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Preprint ARTICLE | doi:10.20944/preprints202403.0992.v1

Epidemiological Characterization of Dengue Virus Serotypes in Mexico: Implications for Disease Severity

Porfirio Felipe Hernández Bautista, David Alejandro Cabrera Gaytán, Clara Esperanza Santacruz-Tinoco, Alfonso Vallejos Parás, Julio Elias Alvarado Yaah, Bernardo Martínez-Miguel, Yu Mei Anguiano Hernández, Lumumba Arriaga Nieto, Alejandro Moctezuma Paz, Leticia Jaimes Betancourt, Yadira Pérez Andrade, Oscar Cruz Orozco, Gabriel Valle Alvarado, Mónica Grisel Rivera Mahey

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: dengue; RT-qPCR; epidemiological surveillance; serotype

Online: 18 March 2024 (07:27:23 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 ARTICLE | doi:10.20944/preprints202401.1328.v1

Proteomics-Based RT-qPCR and Functional Analysis of 18 Genes in Metronidazole Resistance of Bacteroides fragilis

Bakhtiyar Mahmood, Anna Paunkov, Malgorzata Kupc, Katalin Burián, Erzsébet Nagy, David Leitsch, József Sóki

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Bacteroides, metronidazole, nim, resistance mechanism, RT-qPCR

Online: 17 January 2024 (13:06:47 CET)

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Preprint ARTICLE | doi:10.20944/preprints202306.1920.v1

Selection and Evaluation of Reference Genes for qRT-PCR Analysis in Amorphophallus konjac Based on Transcriptome Data

Yanli Liu, Chengcheng Zhang, Nunung Harijati, Ying Diao, Erxi Liu, Zhongli Hu

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: Amorphophallus; reference genes; RT-qPCR; gene expression

Online: 27 June 2023 (13:43:45 CEST)

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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 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/preprints202310.0104.v1

Dynamic and Seasonal Distribution of Enteric Viruses in Surface and Well Water in Riyadh (Saudi Arabia)

Islem Abid, Albert Blanco, Nawal Al-Otaibi, Susana Guix, Maria Isabel Costadreda, Rosa Maria Pinto, Albert Bosch

Subject: Biology And Life Sciences, Virology Keywords: Hepatitis A; Hepatitis E; Norovirus; Real-time RT-qPCR

Online: 3 October 2023 (04:25:03 CEST)

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Preprint COMMUNICATION | doi:10.20944/preprints202306.2007.v1

Ct-Value from qRT-PCR Can Predict SARS-CoV-2 Virus Assembly and Lineage Assignment Success

Dominik Hadzega, Klaudia Babisova, Michaela Hyblova, Nikola Janostiakova, Peter Sabaka, Pavol Janega, Gabriel Minárik

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; RNA genome assembly; RT-qPCR; SPAdes

Online: 29 June 2023 (02:12:07 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 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/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/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/preprints202407.0991.v1

Potential Performance of Two New RT-PCR and RT-q PCR Methods for Multiplex Detection of Dengue Virus Serotypes 1-4 and Chikungunya Virus in Mosquitoes Allowing Efficient Entomological Surveillance of Both Vector-Borne Diseases

Michel Kiréopori Gomgnimbou, Louis robert wendyam BELEM, Etienne Bilgo, Miriam Félicité Amara, Zouera Laouali, Ali Ouari, Toussaint Bayala, Kobo Gnada, Raymond Kharlis Yao, Moussa Namountougou, Ibrahim Sangaré

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: multiplex rt-pcr; multiplex rt-qpcr; molecular detection; dengue virus; chikungunya virus; mosquitoes; Burkina Faso

Online: 12 July 2024 (08:43:46 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202305.0001.v1

Seroepidemiological and Molecular Survey for Detection of SARS-CoV-2 Infection Among Children in Iran, September 2020 to June 2021: One-Year Cross-sectional Study

Roxana Mansour Ghanaie, Idesbald Boone, Ahmadreza Shamshiri, Abdollah Karimi, Arezu Amirali, Noushin Marhamati, Mohammad Hossein Rostami, Niloofar Pashaei, Shahriar Janbazi, Leila Azimi, Hannan Khodaei, Fatemeh Fallah, Tim Eckmanns, Andreas Jansen, Hamid Reza Baradaran, Maryam Momeny Ourimi, Saeed Maham, Ameneh Elikaei, Masoud Alebouyeh

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: SARS-CoV-2; COVID-19; Children; Seroprevalence; RT-qPCR; Iran

Online: 1 May 2023 (00:16:12 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202405.0256.v1

Mitochondrial Bioenergetics in Placenta of Crossbred Cattle- Deciphering the Association of Mitochondrial Alterations with Retained Placenta

Madhuri S. Lahamge, E.M Sadeesh

Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: oxidative stress; RT-qPCR; Mitochondrial gene expression; bovine; retained placenta; energy

Online: 6 May 2024 (08:24:39 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202405.0129.v1

Antagonism and Synergism Characterize the Interactions Between Four North American Potato Virus Y Strains

Vincent N Fondong, Prakash M. Niraula, Junaid A Cheema, Hashir A Cheema, Dejah S Gaiter, Patricia Baldrich, Blake C Meyers

Subject: Biology And Life Sciences, Virology Keywords: antagonism; infectivity; pathogenicity; Potato virus Y; RT-qPCR; superinfection exclusion; synergism

Online: 2 May 2024 (10:15:13 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202303.0330.v1

Vector Competence of Aedes albopictus for Yellow Fever Virus: Risk of Reemergence of Urban Yellow Fever in Brazil

Rossela Damasceno Caldeira, Joaquim Pinto Nunes Neto, Carine Fortes Aragão, Maria Nazaré Oliveira Freitas, Milene Silveira Ferreira, Paulo Henrique Gomes de Castro, Daniel Damous Dias, Pedro Arthur da Silva Araújo, Roberto Carlos Feitosa Brandão, Bruno Tardelli Diniz Nunes, Eliana Vieira Pinto da Silva, Lívia Caricio Martins, Pedro Fernando da Costa Vasconcelos, Ana Cecília Ribeiro Cruz

Subject: Arts And Humanities, Film, Radio And Television Keywords: infecção experimental; Aedes albopictus; febre amarela; reemergência; RT‒qPCR; isolamento viral

Online: 20 March 2023 (02:01:29 CET)

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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/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 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/preprints202409.0600.v1

Real-Time Monitoring of SARS-CoV-2 Variants in Oklahoma Wastewater through Allele-Specific RT-qPCR

Kristen Shelton, Gargi N Deshpande, Gilson J Sanchez, Jason Vogel, A Caitlin Miller, Gabriel Florea, Erin R Jeffries, Kara B. De Leon, Bradley Stevenson, Katrin Gaardbo Kuhn

Subject: Public Health And Healthcare, Public, Environmental And Occupational Health Keywords: wastewater surveillance; SARS-CoV-2; variant; RT-qPCR; sequencing; early warning; demography; Oklahoma

Online: 9 September 2024 (08:42:34 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202408.2112.v1

Identification of Reliable Reference Genes for Use in Gene Expression Studies in Rat Febrile Seizure Model

Anna A. Kovalenko, Maria V. Zakharova, Alexander P. Schwarz, Olga E. Zubareva, Aleksey V. Zaitsev

Subject: Biology And Life Sciences, Neuroscience And Neurology Keywords: reference gene expression stability; febrile seizures; brain; rat; gene expression analysis; RT-qPCR

Online: 29 August 2024 (04:55:37 CEST)

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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 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/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: Biology And Life Sciences, 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/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/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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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 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/preprints202409.2240.v1

Genome-Wide Identification and Characterization of bHLH Gene Family in Hevea brasiliensis

Zheng Wang, Yuan Yuan, Fazal Rehman, Xin Wang, Tingkai Wu, Zhi Deng, Han Cheng

Subject: Biology And Life Sciences, Plant Sciences Keywords: bHLH transcription factor; Rubber tree; Cis-element; Expression analysis; Transcriptome; Abiotic stress; RT-qPCR; Gene structure; Subcellular localization

Online: 30 September 2024 (07:31:00 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202408.1839.v1

Characterization of Respiratory Viruses in Patients with Acute Respiratory Infection in the City of Barranquilla during the SARS-CoV-2/COVID-19 Emergency

Leonardo Arrieta-Rangel, Yesit Bello-Lemus, Ibeth Luna-Rodriguez, Martha Guerra-Simanca, Valmore Bermúdez, Yirys Díaz-Olmos, Elkin Navarro Quiroz, Lisandro Pacheco-Lugo, Antonio J. Acosta-Hoyos

Subject: Public Health And Healthcare, Public Health And Health Services Keywords: Influenza-like illness; acute respiratory infection; molecular diagnosis; RT-qPCR; epidemiological surveillance; public health; quantitative polymerase chain reaction

Online: 26 August 2024 (13:12:59 CEST)

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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 REVIEW | doi:10.20944/preprints202409.0412.v1

Breast Cancer Adjuvant Radiotherapy and Chemotherapy Sequencing: Sequential, Concomitant, or What Else? A Comprehensive Review on the Adjuvant Combinations Journey

Grazia Lazzari, Ilaria Benevento, Antonietta Montagna, Barbara D'Andrea, Antonella Bianculli, Giovanni Calice, Raffaele Tucciariello, Giovanni Castaldo, Vito Metallo, Angela Solazzo

Subject: Public Health And Healthcare, Public Health And Health Services Keywords: adjuvant chemotherapy; radiotherapy; concomitant RT; sequential RT; timing

Online: 6 September 2024 (07:39:29 CEST)

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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 BRIEF REPORT | doi:10.20944/preprints202312.1077.v1

Effects of Chronic Sleep-Restriction on Transcriptional Regulation of SIRT1 Signaling in Mice White Adipose Tissue

Marco Rendine, Paolo Cocci, Luisa de Vivo, Michele Bellesi, Francesco Alessandro Palermo

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: sleep deprivation; adipose tissue; mouse; qPCR

Online: 14 December 2023 (10:46:15 CET)

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Preprint ARTICLE | doi:10.20944/preprints202109.0421.v1

A Practical Approach for Quantitative Polymerase Chain Reaction, the Gold Standard in Microbiological Diagnosis

Tímea Mosolygó, Krisztián Laczi, Gabriella Spengler, Katalin Burián

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: laboratory practical class; undergraduate teaching; qPCR

Online: 24 September 2021 (09:04:57 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/preprints202401.1298.v2

Development of qPCR Detection Kit for Langya Henipavirus L Gene

Kunbo Yuan, Haoqing Zhu, Tianyu Jiang, Mengting Xu, Shihan Du, Samuel Ken-En Gan

Subject: Biology And Life Sciences, Virology Keywords: Langya Henipavirus; primer design; qPCR; detection kit

Online: 22 January 2024 (10:42:23 CET)

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Preprint ARTICLE | doi:10.20944/preprints202212.0009.v1

A Novel Fluorescent Sensor Based on Aptamer and Qpcr for Determination of Glyphosate in Tap Water

Yong Shao, Run Tian, Jiaqi Duan, Miao Wang, Jing Cao, Zhen Cao, Guangyue Li, Fen Jin, Yongxin She, A. M. El-Aty

Subject: Chemistry And Materials Science, Analytical Chemistry Keywords: Glyphosate; Aptamer; qPCR; SYBR Green I; sensor

Online: 1 December 2022 (04:00:13 CET)

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Preprint ARTICLE | doi:10.20944/preprints202308.2102.v1

Real-Time Classification of Motor Imagery using Dynamic Window-level Granger Causality Analysis of fMRI Data

Tianyuan Liu, Bao L, Chi Zhang, Panpan Chen, WeiChen Zhao, Bin Yan

Subject: Biology And Life Sciences, Neuroscience And Neurology Keywords: BCI, rt-fMRI, MI, DWGC, svm

Online: 31 August 2023 (09:43:14 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202308.1650.v1

The Molecular Characterization of Lineage-IV Peste Des Petits Ruminants Virus and the Development of In-House IELISA for Its Rapid Detection

Tahira Kamal Rana, Saeed-ul-Hassan Khan, Fariha Hassan, Aamer Bin Zahur, Aman Ullah, S. Murtaza Hassan Andrabi, Ghulam Muhammad Ali

Subject: Biology And Life Sciences, Virology Keywords: IELISA; PPRV; RT-PCR; Cost-effective

Online: 23 August 2023 (10:08:12 CEST)

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Peste des Petits Ruminants (PPR), a highly contagious viral disease, causes significant economic losses in sheep and goats. Laboratory diagnosis is crucial to disease control and eradication. Since PPRVs have recently adopted new hosts, genetic diversity within isolates of the same lineage is more likely than if they were host-specific, sheep and goats most often. ELISA detects antibodies and antigens in serology. However, mishandling, environmental conditions (temperature and humidity), storage, and sensitivity issues of commercially available ELISA kits prevent rapid PPR virus detection in third-world countries like Pakistan. In the 2020-21 outbreaks in Pakistan, 325 blood samples, 19 swabs, and 6 virus tissue samples of sheep and goats were collected from Gilgit, Islamabad, and Fateh Jang. These virus isolates were submitted to NCBI for partial N gene sequencing. Antigen was prepared from indigenous virus Using semi-purified antigen from PPRV, an indirect ELISA for the detection of PPR antibodies in goat and sheep serum was developed using MW600922 grown in Vero cells. Dilutions of 1:200 serums and 1:32 antigens improve antibody detection. The N-gene-based analysis revealed a better understanding of PPRV genetic characterization. This study develops an RT-PCR assay to detect PPRV by targeting the N-protein gene. This assay offers an accurate and affordable diagnostic tool for PPRV and partial genome sequencing. Results described that PPRV isolates from the current study have 99.73% and 99.4% similarity to previously published Lahore and Faisalabad isolates from Pakistan, respectively. Compared to previous isolates from NCBI data, the virus showed high divergence rates with the Turkish strain. The comparative analysis between Commercial kit (c-ELISA) and I-ELISA revealed that the former had a high sensitivity of 90.60% and specificity of 85.23% compared with the cELISA kit. By comparing I-ELISA and VNT, we find that the current assay is 100% specific and 82.14 % sensitive. Based on these results, serological surveys for PPR antibodies, on a larger scale, in small ruminants can be conducted with indirect ELISA rather than competitive ELISA. Furthermore, the cost and storage efficiency was highly significant because the currently developed method has a low production cost, which is much lesser than the commercially available kit. Our findings demonstrated a significant breakthrough in terms of cost-effectiveness and storage efficiency, and they are highly recommended for developing countries.

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 REVIEW | doi:10.20944/preprints202210.0291.v1

Detection of Fish Pathogens in Freshwater Aquaculture Using eDNA Methods: A Review

Kailash Bohara, Amit K. Yadav, Pabitra Joshi

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: eDNA; eRNA; fish disease; surveillance; hydrolysis; degradation; qPCR

Online: 19 October 2022 (14:45:21 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201809.0413.v1

Comparison of Quantitative PCR (qPCR) Paenibacillus larvae Targeted Assays and Definition of Optimal Conditions for Its Detection/Quantification in Honey and Hive Debris

Franca Rossi, Carmela Amadoro, Addolorato Ruberto, Luciano Ricchiuti

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Paenibacillus larvae; optimized qPCR; quantification; honey; hive debris

Online: 20 September 2018 (14:13:42 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202309.0559.v1

Optimization of RT-QuIC Assay Duration for Screening Chronic Wasting Disease in White-Tailed Deer

Gokhan Yilmaz, Tamara Morrill, Cian Ward, Gordon Mitchell, Andrei Soutyrine, Hanhong Dan, Min Lin, Jiewen Guan

Subject: Medicine And Pharmacology, Veterinary Medicine Keywords: RT-QuIC; Chronic Wasting Disease; Diagnostics; Optimization

Online: 7 September 2023 (15:45:02 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 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/preprints202406.2043.v1

LINC01354 Associates with Low-Grade Glioma Survival

Jingxuan Xu

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: LINC01354; low-grade glioma; survival; west Chinese population; QPCR

Online: 29 June 2024 (05:55:49 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202308.1692.v1

HRM Accuracy and Limitations as a Species Typing Tool for Leishmania Parasites

Camila Patricio Braga Filgueira, Daniela Pitta-Pereira, Lilian Motta Cantanhêde, Gabriel Eduardo Melim Ferreira, Sayonara Dos Reis, Elisa Cupolillo, Otacilio C. Moreira, Constança Britto, Mariana Côrtes Boité

Subject: Biology And Life Sciences, Parasitology Keywords: HRM; Leishmania; Americas; leishmaniasis; qPCR; parasite typing; HSP70; diagnosis.

Online: 24 August 2023 (09:48:48 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202209.0267.v1

Development of a Technique for Estimating the Moniliophthora Roreri Spore Loads of Cacao Fields

Diana L. Jiménez-Zapata, Manuela Quiroga-Peréz, Manuela Quiroz-Yepes, Alejandro Marulanda-Tobón, Javier C. Alvarez, Sandra Mosquera-López

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: spore trap; qPCR; Moniliasis; Theobroma cacao; Frosty pod rot

Online: 19 September 2022 (07:33:31 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202011.0213.v1

Independent Evolution of Sex Chromosomes in Eublepharid Geckos, a Lineage with Environmental and Genotypic Sex Determination

Eleonora Pensabene, Lukáš Kratochvíl, Michail Rovatsos

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: Gekkota; reptiles; DNA-seq; sex chromosomes; sex determination; qPCR

Online: 5 November 2020 (14:14:53 CET)

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Preprint ARTICLE | doi:10.20944/preprints202405.0166.v1

Bixafen, Prothioconazole, and Trifloxystrobin Alone or in Combination Affect Health Related Gene Expression in Honey Bees from Nutritionally Deprived versus Protein Supplemented Colonies

Aline Y. Kato, Tainá A. L. Freitas, Cássia R. A. Gomes, Thais R. R. Alves, Yara M. M. Ferraz, Matheus F. Trivellato, David De Jong, Jaqueline D. Biller, Daniel Nicodemo

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: contact exposure; detoxification; fungicide; immunity; nutrition; RT-PCR

Online: 3 May 2024 (07:36:53 CEST)

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Preprint BRIEF REPORT | doi:10.20944/preprints202306.1122.v1

Detection of Venezuelan Equine Encephalitis Virus From Brain Samples of Equines With Encephalitis

Bernal León, Josimar Estrella-Morales, Carlos Jiménez

Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: alphavirus; Costa Rica; Venezuelan equine encephalitis; RT-PCRs

Online: 15 June 2023 (10:19:06 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202406.1675.v1

Epidemiology of Brucella Species Circulating in Small Holder Dairy Cattle in Tanzania

Isaac Joseph Mengele, James M. Akoko, Gabriel Shirima, Shedrack Festo Bwatota, Shabani Kiyabo Motto, Luis Enrique Hernandez-Castro, Daniel Mushumbusi Komwihangilo, Eliamoni Lyatuu, Barend Mark de Clare Bronsvoort, Elizabeth Anne Jessie Cook

Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: dairy cattle; brucellosis; qPCR; molecular prevalence; risk factors; Brucella; Tanzania

Online: 25 June 2024 (10:07:18 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202405.0167.v1

Detection Method for Gene Doping in a Mouse Model Expressing Human Erythropoietin from Adeno-Associated Virus Vector-9

Takehito Sugasawa, Atsushi Hirokawa, Norihiro Otani, Yasuharu Kanki, Kieu DM Nguyen, Tohru Takemasa, Koichi Watanabe, Yoshinori Takeuchi, Naoya Yahagi, Yoichiro Takahashi

Subject: Biology And Life Sciences, Other Keywords: gene doping; erythropoietin; mouse model; RNA-seq; TaqMan-qPCR assay

Online: 3 May 2024 (07:17:22 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202401.1369.v1

FlashPCR: Revolutionising qPCR by Accelerating Amplification through Low ∆T Protocols

Stephen Andrew Bustin, Sara Kirvell, Tania Nolan, Gregory L. Shipley

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Reverse transcription; qPCR; COVID-19; molecular diagnostics; point-of-care

Online: 18 January 2024 (12:01:04 CET)

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Preprint ARTICLE | doi:10.20944/preprints202401.0481.v1

Development of a Real-Time PCR Assay for Early Detection of the Eucalyptus Pathogen Quambalaria eucalypti

Roberto Faedda, Gabriela B. Silva

Subject: Biology And Life Sciences, Life Sciences Keywords: Quambalaria eucalypti; Quambalaria shoot blight; qPCR; diagnostics; molecular detection; Eucalyptus.

Online: 5 January 2024 (10:13:13 CET)

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Preprint ARTICLE | doi:10.20944/preprints202311.0196.v1

Molecular Identification of Fungal Species by Multiplex-qPCR in Candidal Vulvovaginitis Specimens and Antifungal Susceptibility

Inés Arrieta-Aguirre, Pilar Menéndez-Manjón, Giulia Carrano, Ander Diez, Íñigo Fernandez de Larrinoa, María-Dolores Moragues

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Vulvovaginal Candidiasis; qPCR; Candida species, antifungal susceptibility, resistance-related mutations

Online: 3 November 2023 (04:02:59 CET)

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Preprint ARTICLE | doi:10.20944/preprints202306.1718.v1

Persistent Infections of Ostreid Herpesvirus 1 in Adult Pacific Oysters, Crassostrea gigas

Konstantin Divilov, Xisheng Wang, Gary B Fleener, Blaine Schoolfield, Christopher Langdon, Ling Jin

Subject: Biology And Life Sciences, Virology Keywords: Pacific oysters; OsHV-1; latent; persistent; qPCR; nested PCR; hemocytes

Online: 25 June 2023 (05:24:35 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202107.0604.v2

RT-qPCR Diagnostics: The “Drosten” Sars-Cov-2 Assay Paradigm

Stephen Bustin, Sara Kirvell, Jim F Huggett, Tania Nolan

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: COVID-19; reverse transcription; qPCR; SARS-CoV-2; molecular diagnosis

Online: 3 August 2021 (15:34:05 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201708.0007.v1

Identification of Microbial Indicators and Free Living Protozoa in Natural Mineral Water Using Cultural and Molecular Methods.

Michele Totaro, Beatrice Casini, Paola Valentini, Mario Miccoli, Pier Luigi Lopalco, Angelo Baggiani

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: natural mineral water; free living protozoa; Nontuberculous mycobacteria; Legionella; qPCR

Online: 3 August 2017 (09:11:03 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202409.0463.v1

Development and Validation of a Combined RT-LAMP Assay for the Rapid and Sensitive Detection of Dengue Virus in Clinical Samples from Colombia

Katherine Escorcia-Lindo, Leidy Hurtado-Gómez, Juan Sebastian Rosero, Nataly Solano Llanos, Camilo Barrios Sánchez, Anderson Diaz Pérez, Yirys Díaz-Olmos, Jennifer García, Yesit Bello-Lemus, Leonardo C Pacheco-Londoño, Antonio J. Acosta-Hoyos, Lisandro A Pacheco-Lugo

Subject: Biology And Life Sciences, Life Sciences Keywords: RT-LAMP; Dengue virus (DENV); Sensitivity; Point-of-Care

Online: 5 September 2024 (12:37:39 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202401.1764.v1

Real-Time Performance Benchmarking of RISC-V Architecture: Implementation and Verification on an EtherCAT-Based Robotic Control System

Taeho Yoo, Byoung Wook Choi

Subject: Engineering, Control And Systems Engineering Keywords: RISC-V; FreeRTOS; PREEMPT-RT; RTOS; EtherCAT; Embedded Linux

Online: 24 January 2024 (14:43:54 CET)

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RISC-V offers a modular technical approach combined with an open, royalty-free instruction set architecture (ISA). This openness allows various researches to incorporate RISC-V into both open and proprietary solutions or services. However, despite its advantages as a fundamental building block for many embedded systems, the escalating complexity and functional demands of real-time applications have made adhering to response time deadlines challenging. This has led to an increased demand for comprehensive development insights for real-time systems based on RISC-V. To improve development efficiency, we offer a detailed performance analysis of RISC-V in comparison to various ISAs. In this paper, we analyze the real-time performance of RISC-V through two real-time approaches based on processor architectures. For RTOS applications, we adopted FreeRTOS and evaluated its performance on HiFive1 Rev B (RISC-V) and STM3240G-EVAL (ARM M) to evaluate real-time performance. For Real-time Linux, we utilized Linux with the Preempt-RT patch and tested its performance on VisionFive 2 (RISC-V), MIO5272 (x86-64), and Raspberry Pi 4 B (ARM A). Through these experiments, we examined the real-time mechanism of each operating system. Additionally, in the Preempt-RT experiments, scheduling latencies were evaluated using cyclictest. Finally, in order to practically show the real-time capabilities of RISC-V, we implemented motion control of a six-axis collaborative robot, which was performed on the VisionFive 2 platform. This implementation provided a comparative result of RISC-V’s performance against the x86-64 architecture of MIO-5272. Ultimately, the results indicated that the real-time performance of RISC-V for real-time applications was slightly inferior to that of the x86-64 architecture. A noticeable achievement of this research was the first implementation of an EtherCAT Master on RISC-V designed for real-time applications featuring a multi-tasking structure. The research offers valuable insights into the real-time capabilities of RISC-V compared to established architectures like x86-64. While RISC-V might not surpass these architectures in real-time performance, its flexibility, modularity, and open nature make it a compelling choice for a wide range of real-time applications. The successful implementation of the EtherCAT Master on RISC-V further expands its potential in the domain of real-time embedded control systems.

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/preprints202304.0512.v1

Comparison of Identification and Quantification of Polyphe-Nolic Compounds in Skins and Seeds of Four Grape Varieties

Zlatina Chengolova, Yavor Ivanov, Tzonka Godjevargova

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: grape skins; seeds; polyphenolic composition; antioxidant potential; RT-HPLC

Online: 18 April 2023 (10:22:09 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202207.0449.v1

Dysregulated Expression of Ion Channels in Sensory Neurons Enhances Action Potential Afterhyperpolarization in Patients with Chronic Kidney Disease–Associated Pruritus

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

Subject: Medicine And Pharmacology, Dermatology Keywords: CKD-aP; ion channels; action potential; hyperpolarization; RT-PCR

Online: 29 July 2022 (04:50:39 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 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/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/preprints202306.1956.v1

Building a Teleost Fish Traceability Program Based on Genetic Data from Pacific Panama Fish Markets

Edgardo Enrique Díaz-Ferguson, Magaly Sánchez De Chial, Maribel Arlene González Torres, Edgardo A. Muñoz T., Magister Olga Chen, Ovidio Durán, Angel Javier Vega, Carlos Ramos Delgado

Subject: Biology And Life Sciences, Aquatic Science Keywords: COI; teleostei; nucleotide diversity; haplotypic diversity; qPCR; demographic history; environmental DNA

Online: 28 June 2023 (07:37:41 CEST)

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Fish tissue samples from 203 adult individuals were collected in the main ports and markets of the Pacific coast of Panama. Molecular identification based on cytochrome oxidase I gene segment of all species was verified GENBANK reference sequences. 34 species from 14 families (Ariidae, Lutjanidae, Caranjidae, Scianidae, Centropomidae, Serranidae, Scombridae, Sphyraenidae, Haemulidae, Gerreidae, Stromotidae, Lobotidae, Malacanthidae, Mugilidae) were identified at species molecular level from 164 sequences. Also, three Caribbean species were molecularly identified among the analyzed samples (Mycteroperca xenarcha, Paralonchurus brasilensis and Lobotes surinamensis). Species diversity was slightly higher in the Gulf of Panama than in the Gulf of Chiriquí. For species with 5 or more individual sequences, genetic diversity and genetic connectivity parameters such as: total number of haplotypes (H), haplotype diversity (Hd), and nucleotide diversity (π) were calculated. Overall, pelagic-migratory species showed higher values of genetic diversity than coastal and estuarine species with some exceptions. Connectivity between Gulf areas was compared using values of genetic distances and genetic differentiation (Fst). High level of connectivity observed between Gulf of Chiriqui and Gulf of Montijo indicates the existence of a single stock in that area for the following species: Scomberomorus sierra, Caranx caninus and Lutjanus guttatus. Demographic history of the most common species was examined using Tajima’s D values suggesting population expansion for two snapper species, L. peru and L. argentiventris, having significant and higher values. Another important contribution from this research was the production of primers and dual labeled probes for environmental DNA detection using qPCR for the five most abundant species (spotted rose snapper, yellow snapper, green jack, Pacific crevalle jack and the Pacific sierra fish). These markers represent a new set of tools for environmental DNA (eDNA) detection and molecular traceability of three commercially important fish species along the supply chain including landing sites and markets of the main fishery areas.

Preprint ARTICLE | doi:10.20944/preprints202202.0286.v1

Assay for Evaluating the Abundance of Vibrio Cholerae and Its O1 Serogroup Subpopulation Directly from Water Without DNA Extraction

Tania Nasreen, Nora A.S. Hussain, Jia Yee Ho, Vanessa Zie Jie Aw, Munirul Alam, Stephanie K Yanow, Yann Felix Boucher

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: cholera; Vibrio cholerae; Vibrio cholerae O1; endemic; toxigenic; abundance and qPCR

Online: 23 February 2022 (06:45:35 CET)

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Preprint ARTICLE | doi:10.20944/preprints201908.0124.v1

A Tunable Nanoplatform of Nanogold Functionalised With Angiogenin Peptides for Anti-angiogenic Therapy of Brain Tumours

Irina Naletova, Lorena Maria Cucci, Floriana D'Angeli, Carmelina Daniela Anfuso, Antonio Magrì, Diego La Mendola, Gabriella Lupo, Cristina Satriano

Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: plasmonics; nanomedicine; theranostics; copper; VEGF; glioblastoma; differentiated neuroblastoma; peptidomimetics; qPCR; actin.

Online: 11 August 2019 (07:13:00 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201710.0011.v1

Spore Dispersal Patterns of Fusarium Circinatum on an Infected Monterey Pine Forest in North-Western Spain

Miloň Dvořák, Patrik Janoš, Leticia Botella, Gabriela Rotková, Rafael Zas

Subject: Biology And Life Sciences, Forestry Keywords: Pine pitch canker; Galicia; spore trap; air sampling; qPCR; seasonal dynamics

Online: 2 October 2017 (16:00:11 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202311.0999.v1

Emergency Department Times Targets for Interhospital Transfer of Patients with Acute Ischemic Stroke

Popa I Daian, Iancu Aida, Petrica Alina, Buleu Florina, Williams Gabriela Carmen, Sutoi Dumitru, Trebuian Iosif Cosmin, Anca Tudor, Mederle A Ovidiu

Subject: Medicine And Pharmacology, Emergency Medicine Keywords: emergency department; ED time targets; acute ischemic stroke; rt-PA

Online: 16 November 2023 (02:32:20 CET)

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Preprint ARTICLE | doi:10.20944/preprints202210.0255.v1

Implementation of a Modular Distributed Fault-tolerant Controller for MMC Applications

Semih Isik, Vasishta Burugula, Mohammed Alharbi, Ali Azidehak, Subhashish Bhattacharya

Subject: Engineering, Electrical And Electronic Engineering Keywords: controller; centralized; distributed; CHIL; fault-tolerant; MMC; prototype; Opal-RT

Online: 18 October 2022 (07:30:28 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202208.0509.v1

Using FTA Cards as a Rapid and Field Tool for Detection and Serotyping of Foot-and-mouth Disease Virus in Libya

Fadila Abosrer, Elfurgani Kraim, Emiliana Brocchi, Giulia Pezzoni, Santina Grazioli, Abdunaser Dayhum, Ibrahim Eldaghayes

Subject: Biology And Life Sciences, Virology Keywords: FTA cards; foot-and-mouth disease; RT-PCR; field; sequence

Online: 30 August 2022 (05:45:36 CEST)

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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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Working Paper BRIEF REPORT

Are we on the Right Way after 200 Days of COVID-19 in Morocco?

Issam Bennis, Amina Nasri Sahraoui, Moulay Mustapha Alaoui

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: COVID-19; SARS-CoV-2; RT-PCR; control strategy; Morocco

Online: 5 November 2020 (10:40:41 CET)

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Historically, 2020 will be remembered as the year of COVID-19 pandemic, that limited people move and their social habits. This virus, becomes the first daily tracked public health burden that leads to more than 1,2 million deaths in the World by the end of October 2020, and until now no countries' best control strategies are cited as the example of long term success.Since March 2^nd, 2020, date of the first SARS-COV-2 detected case in Morocco; many decisions were adopted as COVID-19 control strategies. If the first period of COVID-19 noticed a few numbers of cases and deaths, the second half from July is marked with an exponential increase of the number of cases and a spread in almost all provinces with more intensive care needs and more deaths. The policy analysis approach was followed as a method to define the pitfalls themes and to compare with the updated available international information any significant similarities or divergences. Thus, this report has the aim to present an overview of how the COVID-19 pandemic was dealt in Morocco during these 200 days, by highlighting some discrepancies with corrective advice provided in the first version of the manuscript to be confronted by a Moroccan health policymaker’s community, then to notice the decisions adopted during another one month by the MoH to get better future control results against COVID-19.Unfortunately, despite the MoH decision to increase the diagnostic facilities for molecular tests, the overall number of laboratory tests do not go further than 21000 tests per day. The actual insidious transmission is a dangerous blind threat that dissipates the collaborating efforts, due to this limited number of confirmation and follows up tests.Accurate, standardised and up to ten times per day tests of molecular biology represented by RT-qPCR, to interpret results following the time progress of cycle quantification values is the primary action to be done to enhance the overall control strategy.

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/preprints202305.0869.v1

qPCR System for Alongshan Virus Detection

Alexander Litov, Egor Okhezin, Ivan Kholodilov, Alexandra Polienko, Galina Karganova

Subject: Biology And Life Sciences, Virology Keywords: Jingmenvirus group; Alongshan virus; qPCR; Flavivirus; Yanggou tick virus; tick-borne viruses

Online: 11 May 2023 (14:25:01 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/preprints202407.0601.v1

Epidemiological and Molecular Characterization of HBV Virus Infection in General Population of North Waziristan, Pakistan

Najm Ud Din, Asma Saeed, Ata Ur Rehman, Dawood Khan, Abdul Samad Khan, Arman Ali Shah

Subject: Biology And Life Sciences, Virology Keywords: Epidemiology; Hepatitis B virus; ICT; ELISA; RT-PCR; Genotype; DNA; Pakistan

Online: 8 July 2024 (09:04:34 CEST)

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Background: Hepatitis B virus (HBV), a lethal form of viral hapatitis, is an extra burden on the socioeconomic status of a country. Objectives: The population-based studies to quantify the incidence of hepatitis B. Data sources: in the North Waziristan, formally known as EX-FATA (Federal Administrated Tribal Area), Pakistan, are still rare. Study eligibility criteria: 943 individuals were selected on the basis of signs and symptoms to determine the epidemiology of HBV in the study population. Tests: Hepatitis B virus (HBV). Methods of data synthesis: Among these, 626 were male and 317 were female. All the HBV suspected individual were screened through ICT (Indirect Coombs Test) , ELISA (enzyme-linked immunosorbent assay) and RT-PCR (Re-verse transcription polymerase chain reaction). Results: The results obtained from the screening tests for HBV revealed that RT-PCR based results are more reliable and it indicated that HBV infection is more common in male 41 (6.54%) than female 15 (4.73%). The age range selected for the study was 1-75 years. Age wise analysis indicated that HBV is more prevalent among individuals of age group between 16 to 45 years. This age range also showed higher number of patients having either mild, moderate or elevated viral loads. The HBV genotype D was the most common, present in 62.5% patients. However, 16.07 % patients were having genotype U, 12.5 % genotype C, 8.92 % genotype A, and 7.14% had genotype B. Discussion: The questionnaire based investigation revealed that HBV was most prevalent among married individuals (64.6%), whereas least prevalent among individuals having HBV positive family member (1.4 %). The other risk factors contributed were history of dental procedures (57.8%), ear, nose, piercing, or tattooing and uses of un-disposable syringes (56.5%), transfusion of blood or plasma (42.9%), surgery (41.8%), frequent visits to barber shops (39.45%), and addiction of injectable drugs (38.1%). The current study is providing a clear picture of the alarming situation HBV transmission and emphasis on the need for more effective planing, strategies and policies for the control and prevention of HBV.

Preprint ARTICLE | doi:10.20944/preprints202405.0787.v1

The Recombination of Insertion Sequence Results in Deletion of the 3′ End of the cry1Ac Gene with Concomitant Enhancement of Its Insecticidal Activity

Chunmeng Huang, Yongjun Zhang, Huilin Yu, Chenhui Hou, Haoyuan Guan, Xiuping Chen, Jiajian Xie

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: Transgenic cotton; insect-resistant; MON531; R7569; RACE; RT-PCR; ELISA; LC50

Online: 13 May 2024 (08:20:29 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202402.1094.v1

Development and Evaluation of an In-House Real-Time Rt-Pcr Targeting nsp10 Gene for SARS-CoV-2 Detection

Cyril Chik-Yan Yip, Jane Hau-Ching Poon, Kit-Hang Leung, Wan-Mui Chan, Jonathan Daniel Ip, Allen Wing-Ho Chu, Vincent Chi-Chung Cheng, Kwok-Yung Yuen, Kelvin Kai-Wang To

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; COVID-19; nsp10; real-time RT-PCR; diagnostic

Online: 20 February 2024 (06:07:31 CET)

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Preprint ARTICLE | doi:10.20944/preprints202306.1385.v2

Path for Room-Temperature Superconductivity in Q-Carbon Related Materials

Jagdish Narayan

Subject: Engineering, Other Keywords: BCS superconductivity; RT superconductivity; B-doped Q-carbon; B-doped diamond

Online: 30 October 2023 (09:01:40 CET)

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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 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/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 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/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/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 SHORT NOTE | doi:10.20944/preprints202306.1658.v1

Human KRAS Gene May Be Hard to Detect in Quantitative PCR via Probe Detection Chemistry

Wenfa Ng

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: qPCR assay; probe-based detection; SYBR green; human KRAS gene; human gastric CloTest samples

Online: 23 June 2023 (10:50:59 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: Biology And Life Sciences, Neuroscience And Neurology 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 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 CASE REPORT | doi:10.20944/preprints202406.1985.v1

Case Report: Molecular analyses of cell cycle-related genes in cortical brain tissue of a Rasmussen Encephalitis patient

João Ismael Budelon Gonçalves, Vinicius Rosa de Castro, William Alves Martins, Fernando Antonio Costa Xavier, Jaderson Costa da Costa, Eliseu Paglioli Neto, André Palmini, Daniel Rodrigo Marinowic

Subject: Medicine And Pharmacology, Neuroscience And Neurology Keywords: Rasmussen’s encephalitis; Rasmussen; cell cycle; inflammatory; encephalopathy; BDNF; brain-derived neurotrophic factor; qPCR; array; cytokines.

Online: 28 June 2024 (14:18:08 CEST)

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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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