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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/preprints201605.0002.v1

Thermodynamic and Theoretical Studies of the Imide Derivatives

Ahmed Al-Amiery, Hasan R. Obayes, Mohammed S. Ali, Ghadah H. Alwan

Subject: Physical Sciences, Thermodynamics Keywords: imide, DFT, HOMO, spontaneous, endothermic

Online: 11 May 2016 (07:42:45 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/preprints201803.0116.v1

Experimental and DFT Investigation on the Corrosion Inhibition of Mild Steel by 1,2,3-Triazolereg Ioisomers in 1M Hydrochloric Acid Solution

H. Rahmani, K. Ismaily Alaoui, K.M. Emran, A. El Hallaoui, M. Taleb, S. El Hajji, B. Labriti, E. Ech-chihbi, B. Hammouti, F. El-Hajjaji

Subject: Chemistry And Materials Science, Chemical Engineering Keywords: oxazole-triazole; inhibition corrosion; mild steel; EIS; DFT

Online: 15 March 2018 (05:10:29 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/preprints201610.0022.v1

Transcriptome Profiling Analysis of Wolf Spider Pardosa pseudoannulata (Araneae: Lycosidae) after Cadmium Exposure

Chang-chun Li, Yong Wang, Guo-yuan Li, Yueli Yun, Yu-jun Dai, Jian Chen, Yu Peng

Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: P. pseudoannulata; Cadmium; Transcriptome; RT-qPCR

Online: 8 October 2016 (11:07:25 CEST)

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Preprint COMMUNICATION | doi:10.20944/preprints202203.0010.v1

Analytical Sensitivity of Five SARS-CoV-2 Rapid Antigen Tests for Omicron Versus Delta Variant

Jean-Louis Bayart, Jonathan Degosserie, Julien Favresse, Constant Gillot, Marie Didembourg, Happy Phanio Djokoto, Valérie Verbelen, Gatien Roussel, Celine Maschietto, François Mullier, Jean-Michel Dogné, Jonathan Douxfils

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; variant; Omicron; Delta; antigen; RT-qPCR

Online: 1 March 2022 (09:01:19 CET)

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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/preprints201907.0189.v1

Discrete Two Dimensional Fourier Transform in Polar Coordinates Part II: Numerical Computation and Approximation of the Continuous Transform

Xueyang Yao, Natalie Baddour

Subject: Computer Science And Mathematics, Discrete Mathematics And Combinatorics Keywords: Fourier Theory; DFT in polar coordinates; polar coordinates; multidimensional DFT; discrete Hankel transform; discrete Fourier transform; orthogonality

Online: 16 July 2019 (08:00:00 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201701.0031.v1

Molecular Structure, Luminescent and DFT Computational Studies of Two Novel Europium(III) β-diketonate Complexes

Haifeng Shao, Yanjun Hou, Jinyuan Bai, Haijun Niu

Subject: Chemistry And Materials Science, Organic Chemistry Keywords: TFT; complexes; luminescent; synthesis; Density functional theory (DFT)-computation

Online: 6 January 2017 (09:47:23 CET)

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Preprint ARTICLE | doi:10.20944/preprints201612.0109.v1

Theoretical Studies of Acrolein Hydrogenation to Propenol and Propanal on Au₃ and Au₅

Guo-Jun Kang, Shuai He, Xue-Feng Ren

Subject: Chemistry And Materials Science, Theoretical Chemistry Keywords: acrolein; Au Cluster; DFT

Online: 21 December 2016 (10:15:53 CET)

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Preprint ARTICLE | doi:10.20944/preprints201705.0173.v1

Molecular and Biochemical Characterization of Calmodulin from Echinococcus granulosus

Ning Wang, Xiu-Qin Zhong, Xing-Ju Song, Xiao-Bin Gu, Wei-Ming Lai, Yue Xie, Xue-Rong Peng, Guang-You Yang

Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: Echinococcus granulosus; Calmodulin; Ca2+-binding protein; Immunohistochemical localization; Quantitative RT-PCR

Online: 24 May 2017 (08:07:35 CEST)

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Preprint COMMUNICATION | doi:10.20944/preprints201807.0221.v1

Combination High Energy with Stability: Polynitrogen Explosives N14 and N18

Jifeng Chen, Yi Yu, Yuchuan Li, Siping Pang

Subject: Chemistry And Materials Science, Physical Chemistry Keywords: N14; N18; density functional theory (DFT); high energy; stability

Online: 13 July 2018 (03:35:47 CEST)

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Preprint COMMUNICATION | doi:10.20944/preprints202202.0158.v1

Comparison of Auto Sampling and Passive Sampling Methods for SARS-CoV-2 Detection in Wastewater

Melissa Wilson, Yuanyuan Qiu, Jiaao Yu, Bonita E. Lee, David T. McCarthy, Xiaoli Pang

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; wastewater; passive sampler; autosampler; RT-qPCR

Online: 11 February 2022 (08:38:07 CET)

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Preprint ARTICLE | doi:10.20944/preprints201804.0364.v1

Kinetics and DFT Studies of the Hydrogenation Reactions of Alkenes and Alkynes Catalyzed by (Benzoimidazol-2-ylmethyl)amine palladium(II) Complexes

Thandeka Tshabalala, Stephen Ojwach

Subject: Chemistry And Materials Science, Applied Chemistry Keywords: palladium; catalysts; hydrogenation; kinetics; DFT

Online: 27 April 2018 (16:18:05 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 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 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/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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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 REVIEW | doi:10.20944/preprints201707.0003.v1

Chronic Wasting Disease: Evolution of Diagnostic Testing for a Naturally Occurring Prion Disease

Nicholas J. Haley, Juergen A. Richt

Subject: Medicine And Pharmacology, Veterinary Medicine Keywords: prion, cervids, PMCA, RT-QuIC, diagnosis

Online: 3 July 2017 (17:34:35 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201801.0260.v1

Synthesis, X-ray Crystal Structures, Computational Studies and Catechol Oxidase Activity of New Acylhydrazone Derivatives

Khalid Karrouchi, Smaail Radi, Yousfi El Bekkaye, Nada Kheira Sebbar, Jamal Taoufi Taoufik, Younes Ouzidan, Hazem A. Ghabbour, Yahia Mabkhot, Salim Al-Showiman, Seham Alterary, M’hammed Ansar

Subject: Chemistry And Materials Science, Organic Chemistry Keywords: Acylhydrazone; Pyrazole; X-ray crystallography; DFT/B3LYP; Catecholase activity

Online: 28 January 2018 (12:44:49 CET)

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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/preprints201908.0238.v1

Identification of Potent Inhibitors against Aurora Kinase A Using Molecular Docking and Molecular Dynamics Simulation Studies

Sathishkumar Chinnasamy, Gurudeeban Selvaraj, Aman Chandra Kaushik, Satyavani Kaliamurthi, Asma Sindhoo Nangraj, Chandrabose Selvaraj, Sanjeev Kumar Singh, Ramanathan Thirugnanasambandam, Keren Gu, Donq-qing Wei

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: aurora kinase A; molecular docking; DFT; MD simulation

Online: 23 August 2019 (05:01:40 CEST)

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Preprint REVIEW | doi:10.20944/preprints202005.0142.v1

COVID-19 Clinical and Laboratory Diagnosis Overview

Rania Zayed, Dalia Omran, Abeer Zayed

Subject: Biology And Life Sciences, Virology Keywords: COVID-19; serology; RT-PCR; lab; clinical

Online: 8 May 2020 (12:26:46 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201902.0262.v1

Formation of Potassium 2-Hydroxy-6-naphthoate by Kolbe-Schmitt Carboxylation: A Joint Experimental and Theoretical Study

So-Jin Ahn, Du-Hyeon Kim, Eung-Gun Kim, Yong-Kul Lee

Subject: Chemistry And Materials Science, Organic Chemistry Keywords: 2-Hydroxy-6-naphthoic acid; CO2 fixation; Carboxylation; DFT

Online: 28 February 2019 (07:00:19 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 COMMUNICATION | doi:10.20944/preprints202004.0206.v2

An Approach to Screen COVID-19 Patients Using Diagnostic Kits: With Special Reference to Pakistan

Faiza Durrani, Farhat Zaheer

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: COVID-19; RT-qPCR; liquid phase immunoassay

Online: 30 April 2020 (05:10:43 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/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/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/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/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/preprints201912.0050.v1

Zn(II) Complex for Highly Sensitive and Selective Detection of Acetone at Room Temperature

Mohd. Muddassir, Abdullah Alarifi, Mohammad Usman

Subject: Chemistry And Materials Science, Inorganic And Nuclear Chemistry Keywords: x-ray crystallography; h-bonding; acetone; fluorescence sensing; dft

Online: 4 December 2019 (12:22:21 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/preprints201908.0030.v1

Theoretical Determination of Size Effects in Zeolite-Catalyzed Alcohol Dehydration

Larrissa Y. Kunz, Lintao Bu, Brandon C. Knott, Cong Liu, Mark R. Nimlos, Rajeev S. Assary, Larry A. Curtiss, David J. Robichaud, Seonah Kim

Subject: Chemistry And Materials Science, Physical Chemistry Keywords: biomass pyrolysis; alcohol dehydration; zeolite; DFT; ONIOM

Online: 2 August 2019 (10:50:24 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202204.0091.v1

Evidence-Based Evaluation of PCR Diagnostics for SARS-Cov-2 and The Omicron Variants by Sanger Sequencing

Sin Hang Lee

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: SARS-CoV-2; SARS-CoV; RT-PCR; Sanger sequencing; RT-qPCR; receptor-binding domain (RBD); N-terminal domain (NTD); Omicron; multi-allelic SNPs; false-positive

Online: 12 April 2022 (03:57:29 CEST)

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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 REVIEW | doi:10.20944/preprints202005.0316.v1

Diagnostics and Monitoring of COVID-19 Infection – Current Understanding

Martina Bergant, Ario de Marco

Subject: Biology And Life Sciences, Virology Keywords: RT-PCR; seroconversion; serum biomarkers; SARS-CoV2; neutralizing antibodies

Online: 20 May 2020 (04:10:24 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202008.0681.v1

QUMEC: Software for Quantum Mechanics First Principle Calculation in 3-Dimensional Real Space

Hamed Hosseinzadeh

Subject: Chemistry And Materials Science, Materials Science And Technology Keywords: Quantum mechanics; DFT; Pseudopotential; Total energy calculation; Software

Online: 30 August 2020 (17:37:33 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201911.0042.v1

In Spino-Cerebellar Tissue, Ataxin-2 Expansion Affects Ceramide-Sphingomyelin Metabolism

Nesli-Ece Sen, Aleksandar Arsovic, David Meierhofer, Susanne Brodesser, Carola Oberschmidt, Júlia Canet-Pons, Zeynep-Ece Kaya, Melanie V. Halbach, Suzana Gispert, Konrad Sandhoff, Georg Auburger

Subject: Biology And Life Sciences, Endocrinology And Metabolism Keywords: olivo-ponto-cerebellar atrophy (OPCA); amyotrophic lateral sclerosis (ALS); tauopathy; leukodystrophy; mass spectrometry; RT-qPCR; Ceramide Synthase (CERS2/CERS1); Serine Palmitoyltransferase 2 (Sptlc2); neutral Sphingomyelinase (Smpd3); neutral Ceramidase (Asah2); Fatty Acid Elongase (Elovl1/4/5); SCA34; SCA38; acid Sphingomyelinase (ASMase, Smpd1)

Online: 5 November 2019 (03:04:02 CET)

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Ataxin-2 (ATXN2) acts during stress-responses, modulating mRNA translation and nutrient metabolism. Atxn2 knockout mice exhibit progressive obesity, dyslipidemia and insulin resistance. Conversely, the progressive ATXN2 gain-of-function due to polyGlutamine (polyQ) expansions leads to a dominantly inherited neurodegenerative process named spinocerebellar ataxia type 2 (SCA2), with early adipose tissue loss and late muscle atrophy. We tried to understand lipid dysregulation in a SCA2 patient brain and in an authentic mouse model. Thin layer chromatography of a patient cerebellum was compared to the lipid metabolome of Atxn2-CAG100-KnockIn (KIN) mouse spinocerebellar tissue. The human pathology caused deficits of sulfatide, galactosylceramide, cholesterol, C22/24-sphingomyelin and gangliosides GM1a/GD1b, despite quite normal levels of C18-sphingomyelin. Cerebellum and spinal cord from the KIN mouse showed a consistent decrease of various ceramides, with a significant elevation of sphingosine in the more severely affected spinal cord. Deficiency of C24/26-sphingomyelins contrasted with excess C18/20-sphingomyelin. Spinocerebellar expression profiling revealed consistent reductions of CERS protein isoforms, of Sptlc2 and Smpd3, but upregulation of Cers2 mRNA, as prominent anomalies in the ceramide-sphingosine metabolism. Reduction of Asah2 mRNA correlated to deficient S1P levels. In addition, downregulations for the elongase Elovl1, Elovl4, Elovl5 mRNAs and ELOVL4 protein explain the deficit of very-long-chain sphingomyelin. Reduced ASMase protein levels correlated to the accumulation of long-chain sphingomyelin. Overall, a deficit of myelin lipids was prominent in SCA2 nervous tissue at prefinal stage, not compensated by transcriptional adaptation of several metabolic enzymes. Myelination is controlled by mTORC1 signals, so our human and murine observations are in agreement with the known role of ATXN2 yeast, nematode and mouse orthologs as mTORC1 inhibitors and autophagy promoters.

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/preprints201807.0175.v1

Computational Investigation on the Enantioselective Copper(I)-Catalyzed Addition of Enynes to Ketones

Hanwei Li, Mingliang Luo, Guohong Tao, Song Qin

Subject: Chemistry And Materials Science, Organic Chemistry Keywords: copper-catalysed; enantioselective; DFT

Online: 10 July 2018 (11:54:41 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202009.0324.v1

High Rate of Circulating MERS-CoV in Dromedary Camels at Slaughterhouses in Riyadh, 2019

Taibh Aljasim, Abdulrahman Almasoud, Haya A. Aljami, Mohamed W. Alenazi, Suliman A. Alsagaby, Asma N. Alsaleh, Naif Khalaf Alharbi

Subject: Biology And Life Sciences, Virology Keywords: MERS-CoV; camel; seroprevalence; transmission; ELISA; RT-qPCR; slaughterhouse

Online: 15 September 2020 (03:54:34 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201809.0176.v1

Formamide Adsorption at the Amorphous Silica Surface: a Combined Experimental and Computational Approach

Matteo Signorile, Clara Salvini, Lorenzo Zamirri, Francesca Bonino, Gianmario Martra, Mariona Sodupe, Piero Ugliengo

Subject: Chemistry And Materials Science, Physical Chemistry Keywords: formamide; silica; IR-spectroscopy; DFT

Online: 10 September 2018 (14:36:02 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/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 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/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 ARTICLE | doi:10.20944/preprints201905.0037.v1

Characterization and Antimicrobial Efficacy of Bovine Dermcidin, a Novel Antimicrobial Peptide Gene

Nevien Sabry, Tarek Moussa

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Bos taurus; skin; bovine dermcidin; RT-PCR; antimicrobial activity

Online: 6 May 2019 (08:35:59 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202109.0361.v1

Methodological Investigation for Hydrogen Addition to Small Cage Carbon Fullerenes

Yuri Tanuma, Toru Maekawa, Chris Ewels

Subject: Chemistry And Materials Science, Nanotechnology Keywords: Fullerene; Hydrogenation; DFT; Functionalisation; Growth; xTB; REBO; Interstellar

Online: 21 September 2021 (12:31:21 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201907.0151.v1

Discrete Two Dimensional Fourier Transform in Polar Coordinates Part I: Theory and Operational Rules

Natalie Baddour

Subject: Computer Science And Mathematics, Discrete Mathematics And Combinatorics Keywords: fourier theory; DFT in polar coordinates; polar coordinates; multidimensional DFT; discrete hankel transform; discrete fourier transform; orthogonality

Online: 11 July 2019 (05:09:11 CEST)

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Preprint BRIEF REPORT | doi:10.20944/preprints202005.0193.v1

Added Value of Chest CT in Suspected COVID-19: An Analysis of 239 Patients

Daniel A. Korevaar, Ruud S. Kootte, Loek P. Smits, Joost G. van den Aardweg, Peter I. Bonta, Janke Schinkel, Rene M. Vigeveno, Inge A.H. van den Berk, Maeke J. Scheerder, Bregtje A. Lemkes, Abraham Goorhuis, Ludo F.M. Beenen, Jouke T. Annema

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: COVID-19; diagnostic accuracy; CT; RT-PCR

Online: 11 May 2020 (12:35:08 CEST)

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Introduction: Clinicians have been struggling with the optimal diagnostic approach of patients with suspected COVID-19. We evaluated the added value of chest CT over RT-PCR alone. Methods: Consecutive adult patients with suspected COVID-19 presenting to the emergency department (Academic Medical Center, Amsterdam University Medical Centers, the Netherlands) from March 16^th to April 16^th were retrospectively included if they required hospital admission and underwent chest CT and RT-PCR testing for SARS-CoV-2 infection. The CO-RADS classification was used to assess the radiological probability of COVID-19, where a score of 1-2 was considered as negative, 3 as indeterminate, and 4-5 as positive. CT results were stratified by initial RT-PCR results. For patients with a negative RT-PCR but a positive CT, serology or multidisciplinary discussion after clinical follow-up constituted the final diagnosis. Results: 258 patients with suspected COVID-19 were admitted, of which 239 were included because they had both CT and RT-PCR testing upon admission. Overall, 112 patients (46.9%) had a positive initial RT-PCR, and 14 (5.9%) had a positive repeat RT-PCR. Of 127 patients with a negative or indeterminate initial RT-PCR, 38 (29.9% [95%CI 21.3-39.3%]) had a positive CT. Of these, 13 had a positive RT-PCR upon repeat testing, and 5 had positive serology. The remaining 20 patients were assessed in a multidisciplinary consensus meeting, and for 13 it was concluded that COVID-19 was ‘very likely’. Of 112 patients with a positive initial RT-PCR result, CT was positive in 104 (92.9% [95%CI 89.3-97.5%]). Conclusion: In a high-prevalence emergency department setting, chest CT showed high probability of COVID-19 (CO-RADS 4-5) in 29.9% of patients with a negative or indeterminate initial RT-PCR result. As the majority of these patients had proven or ‘very likely’ COVID-19 after follow-up, we believe that CT helps in the identification of patients who should be admitted in isolation.

Preprint ARTICLE | doi:10.20944/preprints201808.0552.v1

Magnetic Moments and Electron Transport through Chromium-based Antiferromagnetic Nanojunctions

Marco Bragato, Simona Achilli, Fausto Cargnoni, Davide Ceresoli, Rocco Martinazzo, Raffaella Soave, Mario Italo Trioni

Subject: Chemistry And Materials Science, Nanotechnology Keywords: antiferromagnetism; spintronics; electronic transport; DFT; ab initio calculations

Online: 31 August 2018 (15:55:42 CEST)

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Preprint BRIEF REPORT | doi:10.20944/preprints202105.0342.v1

RNA Extraction Alternative Method for SARS-CoV-2 Molecular Diagnosis

Elisa Bianchini, Francesco Rossignolo, Melissa Perfranceschi, Chiara Cazzin, Ronaldo Silva, Fabio Formenti, Francesca Perandin, Cristiana Griffante, Rosaria Remelli, Michela Padovani, Salvatore Scarso, Martina Leonardi, Chiara Piubelli

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: COVID-19; SARS-CoV-2; nasopharyngeal swab; RNA extraction; RT-PCR

Online: 14 May 2021 (14:46:42 CEST)

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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/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/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/preprints202103.0062.v1

A Full Computational Evaluation of Two Novel Chalcone Derivatives as Inhibitors for Colon Cancer Related Proteins.

Manos C. Vlasiou, Christos C. Petrou, Yiannis Sarigiannis, Kyriaki S. Pafiti

Subject: Medicine And Pharmacology, Gastroenterology And Hepatology Keywords: Xanthohumol; Colon cancer; Molecular docking, DFT, ADMET

Online: 2 March 2021 (09:51:01 CET)

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Preprint ARTICLE | doi:10.20944/preprints201901.0212.v1

One-tube RT-PCR for the Simultaneous Detection and Typing Duck Hepatitis A Virus Subtypes 1 and 3

Xueming Chen, Yuhuan Chen, Chunguo Liu, Xiaojun Li, Hongyu Liu, Xiaofei Bai, Ming Liu, Yun Zhang

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: DHAV-1; DHAV-3; Phylogenetic analysis; One-tube RT-PCR; Simultaneously

Online: 22 January 2019 (11:08:19 CET)

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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 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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Working Paper BRIEF REPORT

Positive Rate Is Useful to Evaluate the Sufficiency of RT-PCR Test Availability for COVID-19

Sadao Suzuki

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: COVID-19; RT-PCR test; pre-test probability; positive rate

Online: 5 May 2020 (06:04:41 CEST)

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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 REVIEW | doi:10.20944/preprints202308.1380.v1

The Iodine/Iodide/Starch Supramolecular Complex

Radu Silaghi-Dumitrescu, Szilard Pesek

Subject: Chemistry And Materials Science, Polymers And Plastics Keywords: amylose; iodine; iodide; starch; UV-vis; DFT

Online: 21 August 2023 (03:08:53 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202007.0433.v1

Cu-Doped KCl Unfolded Band Structure and Optical Properties Studied by DFT Calculations

Cesar Castillo-Quevedo, Jose Luis Cabellos, Raul Aceves, Roberto Núñez-González, Alvaro Posada-Amarillas

Subject: Chemistry And Materials Science, Materials Science And Technology Keywords: DFT calculations; unfolding band structure; optical spectrum; KCl

Online: 19 July 2020 (20:22:08 CEST)

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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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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/preprints202107.0215.v1

Molecular Geometry, Vibrational Spectroscopic, Molecular Orbital and Mulliken Charge Analysis of 4-(Carboxyamino)-Benzoic Acid: Molecular Docking and Dft Calculations

S.N. Saravanamoorthy, B. Vasanthi, R. Poornima

Subject: Chemistry And Materials Science, Biomaterials Keywords: DFT; HOMO; LUMO; MEP; FMO; RDG; ADMET

Online: 9 July 2021 (10:22:59 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/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 ARTICLE | doi:10.20944/preprints202109.0415.v2

A Routine Sanger Sequencing Target Specific Mutation Assay For SARS-CoV-2 Variants Of Concern And Interest

Sin Hang Lee

Subject: Biology And Life Sciences, Virology Keywords: Delta variant; Variants of concern; Variants of interest; SARS-CoV-2; Spike protein; Nested RT-PCR; Sanger sequencing; Amino acid mutations; ACE2 RBD; N-terminal domain (NTD)

Online: 2 November 2021 (10:40:46 CET)

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Preprint ARTICLE | doi:10.20944/preprints202103.0689.v1

Mobility Patterns of the Portuguese Population During the First Year of the COVID-19 Pandemic: A Longitudinal Study

Tiago Tamagusko, Adelino Ferreira

Subject: Engineering, Civil Engineering Keywords: COVID-19; mobility patterns; Rt; changepoint; modeling; Portugal; Longitudinal Study

Online: 29 March 2021 (12:31:54 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/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/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/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/preprints202010.0139.v1

A Review of Density Functional Models for the Description of Fe(II) Spin Crossover Complexes

Anton Römer, Lukas Hasecke, Peter Blöchl, Ricardo A. Mata

Subject: Chemistry And Materials Science, Analytical Chemistry Keywords: spin crossover; transition metals; DFT

Online: 6 October 2020 (16:01:57 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/preprints202012.0537.v1

Transferability of Molecular Potentials for 2D Molybdenum Disulphide

Marcin Maździarz

Subject: Chemistry And Materials Science, Biomaterials Keywords: 2D materials; MoS2; molecular potentials; DFT, elastic constants; phonons

Online: 21 December 2020 (15:55:33 CET)

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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/preprints202007.0056.v1

A Theoretical and Experimental Study on the Potential Luminescent and Biological Activities of Diaminodicyanoquinodimethane Derivatives

Edison Rafael Jimenez, Manuel Caetano, Nelson Santiago, F. Javier Torres, Thibault Terencio, Hortensia Rodriguez

Subject: Chemistry And Materials Science, Materials Science And Technology Keywords: Aggregation-induced emission; quinones; fluorescence; TD-DFT; quantum yield

Online: 5 July 2020 (08:38:20 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202110.0186.v1

Experimental and Density Functional Theory (DFT): a Dual Approach for the Adsorption of Cd (II) Ion from Aqueous Solution by Starch-Based Activated Carbon

Saad Melhi, Saeed Ullah Jan, Adnan Ali Khan, Khan Badshah, Saeed Ullah, Bushra Bostan, Zeliha Selamoglu

Subject: Chemistry And Materials Science, Applied Chemistry Keywords: Adsorption; DFT; Starch-based Activated Carbon; Kinetics; Thermodynamics

Online: 12 October 2021 (14:58:07 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202109.0331.v1

Batch Adsorption, Kinetics, and DFT study of Cd(II) Ion From Aqueous Solution By Low-Cost Starch-Based Activated Carbon

Saad Melhi Alshahrani, Bushra Bostan, Saeed Ullah Jan, Adnan Ali Khan, Khan Badsha, Saeed Ullah

Subject: Chemistry And Materials Science, Applied Chemistry Keywords: Adsorption; DFT; Cadmium(II) ion; Activated carbon; Kinetics; Thermodynamics

Online: 20 September 2021 (12:22:22 CEST)

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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/preprints202307.1387.v1

ToBRFV Mexican Strain: Seed Transmission Rate, Efficacy of Seed Disinfection Treatment, and Rapid Sensitive Detection in Seed Lots

Erika Janet Zamora-Macorra, Daniel Lobardo Ochoa-Martínez, Claudia Yaritza Chavarín-Camacho, Rosemarie W Hammond, Katia Aviña-Padilla

Subject: Biology And Life Sciences, Virology Keywords: seed transmission; tobamovirus; diagnostic method; natural hosts; RT-PCR

Online: 20 July 2023 (07:26:38 CEST)

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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/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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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/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/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/preprints202011.0573.v1

Electronic, Magnetic and Optical Properties of XScO₃ (X=Mo, W) Perovskites

Amall Ramanathan, Jamil Khalifeh

Subject: Physical Sciences, Theoretical Physics Keywords: DFT-mBJ; magnetic moments; optical conductivity; perovskites

Online: 23 November 2020 (09:24:43 CET)

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Working Paper ARTICLE

Magnetism and Magnetocystalline Anisotropy of Localized 1H/1T by S Atom Sliding

Eunsung Jekal, Dao Phuong

Subject: Chemistry And Materials Science, Nanotechnology Keywords: DFT calculation; magnetism; MoS

Online: 24 November 2019 (15:42:56 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/preprints202102.0525.v1

Exploring New Scaffolds for the Dual Inhibition of HIV-1 Rt Polymerase and Ribonuclease Associated Functions

Rita Meleddu, Angela Corona, Simona Distinto, Filippo Cottiglia, Serenella Deplano, Lisa Sequeira, Daniela Secci, Alessia Onali, Erica Sanna, Francesca Esposito, Italo Cirone, Francesco Ortuso, Stefano Alcaro, Enzo Tramontano, Peter Matyus, Elias Maccioni

Subject: Chemistry And Materials Science, Analytical Chemistry Keywords: HIV-RT; ribonuclease H; dual inhibitors; docking; putative binding

Online: 23 February 2021 (15:51:40 CET)

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Preprint ARTICLE | doi:10.20944/preprints202006.0280.v1

Expression of Stress-Mediating Genes Is Increased in Term Placentas of Women with Chronic Self-Perceived Anxiety and Depression

Cristina A. Martinez, Ina Marteinsdottir, Ann Josefsson, Gunilla Sydsjo, Elvar Theodorsson, Heriberto Rodriguez-Martinez

Subject: Medicine And Pharmacology, Obstetrics And Gynaecology Keywords: antenatal stress; hair cortisol; term-placentae; RT-qPCR; human

Online: 21 June 2020 (16:30:08 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202304.0676.v1

mech2d: An Efficient Tool for High-Throughput Calculation of Mechanical Properties for Two-Dimensional Materials

Haidi Wang, Tao Li, Xiaofeng Liu, Weiduo Zhu, Zhao Chen, Zhongjun Li, Jinlong Yang

Subject: Physical Sciences, Condensed Matter Physics Keywords: mechanical properties; 2D materials; high-throughput; DFT.

Online: 21 April 2023 (07:20:16 CEST)

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Preprint REVIEW | doi:10.20944/preprints202308.1678.v1

FLASH Radiation Therapy- Key Physical Irradiation Parameters and Beam Characteristics

roya boodaghi malidarre, Hesham M.H. Zakaly

Subject: Public Health And Healthcare, Physical Therapy, Sports Therapy And Rehabilitation Keywords: CONV-RT; FLASH-RT; ultra-high-dose-rate; beam characteristics; pulsed beams; normal tissue sparing

Online: 24 August 2023 (04:10:58 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/preprints202110.0269.v1

The Structural, Elastic, Electronic, Vibrational and Gravimetric Hydrogen Capacity Properties of the Perovskite Type Hydrides: DFT Study

Ülkü Bayhan, İnanç Yilmaz

Subject: Physical Sciences, Chemical Physics Keywords: Hydrogen; DFT; Electronic Properties; Energy Storage; Perovskite type Hydrides

Online: 19 October 2021 (10:37:03 CEST)

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