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Preprint ARTICLE | doi:10.20944/preprints202004.0374.v2

Global Comparison of Changes in the Number of Test-Positive Cases and Deaths by Coronavirus Infection (COVID-19) in the World

Akihiro Hisaka, Hideki Yoshioka, Hiroto Hatakeyama, Hiromi Sato, Yoshihiro Onouchi, Naohiko Anzai

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: COVID-19; coronavirus; infectious disease; infection management; PCR test; mortality; kinetic analysis

Online: 3 June 2020 (05:10:05 CEST)

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Preprint BRIEF REPORT | doi:10.20944/preprints202002.0424.v1

Insufficient Sensitivity of RNA Dependent RNA Polymerase Gene of SARS-CoV-2 Viral Genome as Confirmatory Test using Korean COVID-19 Cases

Soyoun Kim, Dong-Min Kim, Baeckseung Lee

Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: SARS-CoV-2; Korean COVID-19; Wuhan Corona virus; real time PCR Ct Value; Sensitivity; False Negative

Online: 28 February 2020 (12:03:13 CET)

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

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

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

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

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

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Preprint ARTICLE | doi:10.20944/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 REVIEW | doi:10.20944/preprints202005.0234.v1

Epidemiological Challenges in Pandemic Coronavirus Disease (COVID-19): Role of Artificial Intelligence

Abhijit Dasgupta, Abhisek Bakshi, Srijani Mukherjee, Kuntal Das, Soumyajeet Talukdar, Pratyayee Chatterjee, Sagnik Mondal, Puspita Das, Subhrojit Ghosh, Archisman Som, Pritha Roy, Rima Kundu, Akash Sarkar, Arnab Biswas, Karnelia Paul, Sujit Basak, Krishnendu Manna, Chinmay Saha, Satinath Mukhopadhyay, Nitai P. Bhattacharyya, Rajat K. De

Subject: Computer Science And Mathematics, Artificial Intelligence And Machine Learning Keywords: SIRD; Twitter; GHSI; Pre-symptomatic; EHR; Contact tracing; On-line survey; qRT-PCR; X-ray; CT/HRCT; CNN; Autoencoder; Drug affinity; CPI; and Inflation.

Online: 14 May 2020 (11:25:57 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202005.0332.v2

Witnessing Evolution of SARS-CoV-2 through Comparative Phylogenomics: The Proximate Origin is Guangdong, not Wuhan

Özgül Doğan, Ertan Mahir Korkmaz, Mahir Budak, Battal Çıplak, Hasan Hüseyin Başıbüyük

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: coronavirus; substitution rate; positive selection; demographic dynamics

Online: 21 June 2020 (16:10:26 CEST)

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A new form of coronavirus called severe acute respiratory disease coronavirus type 2 (SARS-CoV-2) is currently causing a pandemic. A six-month evolutionary history of SARS-CoV-2 is witnessed by characterising the total genome of 821 samples using comparative phylogenomic approaches. Our analyses produced striking inclusive results that may guide scientists/professionals for the past/future of pandemic. Phylogenetic and time estimation analyses suggest the proximate origin of pandemic strain as Guangdong and the origin time as first half of September 2019, not Wuhan and December 2019, respectively. The viral genome experienced a substitution rate similar to other RNA viruses, but it is particularly high in some of the peptides encoding sequences such as leader protein, E gene, orf8, orf10, nsp10, N gene, S gene and M gene and nsp4, while low in nsp11, orf7a, 3C-like proteinase, nsp9, nsp8 and endoRNase. Most strikingly, the divergence rate of amino acid sequences is high proportional to nucleotide divergence. Additionally, specific non-synonymous mutations in nsp3 and nsp6 evolved under positive selection. The exponential growth rate (r), doubling time (Td) and R₀ were estimated to be 47.43 per year, 5.39 days and 2.72, respectively. Comparison of synapomorphies distinguishing the SARS-CoV-2 and the candidate ancestor bat coronavirus indicates that mutation pattern in nsp3 and S gene enabled the new strain to invade human and become a pandemic strain. We arrive at the following main conclusions: (i) six months evolution of viral genome is nearly neutral, (ii) origin of pandemic is not Wuhan and predates formal reports, (iii) although viral population is ongoing an exponential growth, the doubling time is evolving towards shortening, and (iv) divergence rate of total genome is similar to other RNA viruses, but it is prominently high in some genes while low in some others and evolution in these genes should be closely monitored as their protein products intervening to pathogenicity, virulence and immune response.

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/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 REVIEW | doi:10.20944/preprints202004.0201.v2

Detecting the Coronavirus (COVID-19)

Pravin Pokhrel, Changpeng Hu, Hanbin Mao

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: SARS-CoV-2 Detection, SARS-CoV-2 Antibody Test, SARS-CoV-2 Antigen Test, False Negative, False Positive, Sensitivity, Specificity, Point-of-care testing (POCT), SARS-CoV-2 Mutants

Online: 25 March 2021 (15:33:14 CET)

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The COVID-19 pandemic has created huge damage to society and brought panics around the world. Such panics can be ascribed to the seemingly deceptive features of the COVID-19: compared to other deadly viral outspreads, it has medium transmission and mortality rates. As a result, the severity of the causative coronavirus, SARS-CoV-2, was deeply underestimated by the society at the beginning of the COVID-19 outbreak. Based on this, in this review, we define the viruses with features similar to those of SARS-CoV-2 as the Panic Zone viruses. To contain those viruses, accurate and fast diagnosis followed by effective isolation and treatment of patients are pivotal at the early stage of virus breakouts. This is especially true when there is no cure or vaccine available for a transmissible disease, which is the case for current COVID-19 pandemic. As of January 2021, more than two hundred kits for the COVID-19 diagnosis on the market are surveyed in this review, while emerging sensing techniques for SARS-CoV-2 are also discussed. It is of critical importance to rationally use these kits for the efficient management and control of the Panic Zone viruses. Therefore, we discuss guidelines to select diagnostic kits at different outbreak stages of the Panic Zone viruses, SARS-CoV-2 in particular. While it is of utmost importance to use nucleic acid-based detection kits with low false negativity (high sensitivity) at the early stage of an outbreak, the low false positivity (high specificity) gains its importance at later stages of the outbreak. When a society is set to reopen from the lock-down stage of the COVID-19 pandemic, it becomes critical to have antibody based immunoassay kits with high specificity to identify people who can safely return to the society after their recovery of SARS-CoV-2 infections. Given that the emergence of mutant viruses at the beginning of 2021 has complicated current battle against the COVID-19, we also discussed approaches and guidelines to detect viral mutants in the middle of the second wave of the pandemic that started at the end of 2020. Finally, since a massive attack from a viral pandemic requires a massive defense from the whole society, we urge both government and private sectors to research and develop more affordable and reliable point-of-care testing (POCT) kits, which can be used massively by the general public (and therefore called as massive POCT) to contain Panic Zone viruses in future.

Preprint OPINION | doi:10.20944/preprints201608.0016.v1

Dark Side of Molecular Techniques: How to Fix It ?

Vikash Bhardwaj

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: parallel DNA; antiparallel DNA; PCR; CRISPR; nucleic acid hybridization; microarray; siRNA

Online: 2 August 2016 (10:42:27 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202012.0094.v3

“Clinician’s Probability Calculator” to Convert Pre-Test to Post-Test Probability of COVID-19, Based on Method Validation from Each Laboratory

Zoe Brooks, Saswati Das, Tom Pliura

Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: COVID-19; SARS-COV-2; False-Positive; False-Negative; Likelihood Ratio; Probability; Calculator; Interpretation

Online: 3 March 2021 (10:08:27 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/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/preprints201811.0395.v1

Rapid Diagnosis of Capnocytophaga canimorsus Septic Shock in an Immunocompetent Individual Using Real-Time Nanopore Sequencing

Seweryn Bialasiewicz, Tania P.S. Duarte, Son H. Nguyen, Vichitra Sukumaran, Alexandra Stewart, Sally Appleton, Miranda E. Pitt, Arnold Bainomugisa, Amy V. Jennison, Rikki Graham, Lachlan J.M. Coin, Krispin Hajkowicz

Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: nanopore sequencing; droplet digital PCR; Capnocytophaga canimorsus; diagnosis; sepsis

Online: 16 November 2018 (09:45:38 CET)

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Preprint ARTICLE | doi:10.20944/preprints201704.0102.v1

Age-Related Diseases as Vicious Cycles

Aleksey V. Belikov

Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: aging; age-related disease; mortality rate; positive feedback loop; vicious cycle

Online: 18 April 2017 (02:45:04 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/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/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 REVIEW | doi:10.20944/preprints202006.0284.v1

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

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

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

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

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

Preprint ARTICLE | doi:10.20944/preprints201703.0162.v1

Evaluation of the Effects of Airborne Particulate Matter on Bone Marrow-Mesenchymal Stem Cells (BM-MSCs): Cellular, Molecular and Systems Biological Approaches

Muhammad Abu-Elmagd, Mansour A Alghamdi, Magdy Shamy, Mamdouh I Khoder, Max Costa, Mourad Assidi, Roaa Kadam, Haneen Alsehli, Mamdooh Gari, Peter Natesan Pushparaj, Gauthaman Kalamegam, Mohammed Al-Qahtani

Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: Particulate matter; BM-MSCs; cell proliferation; cell death; qRT-PCR; IPA

Online: 20 March 2017 (16:33:56 CET)

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Preprint REVIEW | doi:10.20944/preprints201707.0003.v1

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

Nicholas J. Haley, Juergen A. Richt

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

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

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Preprint ARTICLE | doi:10.20944/preprints202006.0279.v2

COVID-19 Testing – Impact of Prevalence, Sensitivity, and Specificity on Patient Risk and Cost

Zoe C. Brooks, Saswati Das

Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: COVID19; risk; clinical; metrics; cost; false-positive; false-negative; prevalence; sensitivity; specificity

Online: 9 July 2020 (15:57:30 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202006.0032.v1

Emergence of RBD and D614G Mutations in Spike Protein: An Insight from Indian SARS-CoV-2 Genome Analysis

VINAYAGAM SAMYUKTHA, VENKATESAN NAVEEN KUMAR

Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: SARS-CoV-2; Spike protein; COVID-19; Mutation; hACE2 Receptor; Real-time PCR; Vaccine

Online: 4 June 2020 (08:48:03 CEST)

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Currently, entire world is crumbled due to COVID-19 caused by novel SARS-CoV-2. Globally, over 5 million people are infected by SARS-CoV-2 with 6% fatality rate. The surface spike (S) protein plays a key role in the pathogenesis of SARS-CoV-2 by mediating viral entry through human angiotensin converting enzyme 2 (hACE2) receptors on the host cell and there is a big global race to find viral neutralizing antibodies and vaccine against S protein of SARS-CoV-2. Since SARS-CoV-2 evolved into 10 different clades in a very short span, a study on sipke protein mutation is essential to have effective vaccine coverage globally. Based on the mutation analysis of S protein from 166 Indian SARS-CoV-2 genome, a total of 40 different SNPs comprising of 14 synonymous and 26 non-synonymous mutations were observed, and notably, Indian S protein diverged into two major clusters, D614 and G614, with 11 different types. Majority of Indian strains fall in A2a and O clusters. Alarmingly, we have observed six SNPs at RBD and notably two of them at RBM (S438F and S494P). S494P SNP, similar to Bat–SARS like-CoV, may indicate a low ACE2 binding affinity. Interestingly 38% of Indian strains harbor a characteristic D614G SNP which was found predominantly in A2a cluster, mostly comprising USA and European strains with high disease severity. The association of disease severity with D614G SNP is well-correlated in states with high death rate except Maharashtra. Notably, more than 50% of D614G mutation were observed in Northern part of India and 14% in Southern part but not in Kerala and Tamil Nadu strains. Highly conserved motif, D614 (608-VAVLYQDVNCT-618) in upstream and also few downstream, of S1/S2 furin cleavage site may indicate specific key role in efficient interaction with host proteases in pathogenesis. Further studies are warranted to clarify the impact of SD614G SNP association to disease severity . Interestingly, C2367T (Y789Y) synonymous SNP is observed in 37% of Indian strains and notably similar SNPs with degeneracy bases were observed which is a key indication for the possibility of misdiagnosis by Real-Time PCR and revised strategies are needed for the precise diagnosis. Circulation of high number of signature SNPs [D614G and C2367T (Y789Y)] in certain states may be an early indication of emergence of community transmission in India. Further large genome sequence data from India will aid in deep understanding on the diversity of circulating SASR-Cov-2 and its impact on disease severity, origin of imported cases to India, community spread, effect on diagnosis and vaccine coverage.

Preprint ARTICLE | doi:10.20944/preprints201705.0206.v1

Genome Characterization of a Novel Binary Toxin-Positive Strain of Clostridium difficile and Comparison with the Epidemic 027 and 078 Strains

Zhong Peng, Sidi Liu, Xiujuan Meng, Wan Liang, Biao Tang, Yuanguo Wang, Juping Duan, Chenchao Fu, Bin Wu, Anhua Wu, Chunhui Li

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Clostridium difficile; ST201; binary toxin-positive; whole genome sequencing; comparative genomic analysis

Online: 30 May 2017 (06:15:11 CEST)

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A novel binary toxin-positive non-027, non-078 Clostridium difficile strain designated LC693 whose sequence type was ST201 was isolated from the fecal sample of a patient with severe diarrhea in China. To understand the pathogenesis basis of C. difficile ST201, this recently recovered isolate LC693 was then chosen for whole genome sequencing. The project finally generated an estimated genome size of approximately 4.07 Mbp. The genome sequence was then analyzed together with the other two ST201 strains VL-0104 and VL-0391 and compared to the epidemic 027/ST1 and 078/ST11 strains. Phylogenetic analysis demonstrated that the ST201 strains belonged to clade 3. Genome size of the three ST201 strains ranged from 4.07 Mb~4.16 Mb, with an average GC content between 28.5%~28.9%. The ST201 genomes contained more than 40 antibiotic resistance genes and 15 of them were predicted to be associated with vancomycin-resistance, suggesting that they may have a strong antibiotic resistance. The ST201 strains contained a typical clade 3 specific PaLoc with a Tn6218 element inserted, and those genes harbored on their PaLoc that participated in the toxin expression and regulation were highly homologues to the epidemic 027 and 078 strains, with the exception of tcdC. A truncated TcdC was found in the ST201 strains, which is suggestive to have a contribution to the toxin production of the ST201 strains. In addition, the ST201 strains contained intact binary toxin coding and regulation genes, which is also proposed to contribute to the virulence. Genome comparison of the ST201 strains with the epidemic 027 and 078 strain identified 641 genes specific for the C. difficile ST201, and a number of them were predicted as fitness and virulence associated genes. The identification of those genes also contributes to the pathogenesis of the ST201 strain. To our knowledge, this is the first study that the genome sequence of C. difficile ST201 was discussed in detail, and the present study would have a contribution to understanding the pathogenesis basis of C. difficile ST201.

Preprint COMMUNICATION | doi:10.20944/preprints201812.0178.v2

Ecological Drivers of Species Distributions and Niche Overlap for Three Subterranean Termite Species in the Southern Appalachian Mountains, USA

Chaz Hyseni, Ryan Garrick

Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: biodiversity; biogeography; competitive exclusion; ecological niche model; molecular taxonomic identification; PCR-RFLP; Reticulitermes; saproxylic; species richness

Online: 17 January 2019 (03:55:36 CET)

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Preprint ARTICLE | doi:10.20944/preprints202109.0415.v2

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

Sin Hang Lee

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

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

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Preprint ARTICLE | doi:10.20944/preprints202011.0626.v1

Isolation and Identification of Gram Positive and Negative Bacteria from Dairy Department Waste Lines at Baraton University

Stella Wanyama

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Isolation; Identification; gram positive; gram negative; tests staining; microbio metabolic activities

Online: 25 November 2020 (08:36:32 CET)

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Preprint ARTICLE | doi:10.20944/preprints202206.0023.v1

Innate Health: A Novel Examination of What Explains Well-being, Prosocial Behavior, and Aggression among Men Living in a UK Prison

Jeanne Catherine, Adriaan Denkers, Anita McGinty

Subject: Social Sciences, Psychology Keywords: well-being; innate health; positive psychology; mental health; three principles; self-control; pro-social behaviors; criminology; incarcerated men; prisoners; inmates

Online: 2 June 2022 (02:57:49 CEST)

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Preprint BRIEF REPORT | doi:10.20944/preprints201911.0214.v1

Unbiasing in the Genome Analysis of Iconic Shark Species

Kazuaki Yamaguchi, Shigehiro Kuraku

Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: shark; genome; longevity; gigantism; positive selection

Online: 18 November 2019 (07:46:50 CET)

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Preprint ARTICLE | doi:10.20944/preprints201807.0287.v2

Engineering a Minimal Cloning Vector from a pUC18 Plasmid Backbone with an Extended Multiple Cloning Site

Jens Staal, Wouter De Schamphelaire, Rudi Beyaert

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: PCR; recombination; cloning; engineering; biotechnology; synthetic biology; synthetic nucleotide; plasmids; repository; minimalism; Escherichia coli; mutagenesis

Online: 15 October 2018 (09:22:22 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202109.0083.v1

Is the Higgs Field a Positive and Negative Mass Planckion Condensate, and Does the LHC Produce Extreme Dark Energy?

Christopher Pilot

Subject: Physical Sciences, Particle And Field Physics Keywords: Winterberg Model; Quantum Vacuum; Higgs Condensate/Composite Model; Two-Component Superfluid/Supersolid Model for the Vacuum; Positive/Negative Planckion Mass, Q-Theory; Non- Linear Heisenberg Spinor Theory; LHC Energies, Dark Energy; Lattice Substructure for Space

Online: 6 September 2021 (10:38:45 CEST)

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Working Paper BRIEF REPORT

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

Sadao Suzuki

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

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

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Preprint ARTICLE | doi:10.20944/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/preprints202108.0053.v2

Protective Factors and Burnout Risk of Teachers During the COVID-19 Pandemic – A Two-Step Cluster Analysis

Camelia-Mădălina Răducu, Elena Stănculescu

Subject: Social Sciences, Psychology Keywords: COVID-19, positive emotionality, professional experience, selfcontrol, teacher burnout, well-being

Online: 26 October 2022 (09:37:02 CEST)

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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/preprints201712.0003.v1

Ventilation Positive Pressure Intervention Effect on IAQ in a School Building with Moisture Problems

Camilla Vornanen-Winqvist, Kati Järvi, Sander Toomla, Kaiser Ahmed, Maria A. Andersson, Raimo Mikkola, Tamas Marik, Laszlo Kredics, Heidi Salonen, Jarek Kurnitski

Subject: Engineering, Civil Engineering Keywords: ventilation; positive pressure; indoor air quality; mycobiota; indoor air questionnaire; moisture damage

Online: 1 December 2017 (07:06:04 CET)

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Preprint ARTICLE | doi:10.20944/preprints201904.0285.v1

Detection of Transgenes in Gene Delivery Model Mice by Adenoviral Vector Using ddPCR

Takehito Sugasawa, Kai Aoki, Koichi Watanabe, Koki Yanazawa, Tohru Natsume, Tohru Takemasa, Kaori Yamaguchi, Yoshinori Takeuchi, Yasuko Yoshida, Katsuyuki Tokinoya, Nanami Sekine, Kaoru Takeuchi, Haruna Ueda, Yasushi Kawakami, Satoshi Shimizu, Kazuhiro Takekoshi

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: gene doping; gene therapy; droplet digital PCR; adenoviral vector

Online: 25 April 2019 (12:45:49 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/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/preprints202101.0147.v1

A Proposed Model of Dehumanisation and Its Relevance to Dehumanisation in Dementia Care

Hana Speering, Lara Speering

Subject: Social Sciences, Psychology Keywords: Dehumanisation; dementia care; healthcare education; residential aged care facilities; positive dehumanisation; negative dehumanisation

Online: 8 January 2021 (11:23:42 CET)

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

COVID-19 Clinical and Laboratory Diagnosis Overview

Rania Zayed, Dalia Omran, Abeer Zayed

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

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

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Preprint ARTICLE | doi:10.20944/preprints201709.0127.v2

A New Proof of Smoryński’s Theorem

Apoloniusz Tyszka

Subject: Computer Science And Mathematics, Logic Keywords: Davis-Putnan Robinson-Matiyasevich theorem; Diophantine equation which has at most finitely many solutions in non-negative integers; Diophantine equation which has at most finitely many solutions in positive integers; Diophantine equation which has at most finitely many integer solutions; Hilbert’s Tenth Problem; Matiyasevich’s theorem; recursively enumerable set; Smoryński’s theorem

Online: 27 September 2017 (04:05:45 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 ARTICLE

Turkish Adaptation of the Positive-Negative Relationship Quality (PN-RQ) Scale: A Reliability and Validity Study

Arzu Araz, Duygu Güngör, Eda Aşçı

Subject: Social Sciences, Psychology Keywords: positive-negative relationship quality; reliability; validity; confirmatory factor analysis (CFA); bifactor

Online: 16 September 2019 (16:33:17 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201805.0144.v1

ISSR-Markers Assisted Genetic Diversity Assessment of Acid Lime [Citrus aurantifolia (Christm.) Swingle] Germplasm of Eastern Nepal

Nabin Narayan Munankarmi, Neesha Rana, Tribikram Bhattarai, Ram Lal Shrestha, Bal Krishna Joshi, Bikash Baral, Sangita Shrestha

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: citrus breeding; diversity; genetic similarity; Lime; molecular markers; PCR

Online: 9 May 2018 (11:05:37 CEST)

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Acid lime [Citrus aurantifolia (Christm.) Swingle] is a fruit crop, enriched with high commercial value and is cultivated in 60 out of 75 districts representing all geographical landscapes of Nepal. Lack of high yielding cultivars is probably one of the main reason for its extremely reduced productivity which warrants a deep understanding of genetic diversity in existing germplasm. Hereby, we aim to access the genetic diversity of acid lime germplasm cultivated at 3-different ecological gradients of eastern Nepal employing PCR-based Inter-Simple Sequence Repeats markers (ISSR). Altogether, 21 polymorphic ISSR markers were used to assess the genetic diversity in 60 acid lime cultivars sampled from different geographical locations. Analysis of binary data matrix was performed on the basis of bands obtained, scoring of the data was done accordingly, and principal coordinate analysis and phenogram were constructed using different computer algorithms. ISSR profiling yielded 234 amplicons, of which 87.18% were found to be polymorphic. The number of amplified fragments ranged from 7-18 with amplicon size ranging from 250-3200 bp. The NTSYS based Cluster analysis using UPGMA algorithm taking Dice Similarity coefficient separated 60 accessions into 2-major and 3-minor clusters. The genetic diversity analysis revealed the highest for Terai and the lowest for High-hill zone. Cluster I comprised of accessions from High-hill and Mid-hill regions revealing the close genetic relationship, whereas cluster II comprised of accessions from all three agro-ecological zones and the exotic varieties. Furthermore, our results revealed the accessions harvested from different geographical gradients were not genetically distinct, but highest diversity was observed in Terai accessions in comparison to the regions belonging to the High and Mid-hills. Thus, our data indicate that the ISSR provides a better option for evaluating the genetic diversity of Nepalese Acid Lime cultivars and furnished significant information, assisting parental selection in current and future breeding programs and germplasm conservation which ultimately may help to provide a technological breakthrough for the farmers of the developing country like Nepal.

Preprint ARTICLE | doi:10.20944/preprints202108.0077.v1

Chikungunya (Togaviridae) and Dengue 2 (Flaviviridae) Viruses Isolated from Aedes aegypti Mosquitoes by qRT-PCR Technique: Xenosurveillance for Arboviruses Circulating in Burkina Faso

Aristide Sawdetuo Hien, Ibrahim Sangaré, Eric L. Parfait Ouattara, Simon P. Sawadogo, Diloma D. Soma, Maiga Hamidou, Abdoulaye Diabaté, Emmanuel Bonnet, Valéry Ridde, Florence Fournet, Carina Kaupra, Jérémy Bouyer, Adly M.M. Abd-Alla, Frances M. Hawkes, Roch K. Dabiré

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: arboviruses; Dengue; Chikungunya; molecular biology; qRT-PCR; Aedes aegypti; Burkina Faso

Online: 3 August 2021 (12:48:01 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201909.0108.v1

Fusarium species and Fusarium mycotoxins in grain of wheat in Poland in 2009 and 2010

Tomasz Góral, Piotr Ochodzki, Linda Kærgaard Nielsen, Dorota Walentyn-Góral

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: biomass, Fusarium head blight, real-time PCR, trichothecenes, zearalenone

Online: 10 September 2019 (11:24:51 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202009.0450.v2

False-negative Molecular Diagnosis of SARS-CoV-2 in Samples with Amplification Inhibitors

Marcelo Fruehwirth, Açucena Veleh Rivas, Andressa Faria Rahyn Fitz, Aline Cristiane Cechinel Assing Batista, Cleypson Vinicius Silveira, Robson Michael Delai

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: COVID-19; rRT-PCR; dilution; viral diagnosis; RNA extraction

Online: 16 October 2020 (11:48:36 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201905.0126.v1

Viral strategies of manipulating autophagy to benefit infection

Ho Him Wong, Sumana Sanyal

Subject: Biology And Life Sciences, Virology Keywords: Autophagy; positive stranded RNA virus; proviral autophagy; viral subversion strategies

Online: 10 May 2019 (14:00:27 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202104.0784.v1

Artificial Compassion—From An AI Scholar

Cindy Mason

Subject: Social Sciences, Anthropology Keywords: Artificial Intelligence, Robots, Compassion, Human Sciences, Positive Plasticity

Online: 30 April 2021 (10:36:45 CEST)

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Preprint REVIEW | doi:10.20944/preprints201909.0212.v1

Viral Innate Immune Evasion and the Pathogenesis of Emerging RNA Virus Infections

Tessa Nelemans, Marjolein Kikkert

Subject: Biology And Life Sciences, Virology Keywords: positive-sense single-stranded rna viruses; innate immune evasion; type 1 interferon; viral pathogenesis; type 3 interferon

Online: 18 September 2019 (17:12:01 CEST)

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

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

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

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

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

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Preprint ARTICLE | doi:10.20944/preprints201910.0147.v1

Whole Genome Alignment Based Development of Molecular Marker for Detecting Leptosphaeria maculans and Leptosphaeria biglobosa, the Causal Agent of Blackleg Disease in Brassicas

Mostari Jahan Ferdous, Mohammad Rashed Hossain, Denison Michael Immanuel Jesse, Jong-In Park, Hee-Jeong Jung, Hoy-Taek Kim, Ill-Sup Nou

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: blackleg; brassica; diagnosis; effector; genome alignment; leptosphaeria biglobosa; leptosphaeria maculans; marker; PCR

Online: 13 October 2019 (16:08:55 CEST)

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

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

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

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

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

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

Preprint ARTICLE | doi:10.20944/preprints201908.0059.v1

The Effect of Recreation in a Snow-Covered Forest Environment on the Psychological Relaxation of Young Females

Ernest Bielinis, Adrian Łukowski, Aneta Omelan, Sergii Boiko, Norimasa Takayama

Subject: Biology And Life Sciences, Forestry Keywords: deciduous forest; female; forest bathing; forest therapy; Positive and Negative Affect Schedule; Profile of Mood States; Restorative Outcome Scale; restoration; Shinrin-Yoku; snow covered forest; Subjective Vitality Scale; winter

Online: 5 August 2019 (08:56:32 CEST)

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Forest recreation can be successfully conducted for the purpose of psychological relaxation, as has been proven in previous scientific studies. During the winter in many countries, when snow cover occurs frequently, forest recreation (walking, relaxation, photography, etc.) is common. Nevertheless, whether forest therapy conducted in a forest environment with a snow cover will also have a positive effect on psychological indicators remains unknown. Furthermore, male subjects frequently participate in forest therapy experiments, whereas females are rarely involved. Thus, in this study, the effectuality of forest recreation during winter and with snow cover was tested on 32 young females. For these reasons, the experiment involved 15-minute periods of relaxation in a forest environment or in an urban environment, in addition to a pre-test under indoor conditions. Four psychological questionnaires (POMS, PANAS, ROS, SVS) were administered to participants before and after interventions. Results showed that participants’ levels of negative mood, as measured by different aspects of the POMS questionnaire (tension-anxiety, anger-hostility, depression-dejection, confusion, fatigue), decreased after exposure to the forest environment. In contrast, both tension-anxiety and anger-hostility increased in the urban environment. The indicator of negative affect from the PANAS questionnaire also increased after exposure to the urban environment, whereas the indicator of positive affect based on PANAS was higher in the forest environment than in the urban environment. Restorativeness and subjective vitality exhibited higher values after exposure to the forest environment in comparison to those from the control and pre-test. The changes in these indicators demonstrates that forest recreation in the snow during winter can significantly increase psychological relaxation in young females, as well as showing that recreation can be successfully conducted under these winter conditions.

Preprint ARTICLE | doi:10.20944/preprints202107.0707.v1

Existential Suffering in Palliative Care: An Existential Positive Psychology Perspective

Paul T. P. Wong, Timothy T. F. Yu

Subject: Social Sciences, Psychology Keywords: Palliative care; Meaning therapy; CALM therapy; COVID-19; Existential positive psychology; Good death; wellbeing; mature happiness; flourishing

Online: 30 July 2021 (14:27:09 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 REVIEW | doi:10.20944/preprints202201.0012.v3

Quantifying Nature Positive

Anna-Mieke Mathilde Vlieg, Shadia Moazzem, Direshni Naiker, Delwyn Gloria Jones

Subject: Environmental And Earth Sciences, Environmental Science Keywords: Nature-Positive; Quantified Benefit Assessment; Security; Wellness; Viability; Gain

Online: 21 April 2022 (17:37:36 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201809.0245.v1

On the Effect of Filling Rate on Positive Macrosegregation Patterns in Large Size Cast Steel Ingots

Chunping Zhang, Abdelhalim Loucif, Mohammad Jahazi, Rami Tremblay, Louis-Philippe Lapierre Boire

Subject: Engineering, Mechanical Engineering Keywords: medium-carbon low-alloy steel; large size ingot; hot-top; filling rate; positive macrosegregation

Online: 13 September 2018 (15:19:42 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 REVIEW | doi:10.20944/preprints201808.0266.v1

Microfluidic Advancements in Classical Biotechnology – A Review

Ishtiaq Ahmed, Zain Akram, Mohammed Hussen Bule, Hafiz M. N. Iqbal

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: microchannel; micro-array; microstructure; biofilms; polydimethylsiloxane; Micro-PCR; reynolds number; micro electro mechanical systems

Online: 15 August 2018 (05:37:59 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/preprints201911.0368.v1

The Role of Perceived Social Support in the Psychological Well-Being of Young Offenders: from Pretrial Detention to Correctional Camps

Fedor Ushkov, Roman Shilko, Ludmila Shaigerova, Alexandra Dolgikh, Olga Almazova, Olga Vakhantseva, Yuri Zinchenko

Subject: Social Sciences, Psychology Keywords: psychological well-being; young offenders; social support; pretrial detention; correctional camps; positive and negative feelings; positive and negative affects

Online: 29 November 2019 (04:16:05 CET)

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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/preprints201909.0142.v1

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

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

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

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

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Preprint ARTICLE | doi:10.20944/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/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/preprints202208.0511.v1

Phytochemical Composition and Antibacterial Activity of Zingiber cassumunar Roxb. against Agricultural and Foodborne Pathogens

Maha A. Alshiekheid, Yheni Dwiningsih, Amal Abdullah Sabour, Jawaher Alkahtani

Subject: Biology And Life Sciences, Plant Sciences Keywords: Zingiber cassumunar Roxb.; essential oils; microencapsulated products; antibacterial activity; agricultural pathogens; foodborne pathogens; gram-positive bacteria; gram-negative bacteria

Online: 30 August 2022 (07:02:54 CEST)

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Zingiber cassumunar Roxb. is a powerful medicinal plant that has been used as traditional medicine to cure respiratory problems, pain, and inflammation in China, Indonesia, Thailand and other Asian countries by using the crude extracts. The objective of this research is to identify phytochemical composition of Z. cassumunar Roxb. and to analyze antibacterial activity of crude extract, purified compounds, and their microencapsulated products of Rhizome Z. cassumunar Roxb. Identification of phytochemical composition in crude extract of rhizome Z. cassumunar Roxb. was achieved by chromatography-mass spectrophotometer. The major phytochemical composition in crude extract of Z. cassumunar Roxb. is essential oils, including terpinen4-ol (37.7%), β-pinene (20.8%), and (E)-1-(3,4-dimethoxyphenyl)but-1-ene (13.3%). Crude extract of Z. cassumunar Roxb. was purified with silica gel flash column chromatography, resulting two purified compounds. The antibacterial activity of crude extract, purified compounds, and their microencapsulated products of Rhizome Z. cassumunar Roxb. were evaluated against agricultural and foodborne pathogens by using disc agar diffusion and broth microdilution techniques. All of the samples studied (crude extracts, purified compounds, and microencapsulated of Z. cassumunar Roxb.) were effective against all the bacteria. Based on the results of the disc-diffusion assay suggested that amongst the samples studied, purified compounds (compound 1 and 2) and microencapsulated purified compounds (compound 1 and 2) exhibited more effective against all the bacteria compared to the crude extracts. Antibacterial activity of the rhizome of Z. cassumunar Roxb. was contributed mainly by the essential oils components as the active compounds. Gram-negative bacteria (X. oryzae, X. translucens, Pseudomonas spp, E. coli, and S. typhimurium) appeared to the most resistant to the crude extracts, purified compounds, and microencapsulated of Z. cassumunar Roxb. compared to the gram-positive bacteria (S. aureus, B. cereus, and L. monocytogenes). Microencapsulated of the tested samples (crude extract, purified compound 1, and purified compound 2) of the rhizome Z. cassumunar Roxb. exhibited high antibacterial activity with no significantly different with the tested samples without microencapsulation. These results suggest potential antibacterial properties of Z. cassumunar Roxb., which useful for agricultural plant health, food preservation, natural therapies, and pharmaceuticals.

Preprint ARTICLE | doi:10.20944/preprints201908.0225.v1

Analysis of Water Bodies under Partial Cloud Conditions Using Satellite Images

Rahul Neware, Mansi Thakare

Subject: Environmental And Earth Sciences, Remote Sensing Keywords: water bodies; satellite images; vector data; SVM; positive and negative buffering; polygons

Online: 21 August 2019 (10:30:16 CEST)

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Working Paper ARTICLE

Interrogating Hope Theory

Jacob Shivley

Subject: Medicine And Pharmacology, Psychiatry And Mental Health Keywords: interrogating hope theory, hope theory, hope, the hope scale, positive psychology

Online: 25 March 2019 (09:53:58 CET)

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

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

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

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

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

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Preprint ARTICLE | doi:10.20944/preprints202010.0221.v1

Canine Filariasis Outbreak in Southwestern Colombia: A Molecular and Epidemiological Study

Nathaly Espinosa, Angelo Rosero, Claudia Lucia Villegas, Isabel Cristina Garcia, Tania Gaviria-Cantin, Alejandra Peña, Beatriz Eugenia Ferro, Luisa Maria Nieto Ramirez

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Dogs; Microfilariae; Acanthocheilonema; PCR-RFLP; Cali; Zoonosis

Online: 12 October 2020 (10:18:10 CEST)

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

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

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

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

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

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

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

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

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

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

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Preprint REVIEW | doi:10.20944/preprints201901.0039.v1

Prevention of Hearing Loss by Alteration of the Systemic Immune System

Hiroshi Iwai, Muneo Inaba

Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: autoimmune sensorineural hearing loss; age-related sensorineural hearing loss; inflammation, immune senescence; interleukin 1 receptor type II -positive T cells; naturally occurring regulatory T cells; immune rejuvenation; thymus

Online: 4 January 2019 (11:37:31 CET)

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Preprint ARTICLE | doi:10.20944/preprints202306.1716.v1

A Physical Mechanism of the Generation of Stable Positive Kinetic Energy Systems and a Qualitative Explanation of the Proportions of the Four Ingredients in the Universe

Huai-Yu Wang

Subject: Physical Sciences, Quantum Science And Technology Keywords: stable system; dark matter; dark energy; positive kinetic energy; negative kinetic energy; cosmic dark radiation background; gravity potential background

Online: 25 June 2023 (05:16:46 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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Working Paper ARTICLE

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

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

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

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

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

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

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

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

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

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Preprint ARTICLE | doi:10.20944/preprints202101.0045.v1

Kombucha Tea as a Reservoir of Cellulose Producing Bacteria: Assessing Diversity Among Komagataeibacter Isolates

Salvatore La China, Luciana De Vero, Kavitha Anguluri, Marcello Brugnoli, Dhouha Mamlouk, Maria Gullo

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Kombucha tea; microbial diversity; bacterial cellulose; Komagataeibacter xylinus; repetitive elements sequence-based rep-PCR; typing

Online: 4 January 2021 (13:24:41 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/preprints202103.0055.v1

Semi-Covariance Coefficient Analysis of Spike Proteins from SARS-CoV-2 and other Coronaviruses for Viral Evolution and Characteristics Associated with Fatality

Jun Huang, Rebecca Spencer, Wangdong Zhang

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Fractional complex moment; SARS-CoV-2; coronaviruses; spike protein sequence; Pearson correlation coefficient; semi-covariance coefficient; positive-correlative and negative-correlative domains

Online: 2 March 2021 (09:30:12 CET)

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Complex modeling has received significant attention in recent years and is increasingly used to explain the statistical phenomenon with increasing and decreasing fluctuations such as the similarity or difference of spike protein charge patterns of coronaviruses. Different from the existing covariance or correlation coefficient methods in traditional integer dimension construction, this study proposes a simplified novel fractional dimension derivation with the exact Excel tool algorithm. It involves the fractional center moment extension to covariance, which ends up a complex covariance coefficient that is better than the Pearson correlation coefficient, in the sense that the nonlinearity relationship can be further depicted. The spike protein sequences of coronaviruses were obtained from the GenBank and GISAID database, including the coronaviruses from pangolin, bat, canine, swine (three variants), feline, tiger, SARS-CoV-1, MERS, and SARS-CoV-2 (including the strains of Wuhan, Beijing, New York, German, and UK variant B.1.1.7) were used as the representative examples in this study. By examining the values above and below the average/mean based on the positive and negative charge patterns of the amino acid residues of the spike proteins from coronaviruses, the proposed algorithm provides deep insights into the nonlinear evolving trends of spike proteins for understanding the viral evolution and identifying the protein characteristics associated with viral fatality. The calculation results demonstrate that the complex covariance coefficient analyzed by this algorithm is capable of distinguishing the subtle nonlinear differences in the spike protein charge patterns with reference to Wuhan strain SARS-CoV-2 for which the Pearson correlation coefficient may overlook. Our analysis reveals the unique convergent (positive correlative) to divergent (negative correlative) domain center positions of each virus. The convergent or conserved region may be critical to the viral stability or viability; while the divergent region is highly variable between coronaviruses suggesting high frequency of mutations in this region. The analyses show that the conserved center region of SARS-CoV-1 spike protein is located at amino acid residues 900, but shifted to the amino acid residues 700 in MERS spike protein, and then to amino acid residues 600 in SARS-COV-2 spike protein, indicating the evolvement of the coronaviruses. Interestingly, the conserved center region of the spike protein in SARS-COV-2 variant B.1.1.7 shifted back to amino acid residues 700, suggesting this variant is more virulent than the original SARS-COV-2 strain. Another important characteristic our study reveals is that the distance between the divergent mean and the maximal divergent point in each of the viruses (MERS>SARS-CoV-1>SARS-CoV-2) is proportional to viral fatality rate. This algorithm may help to understand and analyze the evolving trends and critical characteristics of SARS-COV-2 variants, other coronaviral proteins and viruses.

Preprint ARTICLE | doi:10.20944/preprints202104.0439.v1

One Possible Reinfection with SARS-CoV-2 Validated by 205-days Interval of Re-detection in Sapporo City, Japan

Toshiaki Asakura, Akiko Tamakoshi

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: SARS-CoV-2; COVID-19; reinfection; re-detected positive; Japan

Online: 16 April 2021 (11:09:45 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202102.0597.v1

Surveillance for COVID-19 in the English Football League 2019-2020

Subhashis Basu, Richard Higgins, Aneil Malhotra, Imtiaz Ahmad

Subject: Public Health And Healthcare, Public, Environmental And Occupational Health Keywords: Surveillance; COVID; Football; Infection; Professional; PCR; Elite

Online: 26 February 2021 (08:59:29 CET)

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

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

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

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

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Preprint 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 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 REVIEW | doi:10.20944/preprints202004.0226.v2

The Non-Tragedy of the Non-Linear Commons

Marco Archetti, István Scheuring, Douglas Yu

Subject: Biology And Life Sciences, Other Keywords: positive assortment; public goods; collective action; common-pool resources; cooperation; game theory; group selection; kin selection; social dilemma

Online: 16 June 2020 (12:35:40 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201805.0169.v1

The Presence of Toxic and Non-toxic Cyanobacteria in the Sediments of the Limpopo River Basin: Implications for Human Health

Murendeni Magonono, Paul Johan Oberholster, Shonhai Addmore, Makumire Stanley, Jabulani Ray Gumbo

Subject: Environmental And Earth Sciences, Environmental Science Keywords: cyanobacteria; cyanotoxins; nutrient enrichment; akinetes; harmful algal blooms; PCR; phylogenetic analyses

Online: 10 May 2018 (15:37:51 CEST)

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Preprint REVIEW | doi:10.20944/preprints202106.0285.v1

Quantitative Fluorescent Polymerase Chain Reaction for Prenatal Diagnosis and Its Application in Vietnam: A Literature Review

Thuan Phan

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: QF-PCR; cytogenetics; prenatal diagnosis; aneuploidy; chromosome abnormalities; screening test

Online: 10 June 2021 (09:17:57 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202007.0749.v1

Fatal Interstitial Pneumonia Caused by Bovine Coronavirus in Cows from Southern Italy

Maria Grazia Amoroso, Giuseppe Lucifora, Barbara Degli Uberti, Francesco Serra, Alessandro Di Domenico, Maria Concetta Cuomo, Giovanna De Luca, Francesca Bove, Giorgio Galiero, Giovanna Fusco

Subject: Biology And Life Sciences, Virology Keywords: Bovine coronavirus; intersititial pneumonia; phylogenetic analysis; Real time PCR

Online: 31 July 2020 (13:46:21 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201812.0314.v1

From Individual Resource to Social Capital: The Mechanism of How Political Skill Affect Job Satisfaction and Turnover Intention

Yi Li, Mengqiu Ma

Subject: Business, Economics And Management, Human Resources And Organizations Keywords: political skill; job satisfaction; turnover intention; popularity; positive affect; negative affect

Online: 26 December 2018 (12:16:31 CET)

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Preprint ARTICLE | doi:10.20944/preprints202105.0538.v1

Health Screening of the Reef Forming Scleractinian Cold-Water Corals Lophelia pertusa and Madrepora oculata in a Remote Submarine Canyon on the European Continental Margin, NE Atlantic

John Appah, Sharon Lynch, Aaron Lim, Ruth O'Riordan, Luke O'Reilly, Larissa de Oliveira, Andrew James Wheeler

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: Lophelia pertusa; Haplosporidia; Vibrio; Rickettsiales-like organisms; Histology; PCR; Pathogen; Cold-water corals

Online: 24 May 2021 (08:20:11 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201902.0172.v4

Protein-Encoding RNA-to-RNA Information Transfer in Mammalian Cells: Principles of RNA-Dependent mRNA Amplification

Vladimir Volloch

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: RNA-dependent amplification of mammalian mRNA; physiologically occurring intracellular PCR, iPCR; RNA-dependent RNA polymerase, RdRp; chimeric RNA; sense-strand RNA; antisense-strand RNA

Online: 12 June 2019 (12:21:59 CEST)

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The transfer of protein-encoding genetic information from DNA to RNA to protein, a process formalized as the “Central Dogma of Molecular Biology”, has undergone a significant evolution since its inception. It was amended to account for the information flow from RNA to DNA, the reverse transcription, and for the information transfer from RNA to RNA, the RNA-dependent RNA synthesis. These processes, both potentially leading to protein production, were initially described only in viral systems, and although RNA-dependent RNA polymerase activity was shown to be present, and RNA-dependent RNA synthesisfound to occur, in mammalian cells, its function was presumed to be restricted to regulatory. However, recent results, obtained with multiple mRNA species in several mammalian systems, strongly indicate the occurrence of protein-encoding RNA to RNA information transfer in mammalian cells. It can result in the rapid production of the extraordinary quantities of specific proteins as was seen in cases of terminal cellular differentiation and during cellular deposition of extracellular matrix molecules. A malfunction of this process may be involved in pathologies associated either with the deficiency of a protein normally produced by this mechanism or with the abnormal abundanceof a protein or of its C-terminal fragment. It seems to be responsible for some types of familial thalassemia and may underlie the overproduction of beta amyloid in sporadic Alzheimer’s disease. The aim of the present article is to systematize the current knowledge and understanding of this pathway. The outlined framework introduces unexpected features of the mRNA amplification such as its ability to generate polypeptides non-contiguously encoded in the genome, its second Tier, a physiologically occurring intracellular polymerase chain reaction, iPCR, a Two-Tier Paradox and RNA Dark Matter. RNA-dependent mRNA amplification represents a new mode of genomic protein-encoding information transfer in mammalian cells. Its potential physiological impact is substantial, it appears relevant to multiple pathologies and its understanding opens new venues of therapeutic interference, it suggests powerful novel bioengineering approaches and its further rigorous investigations are highly warranted.

Preprint ARTICLE | doi:10.20944/preprints202109.0224.v1

Drought Stress Described by Transcriptional Responses of Picea Abies under Pathogen Heterobasidion Parviporum Attack

Xenia Hao-Yi Yeoh, Blessing Durodola, Kathrin Blumenstein, Eeva Terhonen

Subject: Biology And Life Sciences, Forestry Keywords: Drought; Norway spruce; Heterobasidion; RNA-seq; qRT-PCR

Online: 14 September 2021 (08:19:04 CEST)

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The major threats to the sustainable supply of forest tree products are adverse climate, pests and diseases. Climate change, exemplified by increased drought, poses a unique threat to global forest health. This is attributed to the unpredictable behavior of forest pathosystems, which can favor fungal pathogens over the host under persistent drought stress conditions in the future. Currently, the effects of drought on tree resistance against pathogens are hypothetical, thus research is needed to identify these correlations. Norway spruce (Picea abies) is one of the most economically important tree species in Europe, and is considered highly vulnerable to changes in climate. Dedicated experiments to investigate how disturbances will affect the Norway spruce - Heterobasidion sp. pathosystem are important, in order to develop different strategies to limit the spread of H. annosum s.l. under the predicted climate change. Here, we report a transcriptional study to compare Norway spruce gene expressions to evaluate the effects of water availability and the infection of Heterobasidion parviporum. We performed inoculation studies of three-year-old saplings in a greenhouse (purchased from a nursery). Norway spruce saplings were treated in either high (+) or low (-) water groups: high water group received double the water amount than the low water group. RNA was extracted and sequenced. Similarly, we quantified gene expression levels of candidate genes in biotic stress and jasmonic acid (JA) signaling pathways using qRT-PCR, through which we discovered a unique preferential defense response of H. parviporum-infected Norway spruce under drought stress at the molecular level. Disturbances related to water availability, especially low water conditions can have negative effects on the tree host and benefit the infection ability of the pathogens in the host. From our RNA-seq analysis, 114 differentially expressed gene regions were identified between high (+) and low (-) water groups under pathogen attack. None of these gene pathways were identified to be differentially expressed from both non-treated and mock-control treatments between high (+) and low (-) water groups. Finally, only four genes were found to be associated with drought in all treatments.

Preprint ARTICLE | doi:10.20944/preprints201909.0148.v1

Identification of Candida Species from Clinical Samples in a Honduran Tertiary Hospital

Kathy Montes, Bryan Ortiz, Celeste Galindo, Isis Figueroa, Sharleen Braham, Gustavo Fontecha

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Candida spp.; PCR-RFLP; Honduras; HardyCHROM®; MicroScan®

Online: 15 September 2019 (03:30:16 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/preprints202201.0164.v1

Neoadjuvant Pertuzumab plus Trastuzumab in Combination with Docetaxel and Carboplatin in Patients with HER2 Positive Breast Cancer: Real-World Data from a National Institute of Oncology in Poland.

Agnieszka Irena Jagiełło-Gruszfeld, Magdalena Rosinska, Malgorzata Meluch, Katarzyna Pogoda, Anna Niwińska, Renata Sienkiewicz, Aleksander Grous, Pawel Winter, Zbigniew I. Nowecki

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: breast cancer,; neoadjuvant chemotherapy; elederly; HER2- positive; pathological complete response; safety

Online: 12 January 2022 (13:31:16 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/preprints202201.0038.v1

Part 1 - Looking Back and Looking Around: How Parents, Coaches and Athletes See Psychosocial Development in Adolescent Performance Sport.

Sergio Lara-Bercial, Jim McKenna

Subject: Social Sciences, Psychology Keywords: Positive youth development, youth sport, realist evaluation, life skills, personal development, psychosocial development.

Online: 5 January 2022 (12:39:46 CET)

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