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Preprint ARTICLE | doi:10.20944/preprints202401.1468.v1

Diagnostic Efficiency of CTV and HSVd for Early and Mixed Infections Using Bioamplification in Citrus Arizona 861-S1 and RT‒PCR Compared to Direct RT‒PCR

Claudio A. Henriquez, Natalia Riquelme, Alejandra Larach, Ximena Besoain

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Virus-viroid detection; Mixed infections; Comparison of diagnostic methods; CTV; HSVd; Bioamplification

Online: 19 January 2024 (07:52:21 CET)

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Preprint ARTICLE | doi:10.20944/preprints202211.0030.v1

PCR-based Detection of Typhoidal Salmonella from Human Clinical Samples and Evaluation of Traditional PCR, Nested-PCR and Widal Test in Pune, India

Abas O. Hadi, Hussein Alburkat, Taisir Abdulelah Kadhim, Ammar M S Al-Helli, Mustafa Hamza Ghazi, Yasir Abdulameer N. Aldabbagh, Reem Numaan Talib, Sama Hussein Ali, Noor Hameed Imran, Ruaa Almohsen, Turki Muftin Saad, Pallavi Mandave

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: PCR; Salmonella Typhi; Widal Test; BHI

Online: 1 November 2022 (12:43:58 CET)

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Preprint ARTICLE | doi:10.20944/preprints202306.2136.v1

Multiplex Real-Time RT-PCR Assays for Detection and Differentiation of Porcine Enteric Coronaviruses

Christina M. Lazov, Alice Papetti, Graham J. Belsham, Anette Bøtner, Thomas Bruun Rasmussen, Maria Beatrice Boniotti

Subject: Biology And Life Sciences, Virology Keywords: Virus diagnosis; RNA; recombinant virus; alphacoronavirus; deltacoronavirus; porcine epidemic diarrhea virus (PEDV); transmissible gastroenteritis virus (TGEV); swine enteric coronavirus (SeCoV); porcine deltacoronavirus (PDCoV)

Online: 29 June 2023 (13:22:32 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 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/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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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/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/preprints201702.0011.v1

Simulation Analysis of Solution Transportation Absorption Chiller with the Capacity from 25 RT to 1000 RT

Koji Enoki, Fumi Watanabe, Seigo Tanaka, Atsushi Akiwawa, Toshitaka Takei

Subject: Engineering, Energy And Fuel Technology Keywords: absorption chiller; thermal energy transportation; solution transportation; ammonia-water; COP; simulation

Online: 4 February 2017 (07:49:12 CET)

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Preprint ARTICLE | doi:10.20944/preprints202409.1366.v1

Cycle Threshold Values of SARS-CoV-2 RT-PCR During Outbreaks in Nursing Homes: A Retrospective Cohort Study.

Juan Carlos Gasco-Laborda, Maria Gil-Fortuño, Maria Dolores Tirado-Balaguer, Noemi Meseguer-Ferrer, Oihana Sabalza-Baztán, Óscar Pérez-Olaso, Iris Gómez-Alfaro, Sandrine Poujois-Gisbert, Noelia Hernández-Pérez, LLedó Lluch-Bacas, Viorica Rusen, Alberto Arnedo-Pena, Juan Bautista Bellido-Blasco

Subject: Public Health And Healthcare, Public Health And Health Services Keywords: SARS-CoV-2; PCR; cycle threshold; infections; nursing homes; outbreaks; retrospective cohort

Online: 18 September 2024 (11:47:21 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202406.1643.v1

Nested Pattern Detection and Unidimensional Process Characterization

Gerardo L. Febres

Subject: Computer Science And Mathematics, Artificial Intelligence And Machine Learning Keywords: patterns; nested patterns; information; entropy; ordered structure; redundancy

Online: 24 June 2024 (11:09:49 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202311.1127.v1

Machine Learning Application to Brain Diseases Detection

Aleksandar Simović, Maja Lutovac-Banduka, Kristina Davidović, Snežana Lekić

Subject: Computer Science And Mathematics, Artificial Intelligence And Machine Learning Keywords: machine learning; application; classification; brain diseases; detection

Online: 17 November 2023 (15:32:16 CET)

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Preprint ARTICLE | doi:10.20944/preprints202209.0439.v1

SARS-CoV-2 Detection in Fecal Samples in Sym-asymptotic Patients with Typical Findings of COVID-19 on Ag-RDT and SARS-CoV-2 RT-PCR Tests

Richard Odongo Magwanga, Benson Onyango, Alfred Ochieng, Shehu Shagari Awandu, Pamela Were, Joy Nyangasi Kirungu, Marceline Adhiambo Oloo, Erick Muok, Stephen Munga, Fredrick Ogutu, Angeline Orwa, Fredrick Okumu, Clayton Onyango, Dorothy Awuor, Francis Orata, Justine Ochieng’-Midega, Bonface Oure, Regina Nyunja, Fredrick Ade, Sharley Indechi, Erick Okuto, Benson Estambale

Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: COVID19; SARS-CoV-2 virus; Oro-nasopharyngeal; fecal; vaccination; asym-symptomatic; rapid diagnostic test

Online: 28 September 2022 (11:51:21 CEST)

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Coronavirus is a disease caused by a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which emerged as a global pandemic in 2019 from Wuhan, China. Since its emergence, it has caused immense suffering to human life, 6.27 million lives have been lost, movement curtailed and social dynamics disrupted. The golden standard for getting samples for SARS-CoV-2 detection is through oral- nasopharyngeal swab, this method of sample collection is invasive and uncomfortable, thus stigmatized the general population, and thereby impeded the progress of controlling the spread through mass testing. Being a contact disease, mechanisms to encourage mass testing is key to reduce the spread. This study thus developed a complimentary sample type to test for SARS-CoV-2, the use of human feces. Fecal samples were collected from 100 asym-symptomatic individuals suspected to be infected with COVID-19, virus RNA was then extracted and profiled through Real Time Polymerase Chain Reaction (RT-qPCR). The antigen rapid diagnostic test revealed high positivity rate of 44%, but the real time polymerase chain reaction results on nasopharyngeal and fecal samples revealed a significant variation, high number of the patients tested positive with stool samples compared to the nasopharyngeal swabs, with 43 and 37%, respectively. SARS-CoV-2 virus was detected in both symptomatic and asymptomatic individuals; however, the symptomatic registered a higher positivity of 25% compared to 20% among the asymptomatic patients. Vaccination only lowered the risk of infection, fully and partially vaccinated lowered the infection level to 10% compared to 20% among the unvaccinated. Finally, gender parity in relation to COVID19 was evaluated, more females (56%) compared to males were recruited in this study, out of which (20; 43.4%) were positive, and 26 (56.6%) were negative based on fecal RT-qPCR outcomes. Based on the outcome of this study, rapid diagnostic test (Ag-RDT) however cheap and or fast does not provide accurate information, moreover, the virus does not stay longer within the Oro-nasopharyngeal region, thus the invalid or negative results, thus use of feces should be adopted as a confirmatory test to ascertain the COVID19 status of an individual.

Preprint ARTICLE | doi:10.20944/preprints202308.0387.v1

Acquisition of Humoral Immune Responses in Convalescent Japanese People with SARS-CoV-2 (COVID-19) Infection in 2021

Koshiro Monzen, Takanori Watanabe, Toshihiro Okabe, Hisakuni Sekino, Hironori Nakagami, Ryuichi Morishita

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: COVID-19; SARS-CoV-2; Convalescent serum; Neutralizing antibody

Online: 4 August 2023 (12:35:21 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202311.0446.v1

Symbolic Analysis of Classical Neural Networks for Deep Learning

Maja Lutovac-Banduka, Igor Franc, Vladimir Milićević, Nemanja Zdravković, Nikola Dimitrijević

Subject: Computer Science And Mathematics, Artificial Intelligence And Machine Learning Keywords: machine learning; visual programming language; closed-form expression; theoretical justification; feature extraction; complexity; optimization and validation

Online: 7 November 2023 (11:25:29 CET)

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Working Paper ARTICLE

Two Nested Limit Cycles in Two-Species Reactions

Ilona Nagy, Valery G. Romanovski, János Tóth

Subject: Computer Science And Mathematics, Analysis Keywords: Limit cycles; Two-species reactions; Third order reaction step; Hopf bifurcation

Online: 25 August 2020 (10:27:34 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202007.0199.v1

Generation and Application of Nested Entanglement in Matryoshka Quantum Resource-States

Mrittunjoy Guha Majumdar

Subject: Physical Sciences, Quantum Science And Technology Keywords: Quantum Computation; Multipartite Entanglement; Quantum State Sharing

Online: 10 July 2020 (01:40:52 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202408.1620.v1

MFGFF-BiLSTM-EGP: A Chinese Nested Named Entity Recognition Model for Chicken Disease Based on Multiple Fine-Grained Feature Fusion and Efficient Global Pointer

Xiajun Wang, Cheng Peng, Qifeng Li, Qinyang Yu, Liqun Lin, Pingping Li, Ronghua Gao, Wenbiao Wu, Ruixiang Jiang, Ligen Yu, Luyu Ding, Lei Zhu

Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: nested named entity recognition; chicken disease; multiple fine-grained feature fusion; RoBERTa; efficient global pointer

Online: 22 August 2024 (07:41:02 CEST)

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Preprint REVIEW | doi:10.20944/preprints202311.1089.v1

White Paper Textile Fibre Recycling Technologies

Birgit Stubbe, Stijn Van Vrekhem, Sofie Huysman, Rémi G. Tilkin, Isabel De Schrijver, Myriam Vanneste

Subject: Chemistry And Materials Science, Paper, Wood And Textiles Keywords: textile recycling; fibre-to-fibre recycling; textile sorting; textile disassembly; digital textile platforms

Online: 17 November 2023 (08:49:16 CET)

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Preprint REVIEW | doi:10.20944/preprints202401.1473.v1

Nested Markets and the Transition of the Agri-Marketing System towards Sustainability

Pierluigi Milone, Flaminia Ventura

Subject: Social Sciences, Sociology Keywords: Market; Reciprocity; Agency; neo-institutional economy; network analysis

Online: 19 January 2024 (06:59:45 CET)

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We are currently witnessing a strong global transition towards new, more sustainable models of development and consumption. This transition is both activating and highlighting a series of discrepancies between the various actors in agri-food marketing systems, including the institutions that govern regulatory and trade aspects. These discrepancies highlight how, on a global level, the agri-marketing system is unable to provide adequate responses to the new principles of sustainability that are increasingly expected by civil society. This inability is often linked to the phenomena of opportunism, information asymmetries and lock-in effects (resulting from the slowness or inability of some sectors or actors to evolve technologically and culturally). The control of all these factors is often ineffective and often involves high transaction costs . These conditions lead the global market into an ongoing state of failure, creating structural holes, in which new forms of exchange are born, in response to the principles mentioned above. We identify these as nested markets: hybrid market forms that, thanks to new information technologies, create a new form of proximity that transcends the classical concept of physical proximity. This new proximity directly links producers and consumers in relationships based mainly on two substantial values: reciprocity and reputation. Both of these values significantly reduce transaction costs which today play an increasing role in determining the form and repetition of exchanges. This condition is difficult to interpret from classical and neo-classical economic theories. To do so it is necessary to use a multidisciplinary approach. In this article we combine neo-institutional theory and network analysis to interpret phenomena that are increasingly emerging in all areas of the world. Using these two theories, and case studies from Brasil, North America, China and Europe, we try to highlight how the market is not only the place where the price of products and of their quantities are formed. Market is a complex social spaces, where more-or-less stable relationships are formed, based on the values of reciprocity and reputation that determine behaviour and codes of conduct aimed at containing opportunism and encouraging sustainable, autonomous, forms of self-regulation. These relationships are also the driving forces that ensure the ongoing continuation of the exchanges and the diffusion and preservation of knowledge over time and space. These relationships represent the beating heart of nested markets and their dynamic ability to adapt to the continuous changes that occur in the socio-economic and environmental context in which they are rooted. In this way sustainability is built as an expression of the co-production between different actors (producers, consumers, institutions) and natural resources.

Preprint ARTICLE | doi:10.20944/preprints202305.0623.v1

Estimation of Expectations and Variance Components in Two-Level Nested Simulation Experiments

David Fernando Muñoz

Subject: Computer Science And Mathematics, Computational Mathematics Keywords: Bayesian forecasting; stochastic simulation; parameter uncertainty; two-level simulation

Online: 9 May 2023 (09:24:32 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201806.0482.v1

Nested Stochastic Valuation of Large Variable Annuity Portfolios: Monte Carlo Simulation and Synthetic Datasets

Guojun Gan, Emiliano Valdez

Subject: Computer Science And Mathematics, Probability And Statistics Keywords: Monte Carlo; regime-switching multivariate black-scholes; metamodeling; variable annuity; portfolio valuation

Online: 29 June 2018 (11:31:49 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202404.0262.v1

Evaluation of Sensitivity and Applicability of a Droplet Digital Pcr Assay for Simultaneous Detecting Pseudomonas aeruginosa and Pseudomonas fragi in Foods

Ju Huang, Ligong Zhai, Junyin Wang, Xiaotian Sun, Baoshi Wang, Zhaohui Wei

Subject: Biology And Life Sciences, Food Science And Technology Keywords: Pseudomonas aeruginosa; Pseudomonas fragi; simultaneous detection; droplet digital PCR

Online: 3 April 2024 (16:17:11 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202310.0540.v1

Dual-Band Nested Circularly Polarized Antenna Array for 5G Automotive Satellite Communications

Umais Tayyab, Ashish Kumar, Hans-Peter Petry, Muhammad Ehtisham Asghar, Matthias A Hein

Subject: Engineering, Electrical And Electronic Engineering Keywords: 5G; dual-band; nested antenna array; circular polarization; non-terrestrial network; link budget; automotive applications; data rate

Online: 10 October 2023 (02:34:30 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/preprints202402.1112.v1

Cellular Immunity of SARS-CoV-2 in the Borriana COVID-19 Cohort: A Nested Case-Control Study

Salvador Domenèch-Montoliu, Joan Puig-Barberà, Maria Rosario Pac-Sa, Alejandro Orrico-Sanchez, Lorna Gómez-Lanas, Diego Sala-Trull, Carmen Domènech-León, Alba Del Rio-González, Manuel Sanchez-Urbano, Paloma Satorres-Martinez, Laura Aparisi-Esteve, Gema Badenes-Marques, Roser Blasco-Gari, Juan Casanova-Suarez, Maria Gil-Fortuño, Noelia Hernández-Pérez, David Jovani-Sales, Laura López-Diago, Cristina Notari-Rodríguez, Oscar Pérez-Olaso, María Angeles Romeu-Garcia, Raquel Ruíz-Puig, Alberto Arnedo-Pena

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: COVID-19; SARS-CoV-2 infection; cellular immunity; T cells; CD4+; CD8+; humoral immunity; Anti-S antibodies Anti-N antibodies; nested case-control; associated factors

Online: 20 February 2024 (09:01:39 CET)

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Preprint ARTICLE | doi:10.20944/preprints202104.0299.v1

Optimizing Droplet Digital PCR for Environmental Samples

Vasilis Kokkoris, Eric Vukicevich, Andrew Richards, Corrina Thomsen, Miranda Hart

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: ddPCR, droplet digital PCR, environmental samples, environmental DNA, soil microbiology

Online: 12 April 2021 (12:48:11 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202211.0203.v1

Cost-Effective PCR-Based Identification of Tunga penetrans (Siphonaptera) Larvae Extracted From Soil Samples Containing PCR Inhibitor-Rich Material

Billy L. Amugune, Abneel K. Matharu, Paul Ouma, Francis Mutebi, Lynne Elson, Ulrike Fillinger, Jürgen Krücken

Subject: Biology And Life Sciences, Insect Science Keywords: Tungiasis; Tunga penetrans; molecular entomology; DNA isolation; Phusion® polymerase; FIREpol® Taq polymerase; low-cost PCR,

Online: 10 November 2022 (11:19:42 CET)

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Preprint ARTICLE | doi:10.20944/preprints202307.2116.v1

Design of a Dual-Band WiFi Antenna Using the Theory of Characteristic Modes and Nested Chinese Characters

Zhonggen Wang, Mingqing Wang, Wenyan Nie

Subject: Engineering, Electrical And Electronic Engineering Keywords: characteristic mode; Chinese characters; WiFi; high isolation

Online: 31 July 2023 (11:42:23 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202208.0536.v1

Prediction of Bay of Bengal Extremely Severe Cyclonic Storm "Fani” Using Moving Nested Domain

Kuvar Satya Singh, Sridhara Nayak, Suman Maity, Hara Prasad Nayak, Soma Dutta

Subject: Environmental And Earth Sciences, Atmospheric Science And Meteorology Keywords: WRF model; Moving-nest; Fani; Bay of Bengal; Wind Speed

Online: 31 August 2022 (07:48:18 CEST)

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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 REVIEW | doi:10.20944/preprints202403.1182.v1

Present and Future Applications of Digital PCR in Infectious Diseases Diagnosis

Laura Sancha Domínguez, Ana Cotos Suárez, María Sánchez Ledesma, Juan Luis Muñoz Bellido

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: dPCR; digital PCR; infection; bacteria; virus; parasites

Online: 20 March 2024 (08:24:31 CET)

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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/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/preprints202409.1390.v1

Droplet Digital Pcr Enhances Sensitivity and Accuracy in Canine Distemper Virus Detection

Victoria Iribarnegaray, Guillermo Godiño, Camila Larrañaga, Kanji Yamasaki, José Manuel Verdes, Rodrigo Puentes

Subject: Medicine And Pharmacology, Veterinary Medicine Keywords: droplet Digital PCR; canine distemper virus; molecular diagnosis

Online: 18 September 2024 (10:24:27 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202408.1177.v1

A PCR-Based Approach for Early Diagnosis of Head and Neck Aspergillosis

Thaís Ellen Chaves Gomes, Victor Coutinho Bastos, Douglas Boniek, Mário Romañach, Fernanda Faria Rocha, Roberta Rayra Martins Chaves, Ricardo Santiago Gomez

Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: Aspergillosis; Aspergillus; PCR; Diagnosis

Online: 15 August 2024 (14:30:29 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201804.0326.v1

Molecular Characterization of Termitomyces Protoclones through PCR and RFLP Based DNA Typing

Pijush Mallick, Sobhan Roy Chowdhury, Dipanwita Roy, Subhash Kanti Roy, Samir Ranjan Sikdar

Subject: Biology And Life Sciences, Horticulture Keywords: DNA markers; edible mushroom; genome stability; protoplast regeneration

Online: 25 April 2018 (08:26:25 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201611.0125.v1

Up-regulation of Lamin A/C Expression in Epstein-Barr Virus Immortalized B Cells and Burkitt Lymphoma Cell Lines of Activated B Cell Phenotype

Ferenc Bánáti, Anita Koroknai, Kálmán Szenthe, Tamás Tereh, Nóra Kovács, Anita Hidasi, Barbara Bánkuti, Krisztina Buzás, Frederic Lemnitzer, Zsolt Ruzsics, Susan Szathmary, Hans Wolf, Dániel Salamon, János Minárovits, Hans-Helmut Niller

Subject: Biology And Life Sciences, Virology Keywords: Lamin, EBV latency, transformation, epigenetic regulation, activated B cell

Online: 24 November 2016 (17:53:07 CET)

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Preprint ARTICLE | doi:10.20944/preprints202409.0085.v1

Megaselia scalaris and Senotainia tricuspis Infesting Apis mellifera: Genotyping, Detection by Quantitative PCR, and Involvement in the Transmission of Microbial Pathogens

Franca Rossi, Martina Iannitto, Beqe Hulaj, Paola Manocchio, Francesca Gentile, Ilaria Del Matto, Massimiliano Paoletti, Lucio Marino, Luciano Ricchiuti

Subject: Biology And Life Sciences, Insect Science Keywords: Parasitoid flies of Apis mellifera; Megaselia scalaris; Senotainia tricuspis; qPCR detection; occurrence in apiaries; genotyping; pathogen transmission

Online: 2 September 2024 (16:30:19 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202404.1390.v1

Suppression PCR-Based Selective Enrichment Sequencing for Pathogen and Antimicrobial Resistance Detection on Cell-Free DNA in Sepsis - A Targeted, Blood Culture Independent Approach for Rapid Pathogen and Resistance Diagnostics in Septic Patients

Mirko Sonntag, Vanessa K. Elgeti, Yevhen Vainshtein, Lucca Jenner, Jan Mueller, Thorsten Brenner, Sebastian O. Decker, Kai Sohn

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: sepsis; antimicrobial resistances; cell-free DNA; precision diagnostics; Next-Generation sequencing; suppression PCR; real-time diagnostics; nanopore sequencing

Online: 22 April 2024 (10:13:14 CEST)

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Preprint CONCEPT PAPER | doi:10.20944/preprints202204.0104.v1

Statistical Modelling and Experimental Design for the Validation of Droplet Digital PCR Methods

Steffen Uhlig, Christopher Weidner, Bertrand Colson

Subject: Computer Science And Mathematics, Mathematical And Computational Biology Keywords: Method validation; droplet digital PCR; orthogonal factorial design; variance components; Poisson assumption; cloglog model; target DNA copies per droplet; Monte Carlo; prediction interval

Online: 12 April 2022 (08:46:49 CEST)

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Preprint COMMUNICATION | doi:10.20944/preprints202007.0279.v1

COVID19 PCR Testing and the Unprecedented Institutional Response in a Low-Resource Setting

Akintunde Orunmuyi, Olukemi Adekanmbi, Adeola Fowotade, Akindele Adebiyi, Adekunle Adeniji, Olukemi Amodu, E. Oluwabunmi Olapade-Olaopa

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: COVID19; sub-Sahara Africa; PCR testing; Capacity building

Online: 13 July 2020 (06:32:48 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201808.0358.v1

Efficient delineation of nested depression hierarchy in digital elevation models for hydrological analysis using level-set method

Qiusheng Wu, Charles R. Lane, Lei Wang, Melanie K. Vanderhoof, Jay R. Christensen, Hongxing Liu

Subject: Environmental And Earth Sciences, Remote Sensing Keywords: depression filling; digital elevation models; hydrological analysis; level-set method; LiDAR; surface depressions

Online: 20 August 2018 (14:13:34 CEST)

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Preprint REVIEW | doi:10.20944/preprints202002.0099.v1

The Determination of HIV-1 RT Mutation Rate, Its Possible Allosteric Effects, and Its Implications on Drug Resistance

Joshua Yi Yeo, Ghin Ray Goh, Chinh Tran-To Su, Samuel Ken-En Gan

Subject: Biology And Life Sciences, Virology Keywords: retroviruses; HIV-1; reverse transcriptase; mutation rate; drug resistance, allostery

Online: 7 February 2020 (11:50:11 CET)

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Preprint ARTICLE | doi:10.20944/preprints202310.1505.v1

Diagnostic Accuracy of Multiplex PCR in Early Onset Neonatal Sepsis

Anja Stein, Daniel Soukup, Peter-Michael Rath, Ursula Felderhoff-Müser

Subject: Medicine And Pharmacology, Pediatrics, Perinatology And Child Health Keywords: neonatal sepsis; early onset sepsis; multiplex PCR; infection; neonate; diagnosis; pathogen detection

Online: 24 October 2023 (08:11:56 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 ARTICLE | doi:10.20944/preprints202006.0012.v1

Psoriasis is Associated with An Increased Risk of Osteoporosis: Follow-Up and Nested Case–Control Studies Using A National Sample Cohort

Jung Woo Lee, Chanyang Min, Chul Hwan Bang, Bong Cheol Kwon, Hyo Geun Choi

Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: psoriasis; osteoporosis; cohort studies; Case-Control Studies; risk factors

Online: 3 June 2020 (05:50:13 CEST)

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

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

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

Subject: 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/preprints202305.2272.v1

The Hypocholesterolemic Potential of the Edible Algae Fucus Vesiculosus: Proteomic and Quantitative PCR Analysis

Rebeca André, Rita Pacheco, Ana Catarina Alves, Hugo M. Santos, Mafalda Bourbon, Maria-Luísa Serralheiro

Subject: Biology And Life Sciences, Food Science And Technology Keywords: Fucus vesiculosus; cholesterol synthesis; cholesterol excretion; , Ezetimibe; , NPC1L1; ABCG5; qRT-PCR; mRNA

Online: 31 May 2023 (14:54:20 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202212.0196.v1

SARS-CoV-2 PCR Persistence and Duration of COVID-19 Symptoms in Health Professionals

Tatiana Schäffer Gregianini, Ludmila Fiorenzano Baethgen, Richard Steiner Salvato, Ivone Andreatta Menegolla, CEVS COVID-19 Team, Ana Beatriz Gorini da Veiga

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: SARS-CoV-2; PCR persistent positive; respiratory infection; COVID-19

Online: 12 December 2022 (09:04:59 CET)

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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/preprints202405.0581.v1

Looking into the Quantification of Forensic Samples with Real-Time PCR

Ugo Ricci, Dario Ciappi, Ilaria Carboni, Claudia Centrone, Irene Giotti, Martina Petti, Alice Brogi, Elisabetta Pelo

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: DNA amplification; polymerase chain reaction; DNA quantification; forensic DNA

Online: 9 May 2024 (10:39:14 CEST)

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The quantification of human DNA extracts from forensic samples plays a key role in the forensic genetics process. Quantification guarantees maximum efficiency and avoids repeated analyses, over amplified samples, or unnecessary examinations. Here, we present our experience using an extremely sensitive real-time-based method with the Quantifiler® Trio DNA quantification kit, which we have explored in the ISO/IEC17025 accredited test validation process conducted in our laboratory. In this study, our focus was on establishing a minimum threshold beyond which DNA typing is unnecessary, by defining the correlation of negative quantification results with the absence of genetic profiles resulting from DNA typing. We investigated the results in the range in which the technique is used (50-0.005 ng/μl). In the validation process of the internally accredited method, we used data from the commercial quantification system, based on the average values of the standard curve using a wide range of samples, including artificially degraded samples. This method was extensively used continuously for nine years to quantify the DNA extract coming from a wide range of samples from criminal cases. The validation allowed us to verify the limits of the technique, especially in the use of the minimum quantities necessary to obtain genetic profiles acceptable for sending to the Italian DNA database. This optimization of the protocol for analysing forensic samples allows us to optimise the protocol for analysing forensic samples. However, the technique is used in our laboratory with a completely manual preparative phase, and we have decided to investigate the contribution of human error more accurately. Thus, in our experience, we have found that it is preferable to use quantification ranges rather than exact limits before deciding how to analyse the extracts via PCR. In addition, here we present some preliminary data related to the analysis of certain samples that initially appeared negative during quantification, applying a concentration method for maximum yield from forensic samples of judicial interest. Our aim is to ensure that no source of evidence is lost in the reconstruction of a criminal event.

Preprint ARTICLE | doi:10.20944/preprints202111.0210.v1

Detection of Klebsiella pneumoniae DNA by PCR-Based CRISPR-lbCas12a System

Shang Wang, Ying Tang, Jiehong Wei, Shan Wang, Guoyu Peng, Yuqing Li, Song Wu

Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: CRISPR-Cas, Nucleic acid detection, Klebsiella pneumonia

Online: 11 November 2021 (12:57:06 CET)

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Preprint ARTICLE | doi:10.20944/preprints201812.0189.v1

Optimisation of DNA Extraction from Individual Sand Flies for PCR Amplification

Lorena G. Caligiuri, Adolfo E. Sandoval, Jose C. Miranda, Felipe A. Pessoa, María S. Santini, Oscar D. Salomón, Nagila F. C. Secundino, Christina McCarthy

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Sand fly; DNA extraction; Calcium; PCR, lysis buffer, Lutzomyia

Online: 17 December 2018 (10:41:28 CET)

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

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

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

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

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

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Preprint ARTICLE | doi:10.20944/preprints202101.0264.v1

Measuring Time-Varying Effective Reproduction (Rt) Numbers for COVID-19 and Their Relationship with Movement Control Order (MCO) in Malaysia

Musa Kamarul Imran, Wan Nor Ariffin, Mohd Mohd Hafiz, Subhi Jamiluddin, Noor Atinah Ahmad, Chen Xin Wee, Tengku Muhammad Hanis, Awang Bulgiba

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: Reproduction number; COVID-19; movement control order; epidemic curve

Online: 14 January 2021 (09:41:02 CET)

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Preprint ARTICLE | doi:10.20944/preprints202403.1144.v1

Development of PCR-Multiplex Assays for Identification of the Herpotrichiellaceae Family and Agents Causing Chromoblastomycosis

Gabriel S.M. Sousa, Rodrigo S. De Oliveira, Alex B. De Souza, Ruan C. Monteiro, Elaine P. T. E. Santo, Luciano C. Franco Filho, Denison L.O. Moraes, Sarah R. De Sá, Silvia H. M. Da Silva

Subject: Biology And Life Sciences, Other Keywords: chromoblastomycosis; phaeohyphomycosis; PCR-Multiplex; Herpotrichiellaceae; sequencing; phenotypic; molecular biology.

Online: 19 March 2024 (12:35:06 CET)

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Preprint ARTICLE | doi:10.20944/preprints202305.1348.v1

Expanded PCR Panel Testing for Identification of Respiratory Pathogens and Coinfections in Influenza-like Illness

Pallavi Upadhyay, Jairus Reddy, Teddie Proctor, Oceane Sorel, Harita Veereshlingam, Manoj Gandhi, Vijay Singh

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: Respiratory tract infections; COVID-19; influenza-like illness; multiplex PCR; syndromic panels

Online: 18 May 2023 (14:10:38 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202007.0740.v1

Speeding Up COVID-19 Detection Using Shaker-Mill Homogenization and a Direct-to-PCR Workflow

Zachary P Morehouse, Caleb M Proctor, Gabriella L Ryan, Rodney J Nash

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: COVID-19; Virus Detection; Viral Diagnostics; Diagnostics; SARS-CoV-2; Coronavirus; PCR

Online: 31 July 2020 (09:31:18 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/preprints202306.0425.v1

Impact of wind generation in the transformation centers of low voltage distribution networks using Opal-RT 5600

Javier Cabrera, Carlos Guerrero, Esteban Franco, Gabriela Araujo

Subject: Engineering, Electrical And Electronic Engineering Keywords: Wind energy; voltage profile; distribution network; simulation

Online: 6 June 2023 (09:35:15 CEST)

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Preprint COMMUNICATION | doi:10.20944/preprints202111.0549.v1

PCR, PLS, or OPLS Evaluation of different regression techniques for hypothesis generation

Avani Ahuja

Subject: Computer Science And Mathematics, Applied Mathematics Keywords: Principal Component Regression, Partial Least Squares, Orthogonal Partial Least Squares, multivariate regression, hypothesis generation, Parkinson’s disease

Online: 29 November 2021 (15:42:03 CET)

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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 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/preprints202308.0284.v1

Designing and Validation of a Droplet Digital PCR Procedure for Diagnosis and Accurate Quantification of Nervous Necrosis Virus

Sandra Souto, José G. Olveira, Carmen López-Vázquez, Isabel Bandín, Carlos P. Dopazo

Subject: Biology And Life Sciences, Virology Keywords: VNNV; Diagnosis; Validation; dPCR; droplet digital PCR.

Online: 3 August 2023 (10:44:12 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202309.1225.v1

Exploration of Temperature-Induced Quantum Proton Tunneling Probability in PCR-Mediated DNA Amplification

Joseph De Luna

Subject: Physical Sciences, Biophysics Keywords: genetics; molecular biology; biophysics; quantum mechanics

Online: 19 September 2023 (05:18:03 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202305.1033.v2

Designing Microfluidic PCR Chip Device Using CFD Software for the Detection of Malaria

Meynard R. Austria, Jon Patrick T. Garcia, Lemmuel L. Tayo, Alvin R. Caparanga, Bonifacio Jr T. Doma

Subject: Engineering, Bioengineering Keywords: polymerase chain reaction (PCR); Computational Fluid Dynamics (CFD); Plasmodium falciparum; microfluidic chip design

Online: 10 August 2023 (10:30:52 CEST)

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Preprint BRIEF REPORT | doi:10.20944/preprints202211.0436.v1

Multiplex PCR Detects Respiratory Viruses at A Much Higher Rate in Kawasaki Disease

Masayuki Nagasawa, Teruyoshi Shimoyama, Sayuri Hashimoto, Ryuichi Nakagawa, Haruna Yokoyama, Mari Okada, Tomohiro Udagawa, Akihiro Oshiba

Subject: Medicine And Pharmacology, Pediatrics, Perinatology And Child Health Keywords: Kawasaki disease; febrile convulsions; respiratory virus; filmarray; multiplex PCR

Online: 23 November 2022 (07:02:54 CET)

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Preprint ARTICLE | doi:10.20944/preprints202407.2169.v1

Spleen Swabs for Sensitive and High-Throughput Detection of African Swine Fever Virus by Real-Time PCR

Christopher Cafariello, Kalhari Goonewardene, Chungwon J Chung, Aruna Ambagala

Subject: Biology And Life Sciences, Virology Keywords: African swine fever; Diagnostics; Tissue homogenate; Spleen swab; Real-time PCR

Online: 26 July 2024 (16:49:52 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202308.0184.v1

Non-Covalent Interactions between dUTP C5-Substituents and DNA Polymerase Result in a Decrease in PCR Efficiency

Olga A. Zasedateleva, Sergey A. Surzhikov, Viktoriya E. Kuznetsova, Valeriy E. Shershov, Victor E. Barsky, Alexander S. Zasedatelev, Alexander V. Chudinov

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: C5-modified dUTPs; A and B family DNA polymerases; PCR amplification; X-ray structure; molecular modeling; non-covalent interactions

Online: 2 August 2023 (08:21:50 CEST)

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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 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/preprints202310.0061.v1

Handheld Ultra-Fast duplex PCR assays and Lateral flow detection and identification of Leishmania parasites for cutaneous leishmanisis diagnosis

Insaf Bel Hadj Ali, Yusr Saadi Ben Aoun, Zeineb Hammami, Oumayma Rhouma, Ahmed Sahbi Chakroun, Ikram Guizani

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: Cutaneous leishmaniases; Molecular diagnosis; Point of care; Leishmania; Molecular target; Palm PCR; Duplex PCR; Lateral Flow immunoassay

Online: 2 October 2023 (09:43:13 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202307.1994.v1

A Colorimetric RT-LAMP Detection of Multiple SARS-CoV-2 Variants of Concern and Lineages from Direct Nasopharyngeal Swab Samples without RNA Isolation

Santiago Enrique Werbajh, Luciana Larocca, Carolina Carrillo, Fabiana Stolowicz, Lorena Ogas, Sergio Pallotto, Solange Cassará, Lilia Mammana, Inés Zapiola, María Belén Bouzas, Adrián Alberto Vojnov

Subject: Biology And Life Sciences, Virology Keywords: COVID-19; SARS-CoV-2; LAMP

Online: 28 July 2023 (13:29:56 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202311.2000.v1

A Simple Inexpensive Alkaline Method for DNA Extraction from Environmental Samples for PCR Surveillance

Abdulkarim Shwani, Bin Zuo, Adnan Alrubaye, Jiangchao Zhao, Douglas Duane Rhoads

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: microbiome; bacteria; DNA extraction; poultry; swine; air sampling

Online: 30 November 2023 (15:40:03 CET)

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Preprint ARTICLE | doi:10.20944/preprints202405.1939.v1

Actinobacillus pleuropneumoniae Serotypes by Multiplex PCR Identification and Evaluation of Lung Lesions in Pigs from Piedmont (Italy) Farms

Matteo Cuccato, Sara Divari, Silvia Ciaramita, Alessandra Sereno, Domenico Campelli, Pier Giuseppe Biolatti, Bartolomeo Biolatti, Francesco Meliota, Enrico Bollo, Francesca Tiziana Cannizzo

Subject: Medicine And Pharmacology, Veterinary Medicine Keywords: Actinobacillus pleuropneumoniae; porcine pleuropneumonia; swine; respiratory diseases; serotyping; multiplex PCR

Online: 29 May 2024 (14:03:53 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202403.0571.v1

Streamlined Two-Step Fragment Analysis PCR and Exome Sequencing of RFC1 for Diagnostic Testing of Suspected CANVAS Patients

Helena Jaklič, Ivana Babič Božović, Borut Peterlin, Anja Kovanda

Subject: Medicine And Pharmacology, Other Keywords: Cerebellar ataxia neuronopathy and vestibular areflexia syndrome (CANVAS); RFC1; genetic testing; genetic diagnostics, ; fluorescent PCR; repeat-primed PCR; repeat-expansion; fragment length analysis

Online: 11 March 2024 (05:36:41 CET)

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Working Paper ARTICLE

Detection of Peanut Allergen by Real Time PCR: Looking For the Suitable Detection Marker as Affected by Processing

Africa Sanchiz, Paulina Sánchez-Enciso, Carmen Cuadrado, Rosario Linacero

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: Real-time PCR; peanut; food allergen; chloroplast marker; DNA isolation

Online: 16 June 2021 (11:33:10 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202309.1487.v1

Simultaneous Detection of Three Subgroups of Avian Leukosis Virus Using the Nanoparticle-Assisted PCR Assay

Miaoli Wu, Shuaiqi Hu, Yujun Zhu, Feng Cong, Shengwang Liu

Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: nanoPCR; avian leukosis virus; ALV-J; detection

Online: 22 September 2023 (04:33:14 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/preprints202010.0379.v1

Evaluation of Reference Genes for qRT-PCR Normalization in Angelica decursiva under Various Experimental Conditions

Yuedong He, Yuan Zhong, Zhenzhen Bao, Weiqi Wang, Xiaoqing Xu, Yanan Gai, Jie Wu

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: qRT-PCR; reference gene; Angelica decursiva; expression stability

Online: 19 October 2020 (12:25:21 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202005.0440.v1

Clinical Performance Analysis and Evaluation of Quantitative Real Time PCR for Diagnosis of Scrub Typhus in North East India

Diptanu Paul, W Valarie Lyngdoh, Himesh Barman, Clarissa Jane Lyngdoh, Kryshanlang Lynrah, Elantamilan Durairaj

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Scrub typhus; qRT PCR; Quantitative PCR; real time PCR; IgM ELISA; North-East India

Online: 27 May 2020 (07:51:25 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202306.1455.v1

Nebulized recombinant tissue plasminogen activator (rt-PA) for acute COVID-19-induced severe respiratory failure: an exploratory proof of concept trial

Pratima Chowdary, Banwari Agarwal, Maria Rita Peralta, Sanjay Bhagani, Simon Lee, James Goldring, Marc Lipman, Emal Waqif, Mark Phillips, Helen Philippou, Jonathan H Foley, Nicola J Mutch, Robert Ariens, Kathleen A Stringer, Federico Ricciardi, Marie Watissée, Derralynn Hughes, Amit Nathwani, Anne Riddell, David Patch, Jim Buckley, Mark De Neef, Rahul Dimber, Cecilia Diaz-Garcia, Honey Patel, Aarti Nandani, Upuli Dissanayake, Nick Chadwick, Ahmed Alkhatip, Peter Watkinson, Eamon Raith, Suveer Singh, Tony Wolff, Rajeev Jha, Simon E Brill, Ameet Bakhai, Alison Evans, Farhat Gilani, Keith Gomez

Subject: Medicine And Pharmacology, Pulmonary And Respiratory Medicine Keywords: Acute respiratory illness; critical care; recombinant tissue plasminogen activator; nebulization, fibrinolytics, COVID-19 pandemic, inhaled medication, targeted therapy

Online: 20 June 2023 (14:59:12 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202103.0109.v1

Identification and Biotyping of Pythium insidiosum Isolated from Urban and Rural Areas of Thailand by Multiplex PCR, DNA Barcode, and Proteomic Analyses

Zin Mar Htun, Aree Laikul, Watcharapol Pathomsakulwong, Chompoonek Yurayart, Tassanee Lohnoo, Wanta Yingyong, Yothin Kumsang, Penpan Payattikul, Pattarana Sae-Chew, Thidarat Rujirawat, Paisan Jittorntam, Chalisa Jaturapaktrarak, Piriyaporn Chongtrakool, Theerapong Krajaejun

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Pythiosis; Pythium insidiosum; Environment isolate; DNA barcode; Biotyping

Online: 2 March 2021 (16:41:34 CET)

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Preprint ARTICLE | doi:10.20944/preprints202311.0771.v1

Monitoring of Fabric Integrity and Attrition Rate of Dual-Active Ingredient Long-Lasting Insecticidal Nets in Tanzania: A Prospective Cohort Study Nested in a Cluster Randomized Controlled Trial

Jackline Lyimo Martin, Eliud Lukole, Louisa A. Messenger, Tatu Aziz, Elizabeth Mallya, Edmund Bernard, Nancy S. Matowo, Jacklin Franklin Mosha, Mark W. Rowland, Franklin W. Mosha, Alphaxard Manjurano, Natacha Protopopoff

Subject: Biology And Life Sciences, Insect Science Keywords: Long-lasting insecticidal net; median function survival; survivoship; attrition; fabric integrity; Tanzania

Online: 13 November 2023 (10:17:43 CET)

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Preprint ARTICLE | doi:10.20944/preprints202409.0370.v1

Comparison of Whole Genome Sequencing versus Pcr Kit for Detection of COVID-19 Variants in Wastewater

Michelle M. Jarvie, Thu N.T. Nguyen, Benjamin Southwell, Derek Wright

Subject: Public Health And Healthcare, Public, Environmental And Occupational Health Keywords: keyword 1; Covid-19 2; PCR 3; Whole genome sequencing 4; Wastewater-based epidemiology

Online: 4 September 2024 (14:49:55 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202406.1226.v1

Digital PCR Validation for Characterization of Quantitative Reference Material of Escherichia coli O157:H7 Genomic DNA

Claudia Patricia Tere-Peña, Martha Nancy Calderon-Ozuna, John Emerson Leguizamón

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: E. coli O157:H7; Reference material; Method validation; digital PCR

Online: 18 June 2024 (11:03:54 CEST)

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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/preprints202305.2110.v1

Research on the Device of Micro Droplet PCR in Microfluidic Chip Based on Constant Pressure Regulation

Luyang Duanmu, Yuanhua Yu, Xiangkai Meng

Subject: Engineering, Control And Systems Engineering Keywords: Constant Pressure Regulation; Micro droplet Digital PCR; Fluorescence Detection; Quantitative Detection

Online: 30 May 2023 (10:31:02 CEST)

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Working Paper ARTICLE

Kompetitive Allele Specific PCR (KASP) Markers for Potato: An Effective Tool for an Increased Genetic Gain

Moctar Kante, Hannele Lindqvist Kreuze, Maria David, Leticia Portal, Manuel Gastelo

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Late blight; PVY; Ryadg; quality control; KASP

Online: 4 October 2021 (17:37:19 CEST)

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Working Paper ARTICLE

Chip-Based Digital Pcr Improves the Detection of Low-Rate pik3ca Mutations in Breast Cancer Patients

Stefano Giannoni-Luza, Oscar Acosta Conchucos, Alexis Germán Murillo Carrasco, Pierina Danos, José Manuel Cotrina Concha, Henry Guerra Miller, Joseph A. Pinto, Alfredo Aguilar Cartagena, Jhajaira M. Araujo, Ricardo Fujita, José Luis Buleje Sono

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Breast cancer; PIK3CA; digital PCR; Sanger sequencing

Online: 5 July 2021 (14:00:22 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202407.1311.v1

Assessing Stability in Renewable Microgrid Using a Novel-Optimized Controller for PVBattery Based Micro Grid with Opal-RT Based Real-Time Validation

Anshuman Satpathy, Naeem M.S. Hannon, Rahimi Baharom, Niranjan Nayak, Snehamoy Dhar

Subject: Engineering, Control And Systems Engineering Keywords: solar PV; duty-cycle; feedback controller; voltage control; IDGC; ELM; irradiance variation; partial shading

Online: 16 July 2024 (09:32:42 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201810.0383.v1

Pathologic Complete Response (pCR) and Survival of Women with Inflammatory Breast Cancer (IBC): An Analysis Based on Biologic Subtypes and Demographic Characteristics

Tithi Biswas, Charulata Jindal, Timothy Fitzgerald, Jimmy Efird

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: Biologic subtypes; diagnosis; inflammatory breast cancer; pCR; survival

Online: 17 October 2018 (11:08:56 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202208.0520.v1

Prevalence of Human Herpesviruses (HHV1-7), and its Clinical Significance in Middle Eastern Pediatric Leukemia Patients Using 2 Independent PCR Assays

Waleed Seif ElDin Mohamed, Hisham Abid Aldabbagh, Hussein Ali Aldughmani, Zeinab Fathy Abdullah, Sara Ahmed Kassem, Iman Adel Abdel-Almoniem, Mohamed Fawzy Ibrahim

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: Multiplex PCR; Real time PCR; Human herpes viruses; clinical significance; Pediatric Leukemia patients

Online: 30 August 2022 (10:30:06 CEST)

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Objectives: Human herpes viruses can cause life-threatening diseases in immunocompromised children, especially leukemic patients. Therefore, the aim of this study is to detect the human herpes viruses (HHV1-7) and to investigate its clinical significance in Middle Eastern Pediatric Leukemia Patients by using 2 Independent PCR assays. Methods: Detection of human herpes virus DNA has been done in blood samples of 200 pediatric leukemia patients in addition to 90 blood donors as a control group using multiplex PCR assays. When a ‘‘positive’’ result was observed, real-time PCR was performed to measure the viral load. Results: The most frequent herpes virus infection in Middle Eastern Pediatric Leukemia cases was CMV, followed by EBV, then HHV6, VZV, HHV7, HSV1, and HSV2, where they were 92/200 (46%), 76/200 (38%), 72/200 (36%), 48/200 (24%), 12/200 (6%), 8/200 (4%), and 2/200 (1%) respectively. Also, there was a statistically significance difference between leukemic patients and their controls regarding CMV, EBV, HHV6, and VZV (P <0.05). Correlation between percentage of co-infection, and clinical parameters for the 7 herpes viruses has been studied, and there is an increase in absolute neutrophilic count (ANC), total leukocyte count (TLC) and duration of fever and neutropenia in age group 6-11 years for HHV6/CMV, then in age group 12-18 years especially for EBV/CMV and CMV/HHV6. Also, our results show that multiplex PCR assay is close to single PCR assay in relation to specificity and sensitivity which in turn prove its validity for early diagnosis of herpes viral infection. Conclusions: Adopting multiplex PCR technique is helpful in screening of virus infections. It will save time, effort, cost effective and will assist in rapid diagnosis. However, the clinical relevance of the virus infection needs to be evaluated by quantitative real-time PCR which in turn will help patient's management by using appropriate antiviral treatment.

Preprint ARTICLE | doi:10.20944/preprints202005.0076.v2

Effect of Instant Controlled Pressure Drop (DIC) Treatment on the Detection of Nut Allergens by Real Time PCR

Africa Sanchiz, Carmen Cuadrado, Joseph Haddad, Rosario Linacero

Subject: Biology And Life Sciences, Food Science And Technology Keywords: Real time PCR; tree nuts; allergen detection; processed foods; thermal processing; pressure processing; DIC processing

Online: 16 May 2020 (19:18:21 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202310.1790.v1

Applying Infrared Thermography to a Latest Residential Building in France: Case Study, Verifying Dwellings National Thermal Regulations RT 2012 Mainly Thermal Bridges Assessment

Harry RAMENAH

Subject: Engineering, Control And Systems Engineering Keywords: thermal bridges; building efficiency; infrared thermography; building energy performance; balcony

Online: 27 October 2023 (11:04:07 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/preprints202311.1203.v1

PCR Array Profiles the Expression of miRNAs Involved in Differentiation of Amniotic Fluid Stem Cells towards Endothelial and Smooth Muscle Progenitor Cells

Florin Iordache, Adriana Ionescu Petcu, Aurelia Magdalena Pisoschi, Loredana Stanca, Ovidiu Ionut Geicu, Liviu Bilteanu, Carmen Curutiu, Bogdan Amuzescu, Andreea Iren Serban

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: microRNA; stem cells; differentiation; endothelial progenitor cells; smooth muscle progenitor cells

Online: 22 November 2023 (15:08:37 CET)

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Preprint ARTICLE | doi:10.20944/preprints202305.0337.v1

Screening and Validation of Internal Reference Genes for Quan-Titative Real-Time PCR Analysis of Leaf Color Mutants in Den-Drobium Officinale

Hua Cao, Han Li, Lin Lu, Yulu Ji, Lulin Ma, Shenchong Li

Subject: Biology And Life Sciences, Plant Sciences Keywords: Dendrobium officinale; leaf color; qRT-PCR; reference gene; leaf color mutant

Online: 5 May 2023 (09:34:44 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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