Materials Science, Electrochemistry Keywords: Hydrogen evolution reaction; Titanium nitride; Oxygen defects; TiNO; linear sweep voltammertry; DFT

Online: 29 March 2024 (10:01:45 CET)

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Preprint REVIEW | doi:10.20944/preprints202308.1932.v1

Recent Advances of Single-atom Metal Supported at Two-dimensional MoS2 for Electrochemical CO2 Reduction and Water Splitting

Jiahao Wang, Xiaorong Gan, Tianhao Zhu, Dan Zhao, Yanhui Ao, Peifang Wang

Subject: Environmental And Earth Sciences, Environmental Science Keywords: single-atom metal; two-dimensional nanomaterials; water splitting; CO2 reduction; catalysis; DFT

Online: 29 August 2023 (08:42:11 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202112.0450.v1

Effect of Internal Donors on Raman and IR Spectroscopic Fingerprints of MgCl2/TiCl4 Nanoclusters Determined by Machine Learning and DFT

Maddalena D' Amore, Toshiaki Taniike, Minoru Terano, Anna Maria Ferrari

Subject: Chemistry And Materials Science, Physical Chemistry Keywords: polymerization catalysis; machine learning; nanoclusters; DFT; Raman spectrum; IR spectrum; Lewis bases

Online: 28 December 2021 (14:04:10 CET)

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Preprint ARTICLE | doi:10.20944/preprints202107.0222.v1

Detection of Heavy Metals in Water Using Graphene Quantum Dots: An Experimental and Theoretical Study

Lorenzo Gontrani, Olivia Pulci, Marilena Carbone, Roberto Pizzoferrato, Paolo Prosposito

Subject: Chemistry And Materials Science, Biomaterials Keywords: Graphene oxide; Quantum Dots; TD-DFT; Absorption; Quenching effect; Concentration; Optical Response

Online: 9 July 2021 (13:22:41 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202008.0153.v1

Determination of Formation Energies and Phase Diagrams of Transition Metal Oxides with DFT+U

Daniel Mutter, Daniel F. Urban, Christian Elsässer

Subject: Chemistry And Materials Science, Materials Science And Technology Keywords: transition metal oxides; density functional theory; DFT+U; materials modelling; phase diagrams

Online: 6 August 2020 (10:32:01 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201806.0110.v2

Novel Insights into the Configurations of Lead(II)-Benzohydroxamic Acid Coordination Compounds in Aqueous Solution: A Combined Experimental and Computational Study

Jianyong He, Haisheng Han, Chenyang Zhang, Yuehua Hu, Dandan Yuan, Mengjie Tian, Daixiong Chen, Wei Sun

Subject: Chemistry And Materials Science, Inorganic And Nuclear Chemistry Keywords: Pb(II)-BHA; lead chemistry; metal-organic collectors; DFT calculation; surface activation

Online: 25 July 2018 (05:29:34 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202405.0220.v1

Selection and Multiplexing of Reverse Transcription Quantitative PCR Tests Targeting Relevant Honeybee Viral Pathogens

Franca Rossi, Ilaria Del Matto, Luciano Ricchiuti, Lucio Marino

Subject: Life Sciences, Biology And Life Sciences Keywords: ; honeybee; viral pathogens; RT-qPCR tests; TaqMan probes; duplex reactions ;

Online: 6 May 2024 (08:43:43 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202311.1062.v1

Identification of Phylogenetically Conserved Nitrogen-Dependent Small RNA across Pseudomonas

Irina Yu Pozdnyakova-Filatova, Evgeniya V Ivanova, Kirill V Petrikov, Ainur Rezhepova, Alina A Frolova, Marina V Zakharova

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: small RNA; Pseudomonas; nitrogen; NtrC; gene expression; RT-qPCR; nitrogen metabolism; carbon/nitrogen homeostasis

Online: 16 November 2023 (10:34:33 CET)

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Preprint ARTICLE | doi:10.20944/preprints202311.0621.v1

Occurrence of Picobirnavirus in Domestic and Wild Animals from Three Cities of Brazilian Amazon

Elaine Hellen Nunes Chagas, Julia Rezende Da Silva, Bruno de Cássio Veloso de Barros, José Wandilson Barboza Duarte Júnior, Fabiolla da Silva dos Santos, Edivaldo Costa Sousa Júnior, Delana Andreza Melo Bezerra, Helder Henrique Costa Pinheiro, Ceyla Maria Oeiras de Castro, Yashpal Singh Malik, Joana D’Arc Pereira Mascarenhas

Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: enteric virus; picobirnavirus; brazilian animals; page, rt-pcr; rdrp gene; phylogenetic analysis; genogroup I

Online: 9 November 2023 (11:24:00 CET)

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Preprint ARTICLE | doi:10.20944/preprints202103.0292.v1

Ke Zhou, Audrey Blanc-Lapierre, Valérie Seegers, Michèle Boisdron-Celle, Frédéric Bigot, Marianne Bourdon, Hakim Mahammedi, Aurélien Lambert, Mario Campone, Martine Bellanger, Jean-Luc Raoul

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: cancer; COVID-19; symptoms; healthcare workers; anosmia; dysgeusia; ageusia; France; serological test; RT-PCR

Online: 10 March 2021 (16:17:48 CET)

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Preprint REVIEW | doi:10.20944/preprints202006.0284.v1

Factors Affecting SARS-CoV-2 (COVID-19) Pandemic, including Zoonotic, Human Transmission and Chain of Infection. Reducing Public Health Risk by Serum Antibody Testing, Avoiding Screening in Unhygienic Places and False PCR Reporting. A Scientific Review

Kamran Mahmood Ahmed Aziz, Abdullah Othman, Waleed Alqahtani, Sumaiya Azhar

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; RT-PCR; antibody; zoonotic; animal transmission; genomics; asymptomatic fraction; herd immunity

Online: 23 June 2020 (13:30:11 CEST)

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Since December 2019, a rapid increase in the number of SARS-CoV-2 (COVID-19) cases was reported worldwide, despite strict infection control and lock down measures. Current paper investigated the actual facts behind this rapid increase in the number of cases. Study of genomic sequence reveals that domestic and wild animals were likely ancestors and zoonotic source for SARS-CoVs, MERS-CoVs, and SARS-CoV-2. Strong evidence suggest that these viruses already existed and replicated in animals and humans during past several decades, exhibiting diverse mutations, evolutions and self-limiting diseases, except during outbreaks. Serious zoonotic reservoir investigations are required to investigate animal transmission of SARS-CoVs and SARS-CoV-2 to limit current pandemic. This might be the reason of increasing number of cases via animals. SARS-CoV-2 has been retrospectively isolated in different studies in August 2019, several months before Wuhan announced. Hence, there is a possibility that viruses existed, went undetected, infecting subclinically, in past several years, and SARS-CoV-2 antigens and neutralizing antibodies may have been present in humans since long time. This might be another reason of increasing number of cases by screening as mass screening and antigen or antibody testing was not carried out in the past years. Randomized controlled trials are required to investigate human to human transmission by touch, as the current evidence is limited with conflicting results. As all SARS-CoVs are basically respiratory viruses, droplet precautions and infection control measures are essential, especially for hospital staff. Increased number of SARS-CoV-2 asymptomatic, or subclinical cases are detected worldwide. This silent phase of transmission can be beneficial for humans. Lack of symptoms eventually lessen virus transmission and reduce the pathogen's long-term survival and provide humoral herd immunity up to several years. Hence, seropositivity with diverse antibodies develops against mutating SARS-CoVs which will confer strong immunity during epidemics. Strategies such as identification, contact tracing and quarantine are costly and practically difficult. Hence, asymptomatic persons can continue their work with droplet precautions and standard infection control procedures, while symptomatic or sick persons can isolate themselves in their homes without the need for strict quarantine until clinical recovery, with reduced hospital visits and minimizing chances of hospital acquired infections. RT-PCR has low sensitivity and specificity, carries a high risk of handling live virus antigens, and requires difficult protocols. As viral load also sharply declines after few days of onset of infection, this technique might overlook infection. Furthermore, SARS-CoV-2 infection may be present in blood when oropharyngeal swabs are negative by RT-PCR. Additionally, RT-PCR usually gives false negative and false positive results and must be interpreted cautiously. This might be again a reason of increasing number of cases by false positive RT-PCR reporting. Moreover, antibodies against SARS-CoVs develop robustly in serum even by reduced amount of antigens. In contrast to RT-PCR, ELISA for diagnosing antibodies against SARS-CoV-2 demonstrates 100% specificity and 100% sensitivity, even in clinically asymptomatic individuals. These antibodies can be used for serologic surveys, monitoring and screening. However, screening tests for SARS-COV-2 should be avoided in unhygienic public places by nasopharyngeal swabs, which carry a high risk of further transmission, co-infection or superinfection. Such highly infectious virus must be isolated and tested in highly sterilized laboratory. Further strict international laws and policies are required to stop the possible spread of experimental viruses, biological warfare and bioterrorism.

Preprint ARTICLE | doi:10.20944/preprints202004.0216.v1

Development of a Field-deployable RT-qPCR Workflow for COVID-19 Detection

Raphael Nyaruaba, Bo Zhang, Caroline Muema, Elishiba Muturi, Greater Oyejobi, Jin Xiong, Bei Li, Zhengli Shi, Caroline Mwaliko, Junping Yu, Xiaohong Li, Hongping Wei

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: COVID-19; SARS-CoV-2; field work; community; diagnosis; rapid detection; inactivation; RT-qPCR

Online: 14 April 2020 (08:41:04 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202308.1966.v1

Computational Discovery of Marine Molecules of the Cyclopeptide Family with Therapeutic Potential

Norma Flores-Holguín, Joan Sebastian Salas-Leiva, Daniel Glossman-Mitnik

Subject: Chemistry And Materials Science, Theoretical Chemistry Keywords: Drug discovery; computational chemistry; conceptual DFT; marine cyclopeptides; chemical reactivity properties; bioavailability scores

Online: 29 August 2023 (09:36:49 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202212.0329.v1

Preparation, Characterization, DFT Calculations, Antibacterial and Molecular Docking Study of Co(II), Cu(II), and Zn(II) Mixed Ligand Complexes

Maged S. Al-Fakeh, Sabri Messaoudi, Faisal Alresheedi, Abuzar Albadri, Wael A El-Sayed, Emran Saleh

Subject: Chemistry And Materials Science, Inorganic And Nuclear Chemistry Keywords: Mixed-Ligands; DFT Calculations; HOMO; LUMO; Antimicrobial; Antioxidant Assays; and Molecular Docking Analysis

Online: 19 December 2022 (07:43:08 CET)

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Preprint ARTICLE | doi:10.20944/preprints202207.0080.v1

A Density Functional Theory and Information-Theoretic Approach Study of Interaction Energy and Polarizability for Base Pairs and Peptides

Dongbo Zhao, Shubin Liu, Dahua Chen

Subject: Chemistry And Materials Science, Theoretical Chemistry Keywords: density functional theory (DFT); information-theoretic approach (ITA); base pairs; peptides; molecular polarizability

Online: 6 July 2022 (03:04:51 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202111.0568.v2

Potential of Hydroxybenzoic Acids From Graptopetalum paraguayense for Inhibiting of Herpes Simplex Virus DNA Polymerase – Metabolome Profiling, Molecular Docking and Quantum-chemical Analysis

Nadezhda Hristova Todorova, Miroslav Angelov Rangelov, Ivayla Nedyalkova Dincheva, Ilian Kostadinov Badjakov, Venelin Georgiev Enchev, Nadezhda Vasileva Markova

Subject: Chemistry And Materials Science, Organic Chemistry Keywords: Graptopetalum paraguayense E. Walter; anti-HSV activities; hydroxybenzoic (phenolic) acids; molecular docking; DFT.

Online: 15 December 2021 (10:58:46 CET)

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Preprint ARTICLE | doi:10.20944/preprints202106.0498.v1

On the Low-Lying Electronically Excited States of Azobenzene Dimers: Transition Density Matrix Analysis

Evgenii Titov

Subject: Chemistry And Materials Science, Theoretical Chemistry Keywords: azobenzene; transition density matrix; exciton; charge transfer; excited states; TD-DFT; ADC(2)

Online: 21 June 2021 (10:20:13 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202101.0488.v1

The Photochemistry of Fe2(S2C3H6)(CO)6(µ-CO) and its Oxidized Form, Two Simple [FeFe]-Hydrogenase CO-Inhibited Models. A DFT and TDDFT Investigation

Federica Arrigoni, Giuseppe Zampella, Luca De Gioia, Claudio Greco, Luca Bertini

Subject: Chemistry And Materials Science, Analytical Chemistry Keywords: Metal-carbonyl complexes; [FeFe]-hydrogenases; density functional theory; time-dependent DFT; organometallic photochemistry

Online: 25 January 2021 (11:43:03 CET)

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Preprint ARTICLE | doi:10.20944/preprints202007.0742.v1

Assessment of the KID Procedure on a Mo–oxo Complex, an Open–Shell System

Jorge Martínez-Araya, Daniel Glossman-Mitnik

Subject: Chemistry And Materials Science, Theoretical Chemistry Keywords: KID protocol; Global Reactivity; Conceptual DFT; Kopmans’ Theorem; Mo–oxo Complexes; Hydrogen production

Online: 31 July 2020 (10:09:50 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201701.0029.v2

Distal [FeS]-Cluster Coordination in [NiFe]-Hydrogenase Facilitates Intermolecular Electron Transfer

Alexander Petrenko, Matthias Stein

Subject: Chemistry And Materials Science, Theoretical Chemistry Keywords: electron transfer; Marcus equation; enzymatic fuel cell; hydrogen oxidation; electrode adsorption; DFT; bioelectrochemistry

Online: 9 January 2017 (02:49:00 CET)

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Preprint ARTICLE | doi:10.20944/preprints202312.0322.v1

Digital Twin of Microgrid for Predictive Power Control to Building

Hao Jiang, Rudy Tjandra, Chew Beng Soh, Shuyu Cao, Donny Cheng Lock Soh, Kuan Tak Tan, King Jet Tseng, Sivaneasan B. Krishnan

Subject: Engineering, Energy And Fuel Technology Keywords: Matlab/Simulink; load demands; microgrid; DER, OPAL-RT; digital twin; energy optimization; Gurobi; sustainable building

Online: 6 December 2023 (05:43:41 CET)

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Preprint ARTICLE | doi:10.20944/preprints202308.0372.v3

Machine Learning Tools Applied for Training Optimization in Handball

Radu Bucea Manea Tonis, Petre Sorin Savin, Laurentiu-Gabriel Talaghir, Veronica Mindrescu

Subject: Social Sciences, Tourism, Leisure, Sport And Hospitality Keywords: complex indicator; isolated action; weighting system; simultaneous action; machine learning(ML); decision tree(C-RT)

Online: 16 October 2023 (08:35:18 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202307.1532.v1

Molecular and Clinical Epidemiology of SARS-CoV-2 Infection Among Vaccinated and Unvaccinated Individuals in a Large Healthcare Organization from New Jersey

José R. Mediavilla, Tara Lozy, Annie Lee, Justine Kim, Veronica W. Kan, Elizabeth Titova, Ashish Amin, Michael Zody, André Corvelo, Dayna M. Oschwald, Amy Baldwin, Samantha Fennessey, Jerry M. Zuckerman, Thomas Kirn, Liang Chen, Yanan Zhao, Kar Fai Chow, Tom Maniatis, David S. Perlin, Barry N. Kreiswirth

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; COVID-19; pandemic; variants; RT-PCR; sequencing; surveillance; vaccination; vaccine breakthrough; comorbidity.

Online: 21 July 2023 (13:55:29 CEST)

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New Jersey was among the first states impacted by the COVID-19 pandemic, with one of the highest overall death rates in the nation. Nevertheless, relatively few reports have been published focusing specifically on New Jersey. Here we report on molecular, clinical, and epidemiologic observations from the largest healthcare network in the state, in a cohort of vaccinated and unvaccinated individuals with laboratory-confirmed SARS-CoV-2 infection. We conducted molecular surveillance of SARS-CoV-2-positive nasopharyngeal swabs collected in nine hospitals from December 2020 through June 2022, using both whole genome sequencing (WGS) and a real-time RT-PCR screening assay targeting spike protein mutations found in variants of concern (VOC) within our region. De-identified clinical data were obtained retrospectively, including demographics, COVID-19 vaccination status, ICU admission, ventilator support, mortality, and medical history. Statistical analyses were performed to identify associations between SARS-CoV-2 variants, vaccination status, clinical outcomes, and medical risk factors. A total of 5,007 SARS-CoV-2-positive nasopharyngeal swabs were successfully screened and/or sequenced. Variant screening identified three predominant VOC, including Alpha (n =714), Delta (n =1,877), and Omicron (n =1,802). Omicron isolates were further sub-typed as BA.1 (n =899), BA.2 (n =853), and BA.4/BA.5 (n =50); the remaining 614 isolates were classified as “Other”. Approximately 31.5% (1,577/5,007) of the samples were associated with vaccine breakthrough infections, which increased in frequency following the emergence of Delta and Omicron. Severe clinical outcomes included ICU admission (336/5007 = 6.7%), ventilator support (236/5007 = 4.7%), and mortality (430/5007 = 8.6%), with increasing age being the most significant contributor to each (p <0.001). Unvaccinated individuals accounted for 79.7% (268/336) of ICU admissions, 78.3% (185/236) of ventilator cases, and 74.4% (320/430) of deaths. Highly significant (p <0.001) increases in mortality were observed in individuals with cardiovascular disease, hypertension, cancer, diabetes, and hyperlipidemia, but not with obesity, thyroid disease, or respiratory disease. Significant differences (p <0.001) in clinical outcomes were also noted between SARS-CoV-2 variants, including Delta, Omicron BA.1, and Omicron BA.2. Vaccination was associated with significantly improved clinical outcomes in our study, despite an increase in breakthrough infections associated with waning immunity, greater antigenic variability, or both. Underlying comorbidities contributed significantly to mortality in both vaccinated and unvaccinated individuals, with increasing risk based on the total number of comorbidities. Real-time RT-PCR-based screening facilitated timely identification of predominant variants using a minimal number of spike protein mutations, with faster turnaround time and reduced cost compared to WGS. Continued evolution of SARS-CoV-2 variants will likely require ongoing surveillance for new VOCs, with real-time assessment of clinical impact.

Preprint ARTICLE | doi:10.20944/preprints202203.0040.v1

Augmented Sensitivity of At-Home Rapid SARS-CoV-2 Antigen Test (RAT) Kits with Computer Vision

Kim Miikki, Lars Miikki, Jenny Wiklund, Alp Karakoç

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; rapid antigen test; RT-PCR test; COVID-19; image processing; Raspberry Pi

Online: 2 March 2022 (08:06:49 CET)

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Preprint ARTICLE | doi:10.20944/preprints202105.0381.v1

Building-Level Wastewater Monitoring for COVID-19 Using Tampon Swabs and RT-LAMP for Rapid SARS-Cov-2 RNA Detection

Aaron Bivins, Megan Lott, Marlee Shaffer, Zhenyu Wu, Devin North, Erin Lipp, Kyle Bibby

Subject: Environmental And Earth Sciences, Water Science And Technology Keywords: SARS-CoV-2; wastewater monitoring; environmental surveillance; RT-LAMP; building-level; near-source; passive sampling

Online: 17 May 2021 (10:07:04 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202104.0688.v1

Direct Quantitation of SARS-CoV-2 Using Droplet Digital PCR in Suspected Samples With Very Low Viral Load

Michela Deiana, Chiara Piubelli, Antonio Mori, Gian Paolo Chiecchi, Giulia La Marca, Martina Leonardi, Davide Treggiari, Anna Beltrame, Lucia Moro, Zeno Bisoffi, Elena Pomari

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: droplet digital PCR; real time RT-PCR; SARS-CoV-2; false negative; viral load; diagnosis

Online: 26 April 2021 (20:09:26 CEST)

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Preprint REVIEW | doi:10.20944/preprints202004.0201.v1

Detecting the COVID-19

Pravin Pokhrel, Changpeng Hu, Hanbin Mao

Subject: Biology And Life Sciences, Virology Keywords: diagnosis; detection kits; RT-PCR; immunoassay; false negative; false positive; sensitivity; point-of-care (POC)

Online: 12 April 2020 (16:50:05 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202308.0395.v1

Novel Grafted Hydrogel for Iron and Ammonia Removal from Ground Water, Synthesis and Computational Chemistry Study

Hanafy M. Abd El-Salam, Ali El Shafey, Mahmoud K. Abdel-Latif

Subject: Environmental And Earth Sciences, Water Science And Technology Keywords: Grafted hydrogel; Ground water; Ammonia and Iron removal efficiency; DFT and MEP; binding Energy

Online: 4 August 2023 (11:32:16 CEST)

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Preprint COMMUNICATION | doi:10.20944/preprints202306.0875.v1

Exploring the Potential Energy Surface of Medium-Sized Aromatic Polycyclic Systems with Embedded Planar Tetracoordinate Carbons: A Guided Approach

Diego Inostroza, Luis Leyva-Parra, Osvaldo Yañez, Andrew L. Cooksy, Venkatesan S. Thimmakondu, William Tiznado

Subject: Chemistry And Materials Science, Theoretical Chemistry Keywords: planar tetracoordinate carbon; silicon-carbon clusters; global minima; DFT computations; chemical bonding analysis; aromaticity

Online: 13 June 2023 (04:30:10 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202301.0387.v1

New Insights in the Synthesis of High Molecular Weight Aromatic Polyamides. Improved Synthesis of Rod-Like PPTA

Guiomar Hernández, Sergio Ferrero, Helmut Reinecke, Camino Bartolomé, Jesús M. Martinez-Ilarduya, Cristina Álvarez, Ángel E. Lozano

Subject: Chemistry And Materials Science, Polymers And Plastics Keywords: polyamidation; in situ silylation; poly(p-phenylene terephthalamide (PPTA); Kevlar; NMR; DFT molecular simulation

Online: 23 January 2023 (02:00:35 CET)

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Preprint ARTICLE | doi:10.20944/preprints202202.0317.v1

Visualization and Comprehension of Electronic and Topographic Contrasts on Cooperatively Switched Diarylethene-Bridged Ditopic Ligand

Imen Hnid, Lihao Guan, Elarbi Chatir, Saioa Cobo, Frederic Lafolet, Francois Maurel, Jean-Christophe Lacroix, Xiaonan Sun

Subject: Chemistry And Materials Science, Nanotechnology Keywords: photochromic; diarylethene; bipyridine; high-resolution scanning tunneling microscopy; cooperative switches; molecular orbital; DFT calculations

Online: 24 February 2022 (13:17:29 CET)

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Preprint CONCEPT PAPER | doi:10.20944/preprints202106.0075.v1

Towards Mapping Chemical Bonds in Nanostructured Materials

Philip N. H. Nakashima, Ding Peng, Xiaofen Tan, Anna N. Mortazavi, Tianyu Liu, Joanne Etheridge, Laure Bourgeois, David R. Clarke

Subject: Physical Sciences, Condensed Matter Physics Keywords: Chemical bonding; nanostructured materials; electron diffraction; quantum crystallography; QCBED; Density Functional Theory; QCBED-DFT

Online: 2 June 2021 (12:19:23 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202008.0690.v1

Virtual Screening of Marine Natural Compounds by Means of Chemoinformatics and CDFT-Based Computational Peptidology

Norma Flores-Holguín, Juan Frau, Daniel Glossman-Mitnik

Subject: Chemistry And Materials Science, Theoretical Chemistry Keywords: Theopapuamides A-D; Virtual Screening; Chemoinformatics; Conceptual DFT; Computational Peptidology; Bioavailability; Bioactivity Scores; ADMET

Online: 31 August 2020 (03:57:38 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202304.0574.v1

Insights into the Genes Involved in ABA Biosynthesis and Perception during Development and Ripening of the Chilean Strawberry Fruit

Maria Alejandra Moya-León, Yazmina Stappung, Elena Mattus-Araya, Raúl Herrera

Subject: Biology And Life Sciences, Plant Sciences Keywords: ABA biosynthesis; ABA perception; Fragaria chiloensis; fruit ripening; NCED; PYR/PYL receptors; phylogenic analysis; RT-qPCR

Online: 19 April 2023 (08:43:03 CEST)

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Working Paper ARTICLE

Fast Detection of SARS-CoV-2 RNA Directly from Respiratory Samples Using a Loop-Mediated Isothermal Amplification (LAMP) Test

Olympia E. Anastasiou, Caroline Holtkamp, Miriam Schäfer, Frieda Schön, Anna Maria Eis-Hübinger, Andi Krumbholz

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: SARS-CoV-2; COVID-19; RT-PCR; nucleic acids; direct testing; loop-mediated isothermal amplification; LAMP

Online: 5 April 2021 (12:21:19 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202402.1527.v1

Multimetallic Cooperative Activation of Dinitrogen by All-Metal Trinuclear rings: A DFT Study

Athanassios C. Tsipis, Spyros M. Siskos

Subject: Chemistry And Materials Science, Inorganic And Nuclear Chemistry Keywords: N2 fixation; Dinitrogen activation; DFT; IR; Raman; Hexametallic clusters; Ruthenium clusters; Osmium clusters; 15N NMR

Online: 27 February 2024 (12:18:31 CET)

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The fixation and activation of the dinitrogen molecule, N2 by hexametallic clusters of the general formula {[(μ2-L)M)]6(μ-η1:η3-Ν2)}0/+6 (L = CH2-, NH2-, PH2-, OH-, SH-, BH2- and NH2-, M = Ru(II) or Os(II)) were scrutinized by means of density functional theory calculations. In these systems, the dinitrogen molecule, acts as a ligand that bridges the two opposite facing triangular metallic rings, cyclo-M3 of the {[(μ2-L)M)]6(μ-η1:η3-Ν2)}0/+6 clusters The hexametallic clusters, that mimick the six Fe cluster of nitrogenase, were found to strongly activate N2, converting it into a hydrazido-like group, N24-. This is substantiated by the calculated N-N bond lengths, Re(N-N) and the stretching frequencies of the N-N bond of dinitrogen, vs(N-N) found in the ranges 1.299 – 1.487 Å and 780 – 1270 cm-1 respectively. Based on the Re(N-N) and vs(N-N) values, the dinitrogen activation depends upon the nature of the hexametallic cluster. Accordingly, the Os(II) clusters were found to activate more strongly the dinitrogen molecule as compared to their Ru(II) counterparts. The nature of the ligand L also affects the extent of the N2 activation by the hexametallic clusters, which follows the order BH2- < NH2- < OH- < CH2- < NH2- < PH2-, SH- for M = Ru(II) and the order BH2- < NH2- < OH- < NH2- < CH2- < PH2- < SH- for M = Os(II). Thus, the strongest N2 activation is observed for the {[(μ2-SH)Os)]6(μ-η1:η3-Ν2)}+6 cluster and the weakest for the {[(μ2-BH)Ru)]6(μ-η1:η3-Ν2)}0 cluster. The calculated Nitrogen-15 NMR isotropic chemical shielding tensors, σiso(15N) exhibit shielding (upfield) upon N2 fixation to the metal centers of the hexametallic clusters, as a results of electron density transfer towards its constituent N nuclei. A multitude of electronic charge distribution partitioning schemes were applied to assist in delineating the bonding properties of the {[(μ2-L)M)]6(μ-η1:η3-Ν2)}0/+6 clusters. Accordingly, it is found that there is a donation/backdonation interaction between the bridging N2 ligand and the two opposing cyclo-M3 rings located on either side. The dinitrogen ligand forms six bonds of mixed covalent/electrostatic nature with the six metal centers of the {[(μ2-L)M)]6)}0/+6 clusters.

Preprint ARTICLE | doi:10.20944/preprints202309.1759.v1

Camphor Sulfonimine Compounds: Bottom-Up Design of MOF’s from Organic Frameworks Based on X-rayS and DFT-D3

Adelino M. Galvão, Joana P. Costa, M. Fernanda N. N. Carvalho

Subject: Chemistry And Materials Science, Theoretical Chemistry Keywords: DFT-D3; self-assembly; camphor sulfonimine; X-ray diffraction; redox properties; complexes; non-bonding interactions

Online: 26 September 2023 (11:19:02 CEST)

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DFT-D3 calculations based on structural X-ray diffraction data obtained for 3-oxo-camphorsulfonyl imine (1), camphorsulfonyl chloride (2) and seven camphor sulfonimines (O2SNC10H13NR, L1-L7) from which L2 (R=4-OHC6H4), L4 (R=4-ClC6H4) and L6 (R=3,5-(CH3)2C6H3) are new, provide information into the intra and inter molecular interactions with concomitant elucidation of the supramolecular arrangement of the compounds. The DFT D3 calculations performed in small clusters of 2 or 3 molecular units reproduce the interactions observed by X-ray analyses showing that as a general trend the structural arrangement of the molecules is driven by electronic rather than by packing parameters. In all compounds the self-assembly of 3D structures involves the sulfonyl imine group ( NSO2) either to establish hydrogen bonds, through the oxygen atoms or non-classic oxygen-aliphatic hydrogen or non-bonding interactions (NBI) which also involve the sulfonyl oxygens. Interestingly, the camphor sulfonimine compounds (L2, L3) having protic groups (R=C6H4X: X=OH, L2 or X=NH2, L3) at the aromatic imine substituents (=NR) present an extra π-π stacking which is absent in the other compounds aromatic derivatives. The X-ray analysis shows that all the reported camphor sulfonimine compounds display the E configuration with respect to the imine substituent (R). The study of the redox behavior of the compounds by cyclic voltammetry allows an insight into the solution properties of the compounds and the rationalization of the molecular interactions that stand in the solid and solution states. Camphor sulfonimine compounds (L) display appropriate binding atoms to coordinate transition metals. The herein results show that monodentate coordination through the nitrogen atom of the sulfonimine 5-membered ring to the {Ag(NO3)} metal center is favored. When this imine nitrogen atom is not itself involved in the Organic Framework DFT-D3 calculations shows that the complexation does not affect the non-covalent interactions that are reproduced in the MOF structure.

Preprint SHORT NOTE | doi:10.20944/preprints202305.1869.v1

2-(5,6-Diphenyl-1,2, 4-Triazin-3-Yl)pyridinium Dichloroiodate (I)

Maria Carla Aragoni, Vito Lippolis, Annalisa Mancini, Anna Pintus, Enrico Podda, James B. Orton, Simon J. Coles, Massimiliano Arca

Subject: Chemistry And Materials Science, Inorganic And Nuclear Chemistry Keywords: 3-(2-pyridyl)-5,6-diphenyl-1,2,4-triazine; polypyridyl donors; SC-XRD; FT-Raman; DFT; ICl

Online: 26 May 2023 (05:44:34 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202305.1726.v1

Spin Frustrated Pyrazolato Triangular CuII Complex. Structure and Magnetic Properties, an Overview.

Walter Cañón-Mancisidor, Patricio Hermosilla-Ibáñez, Evgenia Spodine, Verónica Paredes-García, Carlos J. Gómez-García, Diego Venegas-Yazigi

Subject: Chemistry And Materials Science, Electronic, Optical And Magnetic Materials Keywords: Cu3-3OH complex; pyrazolato ligands; trinuclear complex; Spin Frustration; magnetic susceptibility; antisymmetric exchange; DFT calculations.

Online: 25 May 2023 (03:37:25 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201904.0014.v1

The Utility of Data Transformation for Alignment, de novo Assembly and Classification of Short Read Virus Sequences

Avraam Tapinos, Bede Constantinides, My VT Phan, Samaneh Kouchaki, Matthew Cotten, David L. Robertson

Subject: Biology And Life Sciences, Virology Keywords: Alignment; assembly; taxonomic classification; time series; data transformation; DWT; DFT; PAA; data compression; compressive genomics

Online: 1 April 2019 (13:29:58 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201806.0477.v1

Verdazyls as Possible Building Blocks for Multifunctional Molecular Materials: A case Study on 1,5-Diphenyl-3-(p-iodophenyl)-verdazyl Focusing on Magnetism, Electron Transfer and the Applicability of the Sonogashira-Hagihara Reaction

Hannah Jobelius, Norbert Wagner, Gregor Schnakenburg, Andreas Meyer

Subject: Chemistry And Materials Science, Organic Chemistry Keywords: radicals; exchange coupling; cross-coupling; broken symmetry DFT; EPR spectroscopy; X-ray crystallography; redox chemistry

Online: 28 June 2018 (15:32:47 CEST)

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Preprint SHORT NOTE | doi:10.20944/preprints201703.0158.v1

Triphenylphosphine-(N,N-dimethyldithiocarbamato)-gold(I) Methanol Solvate

Nicolas Bélanger-Desmarais, Christian Reber

Subject: Chemistry And Materials Science, Inorganic And Nuclear Chemistry Keywords: au(I) dithiocarbamate and phosphine complex; Raman spectroscopy; Single crystal X-ray diffraction; DFT calculations

Online: 20 March 2017 (10:00:42 CET)

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Preprint BRIEF REPORT | doi:10.20944/preprints202105.0526.v1

Circulating SARS-CoV-2 Variants in Italy, October 2020-March 2021

Alessia Lai, Annalisa Bergna, Stefano Menzo, Gianguglielmo Zehender, Sara Caucci, Valeria Ghisetti, Francesca Rizzo, Fabrizio Maggi, Francesco Cerutti, Giorgio Giurato, Alessandro Weisz, Chiara Turchi, Bianca Bruzzone, Francesca Ceccherini-Silberstein, Nicola Clementi, Annapaola Callegaro, Fabio Sagradi, Daniela Francisci, Emmanuele Venanzi Rullo, Ilaria Vicenti, Massimo Clementi, Massimo Galli

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: SARS-CoV-2 virus; complete genome sequencing; COVID-19 RT-PCR testing; Spike protein; vi-ral variants

Online: 21 May 2021 (15:12:17 CEST)

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Preprint REVIEW | doi:10.20944/preprints202009.0526.v1

Nucleic Acid and Immunological Diagnostics for SARS-CoV-2: Processes, Platforms and Pitfalls

Avinash Premraj, Abi George Aleyas, Binita Nautiyal, Thaha Jamal Rasool

Subject: Biology And Life Sciences, Virology Keywords: COVID-19 testing; molecular diagnostics; immunological testing; RT-qPCR; ELISA; pool PCR; lateral flow assay; rapid assay

Online: 23 September 2020 (03:33:12 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202006.0275.v1

Analysis of the Primary Presenting Symptoms and Hematological Findings of COVID-19 Patients in Bangladesh

Abu Taiub Mohammed Mohiuddin Chowdhury, Md Rezaul Karim, H.M. Hamidullah Mehedi, Mohammad Shahbaz, Md Wazed Chowdhury, Guo Dan, Shuixiang He

Subject: Medicine And Pharmacology, Hematology Keywords: SARS-CoV-2; COVID-19; real-time RT-PCR; COVID-19 symptoms; COVID-19 hematological findings; Bangladesh

Online: 21 June 2020 (14:47:03 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202310.1193.v1

Synthesis, Structure, DFT and In Silico Studies of Zn (II) Complex with Lipoic Acid: A Potential Antidiabetic Drug

Farkhod Jumabaev, Diyorbek Khayrullaev, Rukhsona Zakirova, Azamat Abdunazarov, Avez Sharipov

Subject: Chemistry And Materials Science, Inorganic And Nuclear Chemistry Keywords: Racemic α-lipoic acid; zinc; metallcomplex, in silico, DFT calculation; molecular docking simulation; target proteins; diabetes

Online: 19 October 2023 (08:09:26 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202011.0047.v1

Stacking Effects on Anthraquinone/DNA Charge-Transfer Electronically Excited States

Gustavo Cárdenas, Juan J. Nogueira

Subject: Chemistry And Materials Science, Analytical Chemistry Keywords: Photodynamic Therapy; Charge Transfer; Electronically Excited States; Anthraquinone; DNA; Molecular Dynamics; TD-DFT; Transition-Density Analysis

Online: 2 November 2020 (14:15:09 CET)

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Preprint ARTICLE | doi:10.20944/preprints201910.0374.v1

The Low Lying Double-Exciton State of Conjugated Diradicals: Assessment of TDUDFT and Spin-Flip TDDFT Predictions

Sofia Canola, Yasi Dai, Fabrizia Negri

Subject: Chemistry And Materials Science, Theoretical Chemistry Keywords: conjugated diradicals; DFT; broken symmetry; double exciton state; TDDFT; spin-flip TDDFT; diradical character; NFOD descriptor

Online: 31 October 2019 (15:29:31 CET)

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Preprint ARTICLE | doi:10.20944/preprints202304.0971.v1

Diagnostic of Patients With COVID-19 Pneumonia Using Passive Medical Microwave Radiometry (MWR)

Berik Emilov, Aleksander Sorokin, Meder Seiitov, Tulegen Chubakov, Sergey Vesnin, Igor Goryanin

Subject: Medicine And Pharmacology, Pulmonary And Respiratory Medicine Keywords: 2019-nCoV; COVID-19; RT-PCR; SARS-CoV-2; Community-acquired pneumonia; Chest CT; microwave radiometry; temperature measurement

Online: 26 April 2023 (08:02:32 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202204.0115.v1

A Quantum-Chemical Study of Boro-Fullerenes B₆₀H₆₀, B₆₀F₃₀H₃₀ , and B₆₀F₆₀

Ofelia B. Oña, Maxime Ferrer, Diego R. Alcoba, Alicia Torre, Luis Lain, Gustavo Massaccesi, Douglas J. Klein, Ibon Alkorta, José Elguero, Josep M. Oliva-Enrich

Subject: Chemistry And Materials Science, Theoretical Chemistry Keywords: boron; fullerenes; chemical bond; electronic structure; DFT; localization; bond order; QTAIM; ELF; Hückeloid model; heat of formation

Online: 13 April 2022 (04:30:00 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202112.0296.v1

Plasmodium falciparum Dihydroorotate Dehydrogenase, Fragment-based Drug Design, 2D-QSAR, DFT Calculation, Lead Optimization, Induced Fit Docking

Opeyemi Iwaloye, Olusola Elekofehinti, Femi Olawale, Prosper Chukwuemeka, Kikiowo Babatomiwa, Ibukun Folorunso

Subject: Medicine And Pharmacology, Pharmacology And Toxicology Keywords: Plasmodium falciparum dihydroorotate dehydrogenase; fragment-based drug design; 2D-QSAR; DFT calculation; Lead optimization; Induced Fit docking

Online: 20 December 2021 (09:39:42 CET)

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Preprint ARTICLE | doi:10.20944/preprints201712.0173.v4

Four Particular Cases of the Fourier Transform

Jens V. Fischer

Subject: Computer Science And Mathematics, Analysis Keywords: Fourier transform; Fourier series; DTFT; DFT; generalized functions; tempered distributions; Schwartz functions; Poisson Summation Formula; discretization; periodization

Online: 21 November 2018 (11:09:28 CET)

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Preprint ARTICLE | doi:10.20944/preprints202208.0392.v1

Comparison of Four Real-time Polymerase Chain Reaction Assays for the Detection of SARS-CoV-2 on respiratory samples from Tunja, Boyacá - Colombia

Lorenzo Hernando Salamanca Neita, Óscar Leonardo Carvajal Rojas, Juan Pablo Carvajal Rojas, Ruth Maribel Forero, Niya Alexandra Segura

Subject: Biology And Life Sciences, Virology Keywords: Severe Acute Respiratory Syndrome-CoV-2 (SARS-CoV2), COVID-19, molecular diagnostics, real-time polymerase chain reaction (RT-qPCR)

Online: 23 August 2022 (03:55:44 CEST)

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Background: Coronavirus disease (COVID-19) is an infectious disease caused by the SARS-CoV-2. In Colombia, many commercial methods are now available to perform the RT-qPCR assays, and the laboratories must evaluate its diagnostic accuracy to ensure reliable results to suspected COVID-19 patients. The purpose of the study was to compare four commercial RT-qPCR assays for detection of SARS-CoV2 virus, from nasopharyngeal swab samples referred to Laboratorio Carvajal IPS, SAS of Tunja, Boyacá - Colombia. Methods: This prospective study was conducted on 152 samples of respiratory tract samples (Nasopharyngeal Swab) from patients with suspected SARS-CoV-2 infection. Diagnostic accuracy of GeneFinderTM COVID-19 Plus RealAmp (In Vitro diagnostic), One-Step Real-Time RT-PCR (Vitro Master diagnostica), Berlin modified protocol and gold standard Berlin protocol (Berlin Charite Probe One-Step RT-qPCR Kit, New England Biolabs) as reference was assessed. Operational characteristics were estimated in terms of sensitivity, specificity, agreement, and predictive values. Results: Using Berlin Charite Probe One-Step RT-qPCR Kit as reference, the sensitivity/specificity for the diagnostic tests were found to be GeneFinderTM COVID-19 Plus RealAmp Kit 100%/92.7%, One-Step Real-Time RT-PCR, One-Step Real-Time RT-PCR 92.75%/67.47%, and Berlin modified protocol 100%/96.39%. The results of four commercially available methods were found to be consistent with those obtained from Berlin Modified protocol analysis for % of the samples and showed good agreement (κ= 0.96). Concordant SARS-CoV2 negative and positive RT-qPCR results were reported for xxx and xxx samples, respectively. Summarize something about the Ct. Conclusion: Our data demonstrate that all commercially available methods are rapid and reliable for the identification of SARS-CoV-2 virus associated with COVID-19. One-Step RT-qPCR Kit and GeneFinderTM COVID-19 Plus RealAmp assay show optimal sensitivity compared with Belin modified protocol. In addition, there is no significant correlation between xxxxx

Preprint ARTICLE | doi:10.20944/preprints202312.1956.v1

Photocatalytic CO2 to CO Reduction with Cyclometalated Pt(II) Complexes of N^C^N Pincer Dipyridylbenzene Ligands: A DFT study

Antonia Sarantou, Athanassios Tsipis

Subject: Chemistry And Materials Science, Theoretical Chemistry Keywords: Photocatalytic CO2 reduction; DFT/TDDFT; Pt(II) pincer complexes; T1 excited state electrochemistry, CO2 fixation/activation by Pt

Online: 28 December 2023 (02:09:16 CET)

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Preprint ARTICLE | doi:10.20944/preprints202307.2130.v1

Redox Chemistry of Pt(II) Complex with Non-Innocent NHC Bis(phenolate) Pincer Ligand: Electrochemical, Spectroscopic and Computational Aspects

Ilya K. Mikhailov, Zufar N. Gafurov, Alexey A. Kagilev, Vladimir I. Morozov, Artyom O. Kantyukov, Ekaterina Zueva, Gumar R. Ganeev, Ilyas F. Sakhapov, Asiya V. Toropchina, Igor A. Litvinov, Galina A. Gurina, Alexander A. Trifonov, Oleg G. Sinyashin, Dmitry G. Yakhvarov

Subject: Chemistry And Materials Science, Applied Chemistry Keywords: cyclic voltammetry; electron paramagnetic resonance; DFT calculations; UV-VIS/NIR; phenoxyl radical; pincer complex; platinum complex; NHC ligand

Online: 1 August 2023 (03:38:51 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202111.0430.v1

Two Compounds of 1-((4-Bromothiophen-2-Yl)Methylene)-2-(Perfluorophenyl)Hydrazine, and 1-((4-Bromo-5-Methylthiophen-2-Yl)Methylene)-2-(Perfluorophenyl)Hydrazine and They Crystal, Molecular and Electronic Properties

Július Sivý, Dušan Bortňák, Daniel Végh, Erik Rakovský

Subject: Chemistry And Materials Science, Analytical Chemistry Keywords: Ab initio DFT/B3LYP/6-311G/Auto calculation; hydrazine; Hirshfeld surface; hydrogen interactions; single-crystal X-ray study

Online: 23 November 2021 (15:03:30 CET)

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Preprint ARTICLE | doi:10.20944/preprints202008.0351.v1

Conceptual DFT-based Computational Peptidology of Marine Natural Compounds: Discodermins A–H

Norma Flores-Holguín, Juan Frau, Daniel Glossman-Mitnik

Subject: Chemistry And Materials Science, Theoretical Chemistry Keywords: discodermins A-H; chemical reactivity theory; conceptual DFT; global and local reactivity descriptors; pKa; bioavailability; bioactivity scores; ADME

Online: 17 August 2020 (04:45:58 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202007.0406.v1

X-Ray Photoelectron Spectroscopy for Determining Interface Dipoles of Self-Assembled Monolayers

Thomas C. Taucher, Egbert Zojer

Subject: Physical Sciences, Condensed Matter Physics Keywords: x-ray photoelectron spectroscopy; XPS; self-assembled monolayer; SAM; collective electrostatic; band-structure calculation; density-functional theory; DFT

Online: 19 July 2020 (10:40:47 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202312.0487.v1

6-Amino-4-Aryl-7-Phenyl-3-(Phenylimino)-4,7-Dihydro-3H-[1,2]dithiolo[3,4-B]pyridine-5-Carboxamides: Synthesis, Biological Activity, Quantum Chemical Studies and In Silico Docking Studies

Victor V. Dotsenko, Alexander V. Bespalov, Anna E. Sinotsko, Azamat Z. Temerdashev, Vladimir K. Vasilin, Ekaterina A. Varzieva, Vladimir D. Strelkov, Nicolai A. Aksenov, Inna V. Aksenova

Subject: Chemistry And Materials Science, Organic Chemistry Keywords: heterocyclization; Michael addition; dithiomalondiamides; dithiolo[3,4-b]pyridines; DFT calculations; reaction mechanism studies; herbicide safeners; molecular docking; ADMET properties.

Online: 7 December 2023 (07:07:11 CET)

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Preprint ARTICLE | doi:10.20944/preprints202309.1037.v1

Evaluation of Standard M10 Assay for Rapid Molecular Diagnosis of SARS-CoV-2, Influenza A/B virus and Respiratory Syncytial Virus (RSV)

Azwani Abdullah, I-Ching Sam, Yin Jie Ong, Chun Hao Theo, Muhammad Harith Pukhari, Yoke Fun Chan

Subject: Medicine And Pharmacology, Clinical Medicine Keywords: respiratory syncytial virus; influenza A virus; influenza B virus; SARS-CoV-2; rapid RT-PCR; diagnostic accuracy; point-of-care testing

Online: 15 September 2023 (05:38:13 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202308.1465.v1

Pfizer-BioNTech mRNA Vaccine Protection among Children and Adolescents Aged 12–17 Years against COVID-19 Infection in Qatar

Khadieja Osman Hassan Elhag, Jesha Mohammedali Mundodan, Juel Bikhash Chowdhry, Rejoice Puthuchira Ravi, Rekaya houda Baaboura, Jeevan Albuquerque, Bilal Riaz, Reem Yusuf Emran, Khatija Batoul, Abdul Mahmood Esameldin, Zinah Al Tabatabaee, Hayat Salaheldin Khogali, Soha Shawqi Albayat

Subject: Public Health And Healthcare, Public Health And Health Services Keywords: Adolescent; children; 12-17 years COVID-19 vaccine; fully vaccinated; partially vaccinated; vaccination status; RT-PCR-positive; Pfizer; BNT162b2; vaccine effectiveness

Online: 22 August 2023 (03:02:19 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201809.0054.v1

THD Reduction in Wind Energy System Using Type-4 Wind Turbine/PMSG Applying the Active Front-End Converter Parallel Operation

Nadia Maria Salgado-Herrera, David Campos-Gaona, Olimpo Anaya-Lara, Aurelio Medina-Rios, Roberto Tapia-Sanchez, Juan Ramon Rodriguez-Rodriguez

Subject: Engineering, Electrical And Electronic Engineering Keywords: Active Front-End converter; back-to-back converter; PMSG; THD; Type-4 wind turbine; wind energy system; Opal-RT Technologies®

Online: 4 September 2018 (05:02:15 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201812.0173.v2

Synthesis, Crystal Structure, DFT studies, Docking Studies and Fluorescent Properties of 2-(Adamantan-1-yl)-2H-isoindole-1-carbonitrile

Jacques Joubert

Subject: Chemistry And Materials Science, Organic Chemistry Keywords: 2-(Adamantan-1-yl)-2H-isoindole-1-carbonitrile; X-ray diffraction; DFT; molecular orbital calculations; fluorescence; docking; nNOS; fluorescent ligand

Online: 14 December 2018 (11:41:20 CET)

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Preprint ARTICLE | doi:10.20944/preprints202310.0519.v1

Optimization of a protocol for launching grapevine infection with the biologically active cDNA clones of a virus

Mehdi Shabanian, Caihong Li, Ali Ebadi, Valerian Dolja, Baozhong Meng

Subject: Biology And Life Sciences, Virology Keywords: Grapevine leafroll disease; Closteroviridae; GLRaV-3cDNA clones; RT-qPCR; Western blot; vacuum agro-infiltration; agro-pricking; agro-drenching; agro-injection; Koch’s postulates

Online: 9 October 2023 (15:17:00 CEST)

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Grapevine leafroll disease (GLRD) is the most globally prevalent and destructive disease complex responsible for significant reductions in grape yield and quality as well as wine production. GLRD is associated with several positive-strand RNA viruses of the family Closteroviridae, designated grapevine leafroll-associated viruses (GLRaVs). However, the specific etiological role of any of these GLRaVs in GLRD has not been demonstrated. Even though GLRaV-3 is considered the chief GLRD agent, little is known about the molecular, cellular and pathological properties of this virus. Such knowledge gap is due to multiple factors, including unavailability of biologically active virus cDNA clones and the lack of reliable experimental systems for launching grapevine infection using such clones. In this work, we have tested four methods for inoculating tissue cultured grapevine plantlets with cDNA clones of GLRaV-3: i) vacuum agro-infiltration; ii) agro-pricking; iii) agro-drenching and iv) agro-injection. We have shown that vacuum agro-infiltration was the most effective among these methods. Further, we examined the impacts of different experimental conditions on the survival and infectivity rate of grapevines after infiltration. To verify the infectivity rate for different treatments, we used RT-PCR, RT-qPCR, and Western blotting. We have found that humidity plays a critical role in the survival of plantlets after agro-infiltration and that the use of RNA silencing suppressor, and dormancy treatment both had strong effects on the infection rates. To our best knowledge, the experimental protocol reported here is the most effective system for launching infection of grapevine using cDNA clones of grapevine viruses featuring up to 70% infection rate. This system has strong potential to facilitate grapevine virology research including fulfillment of Koch’s postulates for GLRD and other major virus diseases as well as the molecular, cellular, and pathological properties of GLRaVs and potentially other important grapevine viruses.

Preprint SHORT NOTE | doi:10.20944/preprints202309.0671.v1

(3-(4-chlorophenyl)-4,5-dihydroisoxazol-5-yl)methyl Benzene-Sulfonate

Loubna Mokhi, Karim Chkirate, Xiaodong Zhang, Mohsine Driowya, Khalid Bougrin

Subject: Chemistry And Materials Science, Organic Chemistry Keywords: Green strategy; One-pot reaction; isoxazoline sulfonate; Ultrasound cavitation; X-ray single-crystal structure analysis; Hydrogen bond; Hirshfeld surface analysis; DFT calculation.

Online: 11 September 2023 (09:58:23 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202306.0990.v1

The copper(II)-Thiodiacetate (Tda) Chelate As Efficient Receptor of N9-(2-Hydroxyethyl)adenine (9heade). Synthesis, Molecular and Crystal Structures, Physical Properties and Dft Calculations of [Cu(tda)(9heade)(H2O)]·2H2O

Carmen Rosales-Martínez, Antonio Matilla-Hernández, Duane Choquesillo-Lazarte, Antonio Frontera, Alfonso Castiñeiras, Juan Niclós-Gutiérrez

Subject: Chemistry And Materials Science, Inorganic And Nuclear Chemistry Keywords: Copper(II); thiodiacetate chelate; synthetic adenine nucleoside; molecular and crystal structure; chelate-nucleoside recognition; water-mediated interligand interactions, physical properties; DFT calculations.

Online: 14 June 2023 (05:32:53 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201912.0248.v1

Polymer Brush Bilayers under Stationary Shear Motion at Non-Linear Response Regime: An Impressive Theoretical Approach

Mike Edwards

Subject: Physical Sciences, Condensed Matter Physics Keywords: polymer brush bilayers; non-linear response regime; non-Newtonian complex fluids; stationary shear motion; density functional theory (DFT); scaling arguments; phenomenological arguments

Online: 19 December 2019 (07:10:21 CET)

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Preprint ARTICLE | doi:10.20944/preprints201809.0532.v1

Hydrogen Oxidation on Ni-Based Electrocatalysts: The Effect of Metal Doping

Elena S. Davydova, Jérémie Zaffran, Kapil Dhaka, Maytal Caspary Toroker, Dario R. Dekel

Subject: Chemistry And Materials Science, Electrochemistry Keywords: metal doping; nickel-based catalyst; transition metals; synthesis; hydrogen oxidation reaction; exchange current density; alkaline medium; DFT; hydrogen binding energy; hydroxide binding energy

Online: 27 September 2018 (04:59:46 CEST)

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