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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/preprints202008.0206.v1

Amplicon Sequence Variant-Based Oral Microbiome Analysis Using QIIME 2

Hugo Maruyama, Ayako Masago, Takayuki Nambu, Chiho Mashimo, Toshinori Okinaga

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: tongue microbiome; salivary microbiome; amplicon sequence variant (ASV); operational taxonomical unit (OTU); denoising; DADA2; taxonomic classifier

Online: 8 August 2020 (09:29:46 CEST)

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Preprint REVIEW | doi:10.20944/preprints202004.0155.v1

COVID-19 Testing: Challenges, Limitations and Suggestions for Improvement

Emily Hu

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: COVID-19; Coronavirus; False-negative; Nucleic Acid Test; Screening; Diagnostic Accuracy; Missed Diagnosis; Epidemic; Infectious Disease

Online: 9 April 2020 (14:37:56 CEST)

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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 ARTICLE | doi:10.20944/preprints201609.0071.v1

Characterization and Development of EST-SSR Markers in Sweet Potato (Ipomoea batatas (L.) Lam)

Jin-Hee Kim, Jun-Hoi Kim, Won-Sam Jo, Jung-Gwan Ham, Il Kyung Chung, Kyung-Min Kim

Subject: Biology And Life Sciences, Plant Sciences Keywords: EST-SSR marker; hexaploid; sweet potato; polymorphic; sequence

Online: 20 September 2016 (11:35:51 CEST)

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According to statistics from the Food and Agriculture Organization, the world population will increase to about 91 million (Asia 51 million, Africa 19 million). A rise in the world’s population means an increased need for food. However, climate change has caused desertification and unpredictable weather, creating problems in the supply and demand of food. Sweet potato (Ipomoea batatas) is an alternative to solving the food problem, as it is one of the world’s most important food crops, especially in developing countries. The tuberous roots of sweet potato are usually used as staple food, animal feed, industrial material, or raw material for alcohol production. In the future, more variations of sweet potato will be needed for breeding this crop. Recently, molecular markers developed for sweet potato have demonstrated good potential for use in genetic selection. In this study, a cDNA library was constructed from the total RNA of sweet potato leaves. A total of 789 copies of the cDNA were cloned in Escherichia coli by employing the pGEM-T Easy vector. Sequencing was carried out by Solgent Co. (Korea). As many as 579 expressed sequence tag–simple sequence repeat (EST-SSR) markers were designed (73.38%) from the known cDNA nucleotide base sequences. The lengths of the developed EST-SSR markers ranged from 100 to 499 bp (average length 238 bp). Their motif sequence types were varied, with most being dinucleotides and pentanucleotides, and the most commonly found motifs were CAGAAT (29.0%) and TCT (2.8%). Based on these SSR-containing sequences, 619 pairs of high-quality SSR primers were designed using WebSat and Primer3web. The total number of primers designed was 144. Polymorphism was evident in 82 EST-SSR markers among 20 Korean sweet potato cultivars tested and in 90 EST-SSR markers in the two parents of a mapping population, Yeseumi and Annobeny. In this study, the hexaploid sweet potato (2n = 6x = 90) EST-SSR markers were developed in the absence of full-sequence data. Moreover, by acting as a molecular tag for particular traits, the EST-SSR marker can also simultaneously identify information about the corresponding gene. These EST-SSR markers will allow the molecular analysis of sweet potato to be done more efficiently. Thus, we can develop high-quality sweet potato while overcoming the challenges from climate change and other unfavorable conditions.

Preprint ARTICLE | doi:10.20944/preprints201607.0003.v6

Farey Sequences and the Riemann Hypothesis

Darrell Cox

Subject: Computer Science And Mathematics, Algebra And Number Theory Keywords: Riemann hypothesis, Farey sequence, Gauss sum associated with a Dirichlet character

Online: 10 August 2016 (11:35:25 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202005.0407.v1

The SARS-CoV-2 Spike Protein D614G Mutation Shows Increasing Dominance and May Confer a Structural Advantage to the Furin Cleavage Domain

Leyan Tang, Allison Schulkins, Chun-Nan Chen, Kurt Deshayes, John S. Kenney

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; spike protein; D614G mutation; genotype distribution; furin cleavage site; secondary structure; sequence analysis; homology modeling

Online: 24 May 2020 (20:31:16 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201609.0098.v1

Oyelola A. Adegboye, Majeed Adegboye

Subject: Computer Science And Mathematics, Probability And Statistics Keywords: ecological niche model; environment; overdispersion; negative binomial; leishmaniasis; infectious disease

Online: 27 September 2016 (10:17:31 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201705.0137.v1

Investigation on Development of Sliding Mode Controller for Constant Power Loads in Microgrids

Eklas Hossain, Ron Perez, Sanjeevikumar Padmanaban, Pierluigi Siano

Subject: Engineering, Electrical And Electronic Engineering Keywords: sliding mode control; constant power load; negative incremental impedance; robustness analysis; chattering reduction; microgrid stability; noise rejection

Online: 18 May 2017 (04:45:56 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201612.0104.v1

Internalization of Negative External Cost of Logistics and Incentive Mechanism

Zhanzhong Wang, Zhouling Tsai, Jing Fu, Guangdong Tian

Subject: Engineering, Control And Systems Engineering Keywords: green logistics; negative externality of logistics; internalization of logistics negative external cost; incentive mechanism

Online: 20 December 2016 (10:37:21 CET)

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Preprint ARTICLE | doi:10.20944/preprints201608.0049.v2

Understanding Farmers’ Decision Making in Agricultural Water Fee Payment in China: The Role of Mental Accounting

Weikang Zhang, Xinhong Fu, Jing Lu, Lin Zhang, Kwamega Michael, Guoqiang Liu, Yuying Liu, Fan Yang

Subject: Business, Economics And Management, Economics Keywords: mental accounting; agricultural water fee; behavioral economics; decision making; information processing; representativeness; negative psychological externalities

Online: 25 August 2016 (10:12:08 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201608.0144.v1

Statistical Study on Crash Frequency Model Using GNB Models of Freeway Sharp Horizontal Curve Based on Interactive Influence of 3 Explanatory Variables

Yanjie Zeng, Xiaofei Wang, Lineng Liu, Xinwei Li, Caifeng Jiang

Subject: Engineering, Civil Engineering Keywords: freeway; crash prediction model (CPM); sharp horizontal curve segment (SHCS); interactive influence among three explanatory variables; generalized negative binomial (GNB)

Online: 15 August 2016 (09:47:37 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201706.0077.v1

Are Mobile Live Animal Programs Educationally Beneficial? A Critical Assessment of the Human Learning Component Underlying Traveling Animal Exhibits

Kathryn Sussman

Subject: Social Sciences, Education Keywords: zoo; mobile zoo; mobile animal exhibits; animal display; mobile live animal programs; negative education

Online: 16 June 2017 (05:32:18 CEST)

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Preprint REVIEW | doi:10.20944/preprints201802.0095.v1

EP4 as a Therapeutic Target for Aggressive Human Breast Cancer

Mousumi Majumder, Pinki Nandi, Ahmed Omar, Kingsley Chukwunonso Ugwuagbo, Peeyush K. Lala

Subject: Biology And Life Sciences, Cell And Developmental Biology Keywords: COX-2; breast cancer; PGE2; EP receptors; stem-like cells; metastasis; angiogenesis; lymphangiogenesis; MicroRNAs; triple negative breast cancer

Online: 13 February 2018 (09:16:54 CET)

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G protein-coupled receptors (GPCRs, also called seven-transmembrane or heptahelical receptors) are a superfamily of cell surface receptor proteins that bind to many extracellular ligands and transmit signals to an intracellular guanine nucleotide-binding protein (G protein). When a ligand binds, the receptor activates the attached G-protein by causing the exchange of Guanosine-5'-triphosphate (GTP) for guanosine diphosphate (GDP). They play a major role in many physiological functions as well as in the pathology of many diseases including cancer progression and metastasis. Only a few GPCR members have been exploited as targets for developing drugs with therapeutic benefit in cancer. Present review deals with the Prostaglandin E receptor EP4, a member of the EP family of GPCR, as a promising newer therapeutic target for treating breast cancer. We show that aberrant over-expression of cyclooxygenase (COX)-2, an inflammation-associated enzyme, occurring in 40-50% of breast cancer patients leads to tumor progression and metastasis due to multiple cellular events resulting from an increased prostaglandin (PG) E2 production in the tumor milieu. They include inactivation of host anti-tumor immune (NK and T) cells, increased immuno-suppressor function of tumor-associated macrophages, promotion of tumor cell migration, invasiveness and tumor-associated angiogenesis (due to upregulation of VEGF-A), lymphangiogenesis (due to upregulation of VEGF-C/D) and a stimulation of stem-like cell (SLC) phenotype in cancer cells. All these events were primarily mediated by activation of the PGE receptor EP4 on tumor or host cells. We show that selective EP4 antagonists (EP4A) could mitigate all these events tested with cells in vitro as well as in vivo in syngeneic COX-2 expressing mammary cancer bearing mice or immune-deficient mice bearing COX-2 over-expressing human breast cancer xenografts. We suggest that EP4A can avoid thrombo-embolic side effects of long term use of COX-2 inhibitors by sparing cardio-protective roles of PGI2 via IP receptor activation or PGE2 via EP3 receptor activation. Furthermore, we identified two COX-2/EP4 induced oncogenic and SLC-stimulating microRNAs - miR526b and miR655, one of which (miR655) appears to be a potential blood biomarker in breast cancer patients, for monitoring SLC-ablative therapies such as with EP4A. We suggest that EP4A will likely produce the highest benefit in aggressive breast cancers such as COX-2 expressing triple-negative breast cancers, when combined with other newer agents such as PD-1 or PD-L1 inhibitors.

Preprint REVIEW | doi:10.20944/preprints201611.0120.v1

Pancreatic Neuroendocrine Neoplasms: Basic Biology, Current Treatment Strategies and Prospects for the Future

Akihiro Ohmoto, Hirofumi Rokutan, Shinichi Yachida

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: pNENs; 2010 WHO classification; Ki-67 index; mitotic count; pNEC; tumor differentiation; whole-exome sequence data; everolimus; sunitinib; platinum regimen

Online: 24 November 2016 (10:59:33 CET)

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Preprint REVIEW | doi:10.20944/preprints201911.0252.v1

From Sequence to Information

Ovidiu Popa, Ellen Oldenburg, Oliver Ebenhöh

Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: data; sequence; information; entropy; genome; gene; proteins; time-series; modeling; meta-genomics; transcriptomics; proteomics; bioinformatics; DNA

Online: 22 November 2019 (02:28:15 CET)

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Preprint ARTICLE | doi:10.20944/preprints202002.0234.v1

Sequence Properties of the MAAP Protein and of the VP1 Capsid Protein of Adeno-Associated Viruses

David G. Karlin

Subject: Biology And Life Sciences, Virology Keywords: adeno-associated virus; protein sequence analysis; overlapping genes; amino acid depletion; cysteine depletion; tyrosine depletion; capsid design; membrane-binding amphipathic helix

Online: 17 February 2020 (02:42:39 CET)

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

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

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

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

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

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

Preprint ARTICLE | doi:10.20944/preprints201901.0088.v1

Signal-to-Noise Ration Evaluation of Luojia 1-01 Satellite Nighttime Light Remote Sensing Camera Based on Time Sequence Images

Wei Wang, Xing Zhong, Zhiqiang Su, Deren Li, Guo Zhang

Subject: Engineering, Control And Systems Engineering Keywords: signal-to-noise ratio; nighttime light imaging; time sequence images; Luojia 1-01; radiative transfer model; radiometric calibration; in-orbit test

Online: 9 January 2019 (15:43:53 CET)

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Preprint REVIEW | doi:10.20944/preprints201706.0059.v1

Pathology of Adult and Paediatric Mitochondrial Myopathies

Rahul Phadke

Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: mitochondrial; muscle biopsy; ragged red; COX-negative; subsarcolemmal; immunohistochemistry

Online: 13 June 2017 (06:23:36 CEST)

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Preprint TECHNICAL NOTE | doi:10.20944/preprints201804.0047.v1

phylotaR: An automated pipeline for retrieving orthologous DNA sequences from GenBank in R

Dominic J. Bennett, Hannes Hettling, Daniele Silvestro, Alexander Zizka, Christine D. Bacon, Søren Faurby, Rutger A. Vos, Alexandre Antonelli

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: BLAST; DNA, open source; phylogenetics; R; sequence orthology.

Online: 4 April 2018 (06:00:40 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201805.0026.v1

Weighted Negative Binomial Poisson-Lindley Distribution with Actuarial Applications

Hossein Zamani, Noriszura Ismail, Marzieh Shekari

Subject: Computer Science And Mathematics, Probability And Statistics Keywords: weighted distribution; Poisson-Lindley distribution; discrete distribution; weighted negative binomial Poisson-Lindley distribution

Online: 2 May 2018 (11:47:51 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202203.0188.v1

Structural Damage Prediction of a Reinforced Concrete Frame Under Single and Multiple Seismic Events Using Machine Learning Algorithms

Petros C. Lazaridis, Ioannis E. Kavvadias, Konstantinos Demertzis, Lazaros Iliadis, Lazaros K. Vasiliadis

Subject: Engineering, Civil Engineering Keywords: Seismic Sequence; Machine Learning Algorithms; Repeated Earthquakes; Structural Damage Prediction; Intensity Measures; Damage Accumulation; Machine Learning; Artificial Neural Network

Online: 14 March 2022 (11:57:51 CET)

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Preprint ARTICLE | doi:10.20944/preprints202011.0056.v1

Exploring the Non-Medical impacts of Covid-19 using Natural Language Processing

Amol Agade, Samta Balpande

Subject: Computer Science And Mathematics, Algebra And Number Theory Keywords: COVID-19; Deep Learning; Natural Language Processing; Topic Modelling; Text Classification; Latent Dirichlet allocation (LDA); Non-negative matrix factorization (NMF)

Online: 2 November 2020 (15:24:20 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/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 REVIEW | doi:10.20944/preprints202003.0351.v1

Genome Editing: An Emerging Tool for Plant Breeders

Anand Kumar, Karansher Sandhu

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: Conventional method; Clustered Regularly Interspaced Short Palindromic Sequence; Genome editing; RNA Interference; TALEN

Online: 23 March 2020 (10:23:45 CET)

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Preprint ARTICLE | doi:10.20944/preprints202203.0357.v1

Negative Electrical Conductivity Metamaterials

Edward Bormashenko

Subject: Chemistry And Materials Science, Materials Science And Technology Keywords: metamaterial; negative electrical conductivity; negative mass; Drude-Lorentz model; negative refraction

Online: 28 March 2022 (08:56:05 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201802.0163.v1

Shaping Light in Backward-Wave Nonlinear Hyperbolic Metamaterials

Alexander K. Popov, Sergey A. Myslivets, Vitaly V. Slabko, Victor A. Tkachenko, Thomas F. George

Subject: Physical Sciences, Optics And Photonics Keywords: optical metamaterials; fundamental concepts in photonics; light-matter interactions at the subwavelength and nanoscale; fundamental understanding of linear and nonlinear optical processes in novel metamaterials underpinning photonic devices and components; advancing the frontier of nanophotonics with the associated nanoscience and nanotechnology; nanostructures that can serve as building blocks for nano-optical systems; use of nanotechnology in photonics; nonlinear nanophotonics, plasmonics and excitonics; subwavelength components and negative index materials; slowing, store, and processing light pulses; materials with such capabilities that could be used for optical sensing, tunable optical delay lines, optical buffers, high extinction optical switches, novel image processing hardware, and highly-efficient wavelength converters

Online: 26 February 2018 (11:24:39 CET)

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Preprint ARTICLE | doi:10.20944/preprints201902.0156.v4

Diophantine Equations with a Finite Number of Solutions: Craig Smorynski's Theorem, Harvey Friedman's Conjecture and Minhyong Kim's Guess

Apoloniusz Tyszka

Subject: Computer Science And Mathematics, Logic Keywords: Davis-Putnam-Robinson-Matiyasevich theorem, Diophantine equation which has at most finitely many solutions in \mbox{non-negative} integers, Hilbert's Tenth Problem, Hilbert's Tenth Problem for Q, Matiyasevich's theorem, recursively enumerable set, Smorynski's theorem

Online: 1 March 2019 (12:58:53 CET)

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Preprint ARTICLE | doi:10.20944/preprints202105.0546.v1

Atezolizumab and Pembrolizumab in Triple-Negative Breast Cancer: A Meta-Analysis

Mahwish Amin, Shaiza Sharif, Waleed Asghar, Humaira Sadaf, Azza Sarfraz, Zouina Sarfraz, Ivan Cherrez-Ojeda

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: triple negative breast cancer; Pembrolizumab; Atezolizumab; chemotherapy; anti-PD-L1; biomarkers; targeted therapies; development of novel drugs

Online: 24 May 2021 (09:23:50 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201803.0174.v1

Whole Genome Transcriptome Analysis of the Association between Obesity and Triple Negative Breast Cancer in Caucasian Women

Tarun Mamidi, Jiande Wu, Paul B. Tchounwou, Lucio Miele, Chindo Hicks

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: gene expression obesity triple negative breast cancer

Online: 20 March 2018 (07:56:33 CET)

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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 ARTICLE | doi:10.20944/preprints202202.0111.v1

Wearable Sensor Based Human Activity Recognition with Transformer

Iveta Dirgová Luptáková, Martin Kubovčík, Jiří Pospíchal

Subject: Computer Science And Mathematics, Computer Science Keywords: Transformer; human activity recognition; time series; sequence-to-sequence prediction

Online: 8 February 2022 (13:09:21 CET)

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Preprint ARTICLE | doi:10.20944/preprints201807.0156.v1

The Complete Genome Sequence of Escherichia coli phage Eco_BIFF

Lauren Cooper, Erica Lasek-Nesselquist, Joseph Wade

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Bacteriophage; Escherichia coli; Genome sequence

Online: 9 July 2018 (16:08:26 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201809.0051.v2

Unbalanced Current Sharing Control in Islanded Low Voltage Microgrids

foad najafi, Matthias Fripp

Subject: Engineering, Electrical And Electronic Engineering Keywords: distributed generation; LV microgrid; negative-sequence current; zero-sequence current; power sharing; unbalance load; voltage control

Online: 5 September 2018 (05:55:55 CEST)

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This paper reports a new control strategy to improve sharing of unbalanced currents in islanded LV microgrids. This technique provides fast and effective sharing of positive-, negative- and zero-sequence currents, and is the first example of zero-sequence current sharing in the literature. The controllers are designed in the stationary frame. The control structure consists of four loops; 1)~the current controller; 2)~the voltage controller; 3)~the droop controller and the 4)~negative and zero sequence current controllers. The output current is considered unknown for the controller and is added to the control system as a disturbance. The proposed controller features a high gain in fundamental and harmonic frequencies, hence a good voltage quality is obtained in the presence of unbalanced and nonlinear loads. To this aim, a proportional-resonant (PR) controller is adopted as the current controller. By using a multi-resonant controller as current controller, a unified control structure is obtained which is suitable for both grid-connected and islanded modes. The voltage controller is designed using a resonant controller so that the voltage can have low VUF and THD in the presence of unbalanced and nonlinear loads. Furthermore, in this paper droop method is applied to the control structure to share real and reactive powers. Simulation studies show that the conventional droop method cannot share the oscillatory part of the output power that is due to the presence of unbalanced loads in the microgrid. This paper relies on using zero and negative sequence virtual impedance controller to share the oscillatory part of output power. By using zero-sequence virtual impedance controller (ZSVIC) and negative-sequence virtual impedance controller (NSVIC), the zero and negative sequence currents in the microgrid are controlled and shared effectively. By compensating zero- and negative-sequence currents locally, the flow of these currents in the microgrid is minimized, and the overall power quality of the islanded LV microgrid is improved.

Preprint REVIEW | doi:10.20944/preprints202008.0516.v1

A Systematic Review on Coronavirus Disease 2019 (COVID-19)

Hira Karim, Muhammad Shahzeb Khan

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: Coronavirus, sequence homology, transmission, virology, diagnosis, virus control, vaccination.

Online: 24 August 2020 (09:31:38 CEST)

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Emerging and reemerging pathogens is a global challenge for public health. Recently, a novel coronavirus disease emerged in Wuhan, Hubei province of China, in December 2019. It is named COVID-19 by World Health Organization (WHO). It is known to be caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) that affects the lower respiratory tract and manifests as pneumonia in humans. Coronaviruses (CoVs) are structurally more complicated as compared to other RNA viruses. This viral epidemic has led to the deaths of many, including the elderly or those with chronic disease or compromised immunity. Viruses cause infection and diseases in humans of varying degrees, upper respiratory tract infections (URTIs) cause common cold while lower respiratory tract infections induce pneumonia, bronchitis, and even severe acute respiratory syndrome (SARS). The costs of COVID-19 are not limited. It equally affects all the medical, sociological, psychological, and economic aspects globally. This is regarded as the third deadly outbreak in the last two decades after Severe Acute Respiratory Syndrome SARS (2002–2003) and Middle East Respiratory Syndrome MERS (2012). Based on the sequence homology of SARS-CoV-2, different animal sources including bats, snakes, and pangolins have been reported as potential carriers of this viral strain. Real-time RT-PCR represents the primary method for the diagnosis of new emerging viral strain SARS-CoV-2. The transmission dynamics suggest that SARS-CoV-2 is transmitted from person-to-person through direct contact or coughing, sneezing, and by respiratory droplets. Several anti-viral treatments including lopinavir/ritonavir, remdesivir, chloroquine phosphate, and abidor are also suggested with different recommendations and prescriptions. Protective and preventive strategies as suggested by various health organization i.e. WHO and US Center for Disease Control and Prevention (CDC) must be adopted by everyone. This review covers the important aspects of novel COVID-19 including characteristics, virology, symptoms, diagnostics, clinical aspects, transmission dynamics, and protective measures of COVID-19.

Preprint ARTICLE | doi:10.20944/preprints202101.0076.v6

Unification of the Electromagnetic Force and Gravity through the Composite Photon

Ian Clague

Subject: Physical Sciences, Acoustics Keywords: Unification; Composite Photon; Negative Mass; Antimatter; Grand Unification Theory, Dark Energy, Dark Matter

Online: 28 October 2021 (10:06:39 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202004.0117.v1

Using Negative Pressure Wound Therapy in the Treatment of Wounds After Fasciotomy in Acute Compartment Syndrome - Retrospective Case Series Study

Jaroslaw P. Miszczuk, Maria Błońska-Staniec, Anna Michalska, Bartosz Stemplewski

Subject: Medicine And Pharmacology, Surgery Keywords: acute compartment syndrome; negative pressure wound therapy; vacuum assisted wound closure; fasciotomy

Online: 8 April 2020 (04:50:32 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202007.0132.v1

SARS-CoV19-2 Spike Protein Mutation Patterns: A Global Scenario

Renukaradhya K. Math, Mallikarjun Goni, Palaksha K. Javaregowda, Ajay S. Khandagale, AjayKumar Oli

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: coronavirus; spike protein; database; sequence alignment; mutation; homology model; hydrophobic amino acids

Online: 7 July 2020 (16:49:04 CEST)

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Preprint REVIEW | doi:10.20944/preprints202108.0058.v1

Genetic and Epigenetic Variations of SARS-Cov-2 and Host Genes and Their Impact in Covid-19 Pandemic

Muhammed Elayadeth Meethal, Punnoth Poonkuzhi Naseef, Mohamed Saheer Kuruniyan, Mansoor C Abdulla, Shyju Ollakkod, Shahul Ebrahim, Godavarma Girish Varma

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: SARS-CoV-2; COVID-19; Phylogenetic analysis; Next generation sequence analysis; Virus-Host interaction; Immunology; Antiviral agents; Vaccine; Virus diagnosis

Online: 2 August 2021 (16:17:24 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/preprints201907.0205.v1

Matrix Sequences of Tetranacci and Tetranacci-Lucas Numbers

Yüksel Soykan

Subject: Computer Science And Mathematics, Algebra And Number Theory Keywords: Tetranacci numbers; Tetranacci matrix sequence; Tetranacci-Tucas matrix sequence

Online: 17 July 2019 (11:10:06 CEST)

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Preprint CASE REPORT | doi:10.20944/preprints201912.0170.v1

Necrotic Skin Infection by Sphingomonas Paucimobilis in Amazonia Region

Talles Henrique Pichinelli Maffei, Frederico Alberto Bussolaro, Arlei Belaus, Alexandra Prevedello, Claudine Thereza-Bussolaro

Subject: Medicine And Pharmacology, Dermatology Keywords: sphingomonas; gram-negative bacterial infection; skin disease; bacterial

Online: 12 December 2019 (10:01:35 CET)

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Preprint ARTICLE | doi:10.20944/preprints202107.0626.v1

A High Efficacy DNA Vaccine Against Tilapia Lake Virus in Nile Tilapia (Oreochromis niloticus)

Nai-tong Yu, Wei-wei Zeng, Jian-hua Wang, Yu-liang Zhang, Xiu-chun Zhang, Zhi-xin Liu

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: tilapia; negative-sense RNA virus; Tilapia lake virus; DNA vaccine

Online: 28 July 2021 (11:11:37 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202208.0338.v1

Newcastle Disease Genotype VII Outbreaks in Poultry across Egypt are associated with Enzootic Prevalence of the Virus in Wild Birds

Amal A.M. Eid, Ashraf Hussein, Ola Hassanin, Reham M. Elbakrey, Rebecca Daines, Jean-Remy Sadeyen, Hanan M.F Abdien, Klaudia Chrzastek, Munir Iqbal

Subject: Biology And Life Sciences, Virology Keywords: migratory birds; Newcastle disease virus-GVII; poultry; phylogenetics; sequence-independent; sin-gle-primer amplification (SISPA); velogenic; whole genome sequencing (WGS)

Online: 18 August 2022 (10:40:10 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201801.0100.v1

Pressure Distribution during Negative Pressure Wound Therapy of Experimental Abdominal Compartment Syndrome in a Porcine Model

Adrienn Csiszkó, Klaudia Balog, Zoltán Attila Godó, Gyula Juhász, Katalin Pető, Ádám Deák, Mariann Berhés, Norbert Németh, Zsolt Bodnár, Zsolt Szentkereszty

Subject: Medicine And Pharmacology, Clinical Medicine Keywords: intra-abdominal pressure; abdominal compartment syndrome; pressure sensor; negative pressure wound therapy; open abdomen;

Online: 11 January 2018 (09:17:10 CET)

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Preprint ARTICLE | doi:10.20944/preprints201910.0217.v1

Aptamer Bead-Mediated Separation of Gram-Negative Bacteria Using Acoustophoresis

Sang Woo Lee, Byungw Woo Kim, Hye-Su Shin, Anna Go, Minho Lee, Dong-ki Lee, Soyoun Kim, Ok Chan Jeong

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: aptamer: acoustophoresis; microfluidics; gram-negative bacteria

Online: 18 October 2019 (11:41:41 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 REVIEW | doi:10.20944/preprints201910.0362.v1

Trend Analysis of Tuberculosis Cases and the Effect of HIV Cases on Tuberculosis Cases in Some West African Countries Using Panel Poisson and Negative Binomial Regression Models

Monday Osagie Adenomon, Gbenga Solomom Akinyemi

Subject: Computer Science And Mathematics, Probability And Statistics Keywords: tuberculosis (TB); human immunodeficiency virus (HIV); Acquired Immune Deficiency Syndrome (AIDS); World Health Organization (WHO); panel data; poisson; negative binomial; regression

Online: 31 October 2019 (04:33:45 CET)

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Preprint ARTICLE | doi:10.20944/preprints202008.0632.v1

Mathematical Blockchain Modeling of Peer-to-Peer Networks for Gene Expression in Cell Population

Jung In Choi

Subject: Computer Science And Mathematics, Mathematical And Computational Biology Keywords: Blockchain; P2P Networks; Nucleobase DNA/RNA sequence; Gene Expression; Cell Population; Epigenetics; Methylation; Consensus; Hash Algorithm; Triple Codons; Protein Synthesis; Cryptocurrency

Online: 28 August 2020 (10:33:42 CEST)

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The study presents a mathematical modeling for supporting the premise that our body is composed of blockchain systems. A cell population is considered a space with peer-to-peer communication networks for applying blockchain protocol. Transaction is defined as gene expression that constantly occurs for protein synthesis in each cell. The transaction process proceeds according to the blockchain protocol with sharing and recording the data on the blockchain ledger. The premise comes from the clues of the previous research such that the cell population is a complex structured network system having cell-to-cell connections. Although individual cells exhibit stochastic nonlinear dynamic behavior, cell population shows consensus behavior that reaches to ensemble through interaction among cells. It is inferred that gene expression is not regulated by the corresponding cell only nor determined by external intelligence such as the brain. This is achieved through a consensus through stochastic interactions between cells over the whole cell population. These findings imply that mathematical blockchain modeling is a suitable for gene expression process. The original contribution of the study is a methodology for applying mathematically the blockchain protocol to the real biological gene expression process. In other words, the DNA sequence is converted into a numeral bit sequence that makes it possible to implement the blockchain protocol. A new DNA sequence scheme is proposed with adding methylated cytosine and adenine as the 5th and 6th bases for including epigenetic information which has profound effect on gene expression and regulation. The methodology was applied to the real biological synthesis process of protein samples. The protein is composed of amino acids that are encoded by triplet codons of 216 kinds with 6 base RNA sequence. The gene expression information is traced backward from a synthesized protein sample, amino acids of codons, RNA transcript up to DNA sequence. One of the results is a numeric value in the form of a bit sequence with which mathematical blockchain modeling is applicable. The cryptographic authentication and the consensus process are mathematically proven to work properly by the blockchain protocol. It implies that the same protein is synthesized, but with different epigenetic data, then protein's latent material properties will certainly be different. Although the result has not been justified by the biologic experiment yet, it is sure that the biological hidden algorithm inside DNA sequence will be revealed by the binary bit-logic with physical on/off states which is mathematically proven. The research will greatly contribute to disease treatment and medicine development as well as epigenetics in the future.

Preprint ARTICLE | doi:10.20944/preprints201802.0126.v1

New Definitons about A^I-Statistical Convergence with Respect to a Sequence of Modulus Functions and Lacunary Sequences

Ömer Kişi, Hafize Gümüş, Ekrem Savaş

Subject: Computer Science And Mathematics, Analysis Keywords: Lacunary sequence; ideal convergence; modulus function

Online: 20 February 2018 (09:15:49 CET)

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Preprint ARTICLE | doi:10.20944/preprints201809.0226.v1

Relation Contractive Selfmaps Involving Cauchy Sequences

Maria Luigia Diviccaro, Salvatore Sessa

Subject: Computer Science And Mathematics, Analysis Keywords: Cauchy sequence; d-self-closed relation; relation contraction; relation preserving

Online: 13 September 2018 (03:16:34 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 REVIEW | doi:10.20944/preprints201808.0087.v1

Mikko J. Lammi, Chengjuan Qu

Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: selenium; selenocysteine; selenoproteins; selenocysteine insertion sequence; nonsense-mediated decay

Online: 4 August 2018 (11:47:34 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201807.0263.v1

Geometry of Chalcogenide Negative Curvature Fibers for CO₂ Laser Transmission

Chengli Wei, Curtis R. Menyuk, Jonathan Hu

Subject: Physical Sciences, Optics And Photonics Keywords: CO2 lasers; negative curvature fibers; chalcogenide glass; fiber loss; mid-IR

Online: 16 July 2018 (08:40:16 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201908.0064.v1

On the Trends of Registered Birth and Death Rates in Nigeria: Evidence from Generalized Linear Models

Monday Osagie Adenomon, Emmanuel Chukwuma Anikweze

Subject: Computer Science And Mathematics, Probability And Statistics Keywords: birth; death; trends; generalized linear models (GLMs); poisson; negative binomial

Online: 5 August 2019 (14:36:49 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202006.0165.v2

Conserved Sequence Features in the Spike Protein Provide Evidence Suggesting the Origin of SARS-CoV-2 (COVID-19)-Related Viruses by Recombination between SARS virus and Another Sarbecovirus

Radhey S. Gupta, Bijendra Khadka

Subject: Biology And Life Sciences, Virology Keywords: Conserved signature indels (CSIs) specific for SARS and SARS-CoV-2-related viruses. Molecular markers distinguishing different clades of Sarbecovirus, Evolutionary relationships between SARS and SARS-CoV-2-related viruses, Origin of SARS-CoV-2 and Pangolin CoV_MP789 viruses, Novel sequence and structural features of spike and nucleocapsid proteins. Genetic recombination.

Online: 26 August 2020 (10:17:16 CEST)

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Both SARS-CoV-2 (COVID-19) and SARS coronaviruses (CoVs) are members of the subgenus Sarbecovirus. To understand the origin of SARS-CoV-2, protein sequences from sarbecoviruses were analyzed to identify highly-specific molecular markers consisting of conserved inserts or deletions (termed CSIs) in the spike (S) and nucleocapsid (N) proteins that are specific for either particular clusters/lineages of these viruses or are commonly shared by specific lineages. Three novel CSIs in the N-terminal domain of the spike protein S1-subunit (S1-NTD) are uniquely shared by the SARS-CoV-2, BatCoV-RaTG13 and most pangolin CoVs, distinguishing this cluster of viruses (SARS-CoV-2r) from all others. In the same positions, where these CSIs are found, related CSIs are also present in two other sarbecoviruses (viz. CoVZXC21 and CoVZC45 forming CoVZC cluster), which form an out group of the SARS-CoV-2r cluster. These three CSIs are not found in the SARS-CoVs. However, both SARS and SARS-CoV-2r CoVs contain two large CSIs in the C-terminal domain of S1 (S1-CTD), which binds the human ACE-2 receptor, that are absent in the CoVZC cluster of CoVs. These results indicate that while the S1-NTD of the SARS-CoV-2r viruses possesses the sequence characteristics of the CoVZC cluster of CoVs, their S1-CTD resembles the SARS viruses. Thus, the spike protein of SARS-CoV-2r viruses has likely originated from a recombination event between the S1-NTD of the CoVZC viruses and the S1-CTD of SARS viruses. This inference is also supported by the amino acid sequence similarity of the S1-NTD and S1-CTD from SARS-CoV-2 compared to the CoVZC and SARS CoVs. We also present evidence that one of the pangolin-CoV_MP789, whose receptor-binding domain is most similar to the SARS-CoV-2, is also derived by a recent recombination between the S1-NTD of the CoVZC CoVs and the S1-CTD of a SARS-CoV-2 related virus. Several other identified CSIs are specific for others clusters of sarbecoviruses including a clade consisting of bat SARS-CoVs (BM48-31/BGR/2008 and SARS_BtKY72). Structural mappings studies show that the identified CSIs are located within surface-exposed loops and form distinct patches on the surface of the spike protein. These surface loops/patches are predicted to interact with other host components and play important role in the biology/pathology of SARS-CoV-2 virus. Lastly, the CSIs specific for the SARS-CoV-2r clade provide novel means for development of new diagnostic and therapeutic targets for these viruses.

Preprint ARTICLE | doi:10.20944/preprints202004.0509.v1

GATA 3 Gene Overexpression Is A Biomarker of Adverse Prognosis for Peripheral T-Cell Lymphoma, Not Otherwise Specified and for ALK-Negative Anaplastic Large Cell Lymphoma: An Exploratory Analysis of 80 Latin American Cases of nodal PTCLs

Luís Alberto de Pádua Covas Lage, Cláudio Vinícius Brito, Débora Levy, Hebert Fabrício Culler, Samuel Campanelli Freitas Couto, Lucas Bassolli, Maria Claudia Nogueira Zerbini, Vanderson Rocha, Juliana Pereira

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: nodal peripheral T-cell lymphomas; peripheral T-cell lymphoma, not otherwise specified (PTCL/NOS); ALK-negative anaplastic large-cell lymphoma (ALCL/ALK-); Angioimmunoblastic T-cell lymphoma (AITL); diagnosis; prognosis; GATA3 gene expression

Online: 29 April 2020 (12:48:00 CEST)

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Background: Nodal peripheral T-cell lymphomas (nPTCLs) encompass a heterogeneous group of mature and aggressive lymphoid malignancies, including peripheral T-cell lymphoma, not otherwise specified (PTCL/NOS), angioimmunoblastic T-cell lymphoma (AITL) and anaplastic large cell lymphoma (ALCL) ALK-positive and ALK-negative. Their differential diagnosis and prognosis are an issue in the clinical practice. Accurate biomarkers to refine the different subtypes of nPTCLs and to stratify their prognosis are essential to improve their treatment approach. The aim of this study was to test the prognostic impact of GATA3 gene expression, and its capability to discriminate the different subtypes of nPTCLs. Patients and Methods: From 2000 to 2017, 80 patients with nPTCLs were eligible for GATA3 gene expression analysis that was assessed retrospectively by quantitative real time PCR (qRT-PCR) of neoplastic biopsies in Formalin-Fixed Paraffin-Embedded samples (FFPE). Results: Median age was 49 years old (IqR 34-59), 43/80 (53.7%) were male. Median follow-up was 1.72 years. Of them, 36.3% were classified as PTCL/NOS, 31.2% ALK-negative ALCL, 21.2% ALK-positive ALCL and 11.3% AITL. The majority of cases had advanced stage (III/IV). Two-year estimated overall survival (OS) and progression-free survival (PFS) were 52.2% and 39.5%, respectively. The median GATA3 gene expression level was 0.49% (range 0 – 7.07) in all cohort, it was 0.11% for ALK-positive ALCL, 0.46% for ALK-negative ALCL, 0.86% for PTCL/NOS and 0.67% for AITL. The difference of GATA3 gene expression among distinct variants of nPTCLs was statistically significant (p < 0.001). GATA3 gene expression levels ≥ 0.71% discriminate PTCL/NOS from ALK-negative ALCL and AITL with sensitivity of 62% and specificity of 80.3%. GATA3 gene expression levels ≥ median was associated with poor 2-year OS for PTCL/NOS (46.7% x 21.4%, p=0.04) and for ALK-negative ALCL (85.7% x 54.5%, p=0.04). Conclusion: Despite the relative small and heterogeneous group of patients with nPTCLs, GATA3 gene overexpression may be an important biomarker associated with poor prognosis in PTCL/NOS and ALK-negative ALCL. Moreover it may also discriminate different subtypes of nPTCLs. Further studies with larger series of patients should confirm our findings.

Preprint ARTICLE | doi:10.20944/preprints202002.0366.v1

Energy-Momentum Tensor and Parameters in Cosmological Model

Ying-Qiu Gu

Subject: Physical Sciences, Astronomy And Astrophysics Keywords: cosmological model; energy-momentum tensor; equation of state; cosmic curvature; cosmological constant; negative pressure; dynamic analysis

Online: 25 February 2020 (07:55:12 CET)

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Preprint ARTICLE | doi:10.20944/preprints201904.0218.v1

A Study on the Determinants of Eco-Innovation of Korean Manufacturing Firms

Cheon Yu, Yun Seop Hwang

Subject: Business, Economics And Management, Business And Management Keywords: eco-innovation; anticipated regulation; self-regulation; industry-specific characteristics; information sourcing openness; multivariate probit model; zero inflated negative binomial model

Online: 19 April 2019 (11:25:06 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202202.0112.v1

Auxetic Structures from Rotating Squares

Julian Plewa, Małgorzata Płońska, Paweł Lis

Subject: Engineering, Mechanical Engineering Keywords: auxetic structures; metamaterials; negative Poisson’s ratio (NPR)

Online: 8 February 2022 (13:15:25 CET)

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Preprint ARTICLE | doi:10.20944/preprints201907.0147.v1

Schizophrenia Phenomenology Revisited: Positive and Negative Symptoms are Strongly Related Reflective Manifestations of an Underlying Single Trait Indicating Overall Severity of Schizophrenia

Abbas Almulla, Hussein Al-Hakeim, Michael Maes

Subject: Medicine And Pharmacology, Psychiatry And Mental Health Keywords: deficit schizophrenia, positive symptoms, negative symptoms, inflammation, neuro-immune

Online: 10 July 2019 (11:02:41 CEST)

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Preprint REVIEW | doi:10.20944/preprints202107.0614.v1

Mixed Effects and Mechanisms of Cannabinoids for Triple-Negative Breast Cancer Treatment

Khanh Tran

Subject: Medicine And Pharmacology, Medicine And Pharmacology Keywords: Triple-negative breast cancer; cannabinoid; marijuana; cell signalling; medicinal plants

Online: 28 July 2021 (08:56:32 CEST)

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Triple-negative breast cancer (TNBC) is a subtype of breast cancer characterized by the lack of estrogen receptors (ER), progesterone receptors, and HER-2 receptors. Thus, TNBC tumours do not benefit from the current therapies targeting ER or HER-2. Therefore, there is an urgent need to develop novel treatment for this subtype of breast cancer. Marijuana is a common name given to Cannabis plants, a group of plants in the Cannabis genus of the Cannabaceae family. Cannabis plants are among the oldest cultivated crops, traced back at least 12,000 years and are well known for their multi-purpose usage, including medicinal purposes. The main active compounds extracted from Cannabis plants are 21-carbon-containing terpenophenolics, which are referred to as phytocannabinoids. Of these, the tetrahydrocannabinol (THC) group contains highly potent cannabinoids, including delta-9-tetrahydrocannabinol (∆9-THC) and delta-8-tetrahydrocannabinol (∆8-THC), which are the most abundant THCs and are largely responsible for psychological and physiological effects of marijuana. The use of Cannabis plants for medicinal purposes was first recorded in 2337 BC in China, where Cannabis plants were used to treat pains, rheumatism, and gout. Recently, several cannabinoids have been approved for a number of treatments, one of which is the treatment of nausea and vomiting caused by chemotherapy in cancer patients. Furthermore, increasing evidence shows that cannabinoids not only attenuate side effects due to cancer treatment, but might also potentially possess direct antitumor effects in several cancer types, including breast cancer. However, anti-tumour activity of marijuana has been variable in different studies and even promoted tumour growth in some cases. In addition, the mechanisms of cannabinoid action in cancer remain unclear. This review summarizes evidence about the mixed actions of cannabinoids in cancer in general and triple-negative breast cancer in particular.

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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Preprint TECHNICAL NOTE | doi:10.20944/preprints201901.0126.v1

Mapping Quantitative Trait Loci onto Chromosome-scale Pseudomolecules in Flax

Frank M. You, Sylvie Cloutier

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: flax; association mapping; genome-wide association study (GWAS); simple sequence repeat (SSR); single nucleotide polymorphism (SNP); quantitative trait loci (QTL); chromosome-scale pseudomolecules

Online: 14 January 2019 (07:19:08 CET)

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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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Working Paper BRIEF REPORT

The Curious Case of the RaTG13 Genome: Time to Revise the Sequence Reporting Standards for Pathogens

Mohit Singla, Saad Ahmad, Chandan Gupta, Tavpritesh Sethi

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: Data Quality; Sequence reporting standards; RaTG13 Sequence; De-novo assembly

Online: 26 July 2021 (12:08:30 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202109.0085.v1

Chick Embryo Experimental Platform for 3D Tissue Engineering Modelling of Cancer Micrometastases for Tumor Biology, Drug Development and Nanomaterials Testing

Anna Guller, Inga Kuschnerus, Vlada Rozova, Annemarie Nadort, Yin Yao, Zahra Khabir, Alfonso Garcia-Bennett, Liuen (Olivia) Liang, Aleksandra Polikarpova, Yi Qian, Ewa M. Goldys, Andrei Zvyagin

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: chick embryo; 3D culture; tumor models in vitro; tissue engineering; metastasis; triple-negative breast cancer; liver; mesoporous silica nanoparticles; doxorubicin; micrometastasis

Online: 6 September 2021 (11:46:54 CEST)

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Working Paper BRIEF REPORT

Identification of Novel Missense Mutations in a Large Number of Recent SARS-CoV-2 Genome Sequences

Hugh Y. Cai, Kimberly K. Cai, Julang Li

Subject: Biology And Life Sciences, Virology Keywords: COVI-19; SARS-CoV-2; virus; mutation; polymorphism; genome sequence

Online: 21 May 2020 (04:09:53 CEST)

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Background: SARS-CoV-2 infection has spread to over 200 countries since it was first reported in December of 2019. Significant country-specific variations in infection and mortality rate have been noted. Although country-specific differences in public health response have had a large impact on infection rate control, it is currently unclear as to whether evolution of the virus itself has also contributed to variations in infection and mortality rate. Previous studies on SARS-CoV-2 mutations were based on the analysis of ~ 160 SARS-CoV-2 sequences available until mid-February 2020.^{2, 3, 4, 5} By mid-April, > 550 SARS-CoV-2 sequences had been deposited in GenBank, and over 8,200 in the GISAID database. Methods: We performed a sequence analysis on 474 SARS-CoV-2 genomes submitted to GenBank up to April 11, 2020 by multiple alignment using Map to a Reference Assembly and Variants/SNP identification. The results were verified on a larger scale, 8,126 hCoV-19 (SARS-CoV-2) sequences from GISAID database. Results: We identified 5 recently emerged mutations in many isolates (up to 40%). Our analysis highlights 5 frequent new mutations that have emerged since late February 2020. These mutations are: one each missense (non-synonymous) mutation in orf1ab (C1059T), orf3 (G25563T) and orf8 (C27964T), one in 5’UTR (C241T), one in a non-coding region (G29553A). The final mutation (G29553A) was found to be almost exclusive to the US isolates. The first 3 mutations are non-synonymous, leading to amino acid substitutions in the viral protein sequence. Except for C241T, all the novel mutations identified are absent in the isolates from Italy and Spain in the SARS-CoV-2 genomes deposited in GenBank and GISAID by April 13, 2020. Conclusion: The results of current study indicate that new mutations are emerging as COVID-19 pandemic are spreading to different countries and that geography specific mutants may exist. The findings of current study lay the foundation for further investigation into the impact of SARS-CoV-2 mutations on disease incidence, severity, and host immune response. In addition, it may also provide insights into vaccine development and serological response detection for the virus.

Preprint ARTICLE | doi:10.20944/preprints202202.0175.v1

Prediction of Linear Cationic Antimicrobial Peptides Active against Gram Negative and Positive Bacteria Based on Machine Learning Models

Ümmü Gülsüm Söylemez, Malik Yousef, Zülal Kesmen, Mine Erdem Büyükkiraz, Burcu Bakır-Güngör

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: antimicrobial peptide prediction; sequence analysis; random forest

Online: 14 February 2022 (11:57:01 CET)

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Preprint ARTICLE | doi:10.20944/preprints201903.0036.v1

Aligning the Aligners: Comparison of RNA Sequencing Data Alignment and Gene Expression Quantification Tools for Clinical Breast Cancer Research

Isaac Raplee, Alexei Evsikov, Caralina Marín de Evsikova

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: breast neoplasms, ductal carcinoma in situ (DCIS), gene expression profiling, high-throughput nucleotide sequencing, infiltrating ductal carcinoma (IDC), paraffin embedding, sequence alignment, transcriptome

Online: 4 March 2019 (10:23:25 CET)

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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/preprints201807.0224.v2

Pseudopterosin Inhibits Proliferation and 3D Invasion in Triple Negative Breast Cancer by Agonizing Glucocorticoid Receptor Alpha

Julia Sperlich, Nicole Teusch

Subject: Medicine And Pharmacology, Pharmacology And Toxicology Keywords: pseudopterosin; triple negative breast cancer; glucocorticoid receptor alpha; dexamethasone; cell proliferation; 3D invasion; tumor spheroid; co-culture; interleukin 6; interleukin 8

Online: 2 August 2018 (06:08:31 CEST)

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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 REVIEW | doi:10.20944/preprints202110.0258.v2

Recent Progress on Methods for Estimating and Updating Large Phylogenies

Paul Zaharias, Tandy Warnow

Subject: Biology And Life Sciences, Cell And Developmental Biology Keywords: phylogeny estimation; multiple sequence alignment; phylogenetic placement; phylogenomics; taxon identification; maximum likelihood

Online: 12 January 2022 (18:56:42 CET)

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Preprint ARTICLE | doi:10.20944/preprints202008.0398.v1

Hyperbolic Rules in Genomes, the Harmonic Progression and Recurrence Sequences in Algebraic Biology

Sergey V. Petoukhov

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: genomes; hyperbolic sequences; harmonic progression; recurrence sequence; harmonic numbers; natural logarithm; logarithmic spiral; biological spirals; tensor product

Online: 19 August 2020 (08:15:03 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201904.0011.v2

Nucleotide Epi-Chains and New Nucleotide Probability Rules in Long DNA Sequences

Sergey Petoukhov

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: DNA sequence; helix; nucleotide frequencies; DNA epi-chains; helical antennas; Fröhlich's theory; long-range coherence; epigenetics; quantum biology; binary representation

Online: 14 May 2019 (06:22:48 CEST)

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Preprint REVIEW | doi:10.20944/preprints202004.0148.v1

Well-defined Conjugated Macromolecules in Sensing

Agata Krywko-Cendrowska, Dawid Szweda, Roza Szweda

Subject: Chemistry And Materials Science, Applied Chemistry Keywords: well-defined macromolecules; sequence-defined macromolecules; sequence-defined polymers; conjugated oligomers; oligo(arylene ethynylene)s; biosensors; sensors; process monitoring

Online: 9 April 2020 (10:06:28 CEST)

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Preprint CONCEPT PAPER | doi:10.20944/preprints201810.0277.v1

Quantitative Network Organization of Interactions Emerging from the Evolution of Sequence and Structure Space of Antibodies: the RADARS Model

József Prechl

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: antibody; network; sequence; structure; clonality; B cell; systems biology; quantitative biology

Online: 12 October 2018 (17:01:13 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202101.0191.v1

Social Systems: Structure, Development and Application of the Fibonacci Sequence

Pavel Brazhnikov

Subject: Social Sciences, Sociology Keywords: economic systems; social structure; ownership; the Fibonacci sequence; surplus value

Online: 11 January 2021 (12:41:23 CET)

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Preprint ARTICLE | doi:10.20944/preprints202011.0041.v1

Negative-Curvature Spacetime Solutions for Graphene

Antonio Gallerati

Subject: Physical Sciences, Acoustics Keywords: negative-curvature spacetime; field theories in lower dimensions; graphene theoretical physics

Online: 2 November 2020 (13:24:36 CET)

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Preprint ARTICLE | doi:10.20944/preprints201908.0247.v1

What do a Longest Increasing Subsequence and a Longest Decreasing Subsequence Know About Each Other?

Elizabeth J. Itskovich, Vadim E. Levit

Subject: Computer Science And Mathematics, Computational Mathematics Keywords: Erd˝os-Szekeres theorem; longest increasing sequence; longest decreasing sequence

Online: 23 August 2019 (11:35:32 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201909.0171.v1

Amplicon Analysis I

Eduardo Pareja-Tobes, Raquel Tobes

Subject: Computer Science And Mathematics, Mathematical And Computational Biology Keywords: Bioinformatics; NGS; DNA sequencing; DNA sequence analysis; amplicons; ultrametric spaces; indexing

Online: 16 September 2019 (16:45:10 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202106.0610.v1

Large-scale Phylogenomic Analysis Provides New Insights Into the Phylogeny of the Order Gadiformes and Evolution of Freshwater Gadiform Species Burbot (Lota lota)

Zhiqiang Han, Chenyan Shou, Manhong Liu, Tianxiang Gao

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: phylogenomic analyses; exon sequence; Gadiformes; Lota lota

Online: 25 June 2021 (09:13:35 CEST)

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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 REVIEW | doi:10.20944/preprints202011.0689.v1

Alternative Invasion Mechanisms and Host Immune Response to Plasmodium vivax Malaria: Trends and Future Directions

Daniel Kepple, Kareen Pestana, Junya Tomida, Abnet Abebe, Lemu Golassa, Eugenia Lo

Subject: Medicine And Pharmacology, Tropical Medicine Keywords: Plasmodium vivax; Erythrocyte Invasion Mechanisms; Duffy Negative; Africa; Immunology; Epidemiology

Online: 27 November 2020 (13:08:59 CET)

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Preprint ARTICLE | doi:10.20944/preprints201911.0033.v4

Circuit-Based Approaches for a Superconducting-Like Behavior with Relatively High Critical Current Density

Shinichi Ishiguri

Subject: Physical Sciences, Condensed Matter Physics Keywords: temperature-independent superconductivity; circuit-approached superconductivity; electron pair; Bose– Einstein condensation; large superconducting energy gap; London equation; Meissner effect; macroscopic wave function; critical current density; negative voltages

Online: 20 February 2024 (22:14:28 CET)

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In general, a superconductor has zero resistance, although it requires significant refrigeration or high pressures with high manufacturing costs, which prevents it into practical applications. In other words, solving these issues implies main superconducting researches. To solve these problems, this paper describes a new type of superconductivity, which is independent for temperatures and which operates without pressures. The principles of the presented system are as follows:First a voltage source, a current source and a load are connected in series. Then, the voltage of the voltage source is adjusted to balance the voltage of the load. Under this condition, the balance of the two voltages provides a zero voltage between the taps of the current source and the generated current from the voltage source becomes zero because of the internal infinite resistance of the current source. As a result, the electric powers generated by the two sources are zero, and therefore, the load cannot generate Joule heating because of energy conservation. However, the current from the current source (not the voltage source) is not zero; therefore, we can predict that the resistance of the load must be zero. As a theory, we derived a new electric field and transient attractive force, which result in a very short coherence of an electron pair because there is not the Coulomb repulsive force due to the existence of the above transient attractive force. Note that both the forces are derived by the Poisson equation, which implies that they cannot be compatible. Therefore, the pair combination energy from spins becomes extremely strong, which is not destroyed by the normal heat energy. Moreover, every center-of-mass motion of electron pair results in the Bose-Einstein condensation and the macroscopic wave function, which produces the London equation (i.e., the Meissner effect). Moreover, by introducing the equivalent circuit, this paper conducted numerical calculations. As a result, we could derive numerically zero resistance and responses for additional static magnetic fields as a discharged current, which implies the Meissner effect. Note that this paper has prepared Appendix section, which provides a guide to reproduce actual experiments and preliminary experimental results. These results in the Appendix indicate the zero resistances and Meissner effects.

Preprint REVIEW | doi:10.20944/preprints201910.0255.v1

Effectiveness of Efflux Pump Inhibitors as Biofilm Disruptors and Resistance Breakers in Gram-negative (ESKAPEE) Bacteria

Akif Reza, J. Mark Sutton, Khondaker Miraz Rahman

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: antimicrobial resistance; biofilm; efflux pump inhibitors; antibiotic potentiation; eskapee pathogens; gram-negative bacteria

Online: 22 October 2019 (10:22:56 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202004.0064.v2

Parvovirus B19 and Human Parvovirus 4 Encode a Homologous “X Protein” in a Reading Frame Overlapping the VP1 Capsid Gene: A VP1/X Overlap in Parvovirus B19 and PARV4

David G Karlin

Subject: Biology And Life Sciences, Virology Keywords: Overlapping genes; overlapping coding sequences; overlapping reading frames; 9 kDa protein; erythroparvovirus; tetraparvovirus; Y region; Y coding sequence; PLA2

Online: 15 September 2023 (11:31:52 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201809.0129.v1

Fibonacci-Mann Iteration for Monotone Asymptotically Nonexpansive Mappings in Modular Spaces

Buthinah A. Bin Dehaish, Mohamed A Khamsi

Subject: Computer Science And Mathematics, Analysis Keywords: Asymptotically nonexpansive mapping, Fibonacci sequence, fixed point, Mann iteration process, modular function spaces, monotone Lipschitzian mapping, Opial condition, uniformly convexity.

Online: 7 September 2018 (10:58:24 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201811.0438.v1

Adiabatic Thermodyhamics

Christian Fronsdal

Subject: Physical Sciences, Fluids And Plasmas Physics Keywords: entropy; thermodynamics; conservative hydrodynamics; rotations; meniscus; planets; negative pressure

Online: 19 November 2018 (09:42:08 CET)

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Preprint ARTICLE | doi:10.20944/preprints202202.0133.v1

Phenotypic Heterogeneity Drives Differential Disease Outcome in Triple Negative Breast Cancer

Archana P. Thankamony, Reshma Murali, Priyanka Chakraborty, Nitheesh Karthikeyan, Binitha Anu Varghese, Vishnu Sunil Jaikumar, Mohit Kumar Jolly, Radhika Nair

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Intratumoral heterogeneity; Triple negative breast cancer (TNBC); Macc1; Phenotypic heteroge-neity

Online: 9 February 2022 (10:40:54 CET)

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Preprint ARTICLE | doi:10.20944/preprints201910.0346.v1

Factors That Enhanced Prevention of Mother-to-Child Transmission of HIV in Nasarawa State of Nigeria Using Logistic, Poisson and Negative Binomial Regression Models

Monday Osagie Adenomon, David Usman

Subject: Computer Science And Mathematics, Probability And Statistics Keywords: Prevention of Mother-to-Child transmission (PMTCT); Human Immunodeficiency Virus (HIV); Acquired Immune Deficiency Syndrome (AIDs); Poisson; negative binomial; logistic; regression

Online: 30 October 2019 (04:06:36 CET)

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Preprint ARTICLE | doi:10.20944/preprints201904.0318.v1

Evaluation of Sequence Learning Models for Large Commercial Building Load Forecasting

Cristina Nichiforov, Grigore Stamatescu, Iulia Stamatescu, Ioana Fagarasan

Subject: Engineering, Control And Systems Engineering Keywords: sequence models; recurrent neural networks; energy modelling; smart buildings

Online: 28 April 2019 (11:47:47 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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Preprint ARTICLE | doi:10.20944/preprints202104.0688.v1

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

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

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

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

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Preprint ARTICLE | doi:10.20944/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/preprints201810.0505.v1

Genomic Islands Confer Heavy Metal Resistance in Mucilaginibacter Kameinonensis and Mucilaginibacter Rubeus Isolated from a Gold/Copper Mine

Yuan Ping Li, Nicolas Carraro, Nan Yang, Bixiu Liu, Xian Xia, Renwei Feng, Quaiser Saquib, Hend A. Al-Wathnani, Jan Roloef van der Meer, Christopher Rensing

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Mucilaginibacer rubeus；Mucilaginibacter kameinonensis; genomic island; evolution; heavy metal resistance; draft genome sequence; CTnDOT

Online: 22 October 2018 (15:21:18 CEST)

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Preprint BRIEF REPORT | doi:10.20944/preprints202004.0009.v5

A Flexible Genome-Scale SARS-CoV-2 Clone Resource

Dae-Kyum Kim, Jennifer J. Knapp, Da Kuang, Aditya Chawla, Patricia Cassonnet, Hunsang Lee, Dayag Sheykhkarimli, Payman Samavarchi-Tehrani, Hala Abdouni, Ashyad Rayhan, Oxana Pogoutse, Etienne Coyaud, Sylvie van der Werf, Caroline Demeret, Anne-Claude Gingras, Mikko Taipale, Brian Raught, Yves Jacob, Frederick P. Roth

Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: SARS-CoV-2; coding sequence collection; gateway-compatible

Online: 7 July 2020 (18:09:21 CEST)

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