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Preprint ARTICLE | doi:10.20944/preprints201805.0330.v1

Genome-Wide Identification and Expression Analyses of the Fibrillin Family Genes Reveal Their Involvement in the Photoprotection in Cucumber

Inyoung Kim, Sang-Choon Lee, Eun-Ha Kim, Kiwhan Song, Tae-Jin Yang, Hyun Uk Kim

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: fibrillin; cucumber; genome-wide; gene expression; high light stress

Online: 24 May 2018 (05:24:00 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201805.0008.v1

Construct Validity of Korean Leisure Sports Instructor Job Crafting Questionnaire Scale (KSIJCQ: Korean Sports Instructor JCQ)

Wook Kyung Kim, Won Chung Chung, Hyu Kyoung Park

Subject: Social Sciences, Sociology Keywords: JCQ; job crafting; construct validity; leisure sports instructor; valid scale

Online: 1 May 2018 (11:36:48 CEST)

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Preprint REVIEW | doi:10.20944/preprints202009.0279.v1

The Population Genetics of Ploidy Change in Fungi

Aleeza C. Gerstein, Nathaniel Sharp

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: selection; mutation; genetic drift; adaptation; ploidy drive; genome instability

Online: 13 September 2020 (11:48:30 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202201.0333.v1

Creating Variant Features to Enhance Covid-19 Predictions with Machine Learning Ensemble

Justin Wood, Wenjia Wang

Subject: Computer Science And Mathematics, Artificial Intelligence And Machine Learning Keywords: Covid-19; Ensemble; Genome sequencing; Machine learning; Variant

Online: 21 January 2022 (15:17:58 CET)

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Preprint ARTICLE | doi:10.20944/preprints202102.0604.v1

Phylogenetic Analysis of the 2020 West Nile Virus (WNV) Outbreak in Andalusia (Spain)

Carlos S. Casimiro-Soriguer, Javier Perez-Florido, Jose L. Fernandez-Rueda, Irene Pedrosa-Corral, Vicente Guillot-Sulay, Nicola Lorusso, Luis Javier Martinez-Gonzalez, José María Navarro-Marí, Joaquin Dopazo, Sara Sanbonmatsu-Gámez

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: West Nile Virus; outbreak; meningoencephalitis; epidemiology; phylogeny; whole genome sequencing

Online: 26 February 2021 (09:46:38 CET)

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Preprint ARTICLE | doi:10.20944/preprints201910.0156.v1

Complete Genomic Sequence of Noni mosaic virus (NoMV), a Novel Potyvirus Associated with a Mosaic Disease in Morinda citrifolia L.

Nai-Tong Yu, Zhi-Ying Cai, Zhongguo Xiong, Yan Yang, Zhi-Xin Liu

Subject: Biology And Life Sciences, Virology Keywords: noni mosaic virus; potyvirus; complete genome; morinda citrifolia l; illumina transcriptomic sequencing

Online: 14 October 2019 (09:29:57 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202102.0208.v1

A Solution of the Cosmological Constant, Using Multiverse Version of Penrose CCC Cosmology, and Enhanced Quantization Compared

Andrew Beckwith

Subject: Physical Sciences, Acoustics Keywords: Minimum scale factor; cosmological constant; space-time bubble; bouncing cosmologies

Online: 8 February 2021 (13:00:28 CET)

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Preprint REVIEW | doi:10.20944/preprints202104.0484.v1

From RNA World to SARS-CoV-2: The Edited Story of RNA Viral Evolution

Zachary W. Kockler, Dmitry A. Gordenin

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: RNA world theory; Viral RNA; Genome stability; Viral evolution; Mutational signatures; RNA dependent RNA polymerase, RdRp; RNA recombination; RNA damage; Hypermutation; APOBEC; ADAR; RNA editing; SARS-CoV-2; rubella virus

Online: 19 April 2021 (13:22:01 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202105.0422.v1

Unlocking LoxP to Track Genome Editing In Vivo

William Gendron, Jeffrey Rubin, Brandon Simone, Stephen Ekker, Michael Barry, Rebecca Nace, Michael Hansen

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: genome editing; CRISPR; Cas9; in vivo editing

Online: 18 May 2021 (11:27:46 CEST)

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Preprint REVIEW | doi:10.20944/preprints202104.0244.v1

Curating and Comparing 114 Strain-Specific Genome-Scale Metabolic Models of Staphylococcus aureus

Alina Renz, Andreas Dräger

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Staphylococcus aureus; MRSA; genome-scale metabolic models; model-driven discovery; strain-specific models

Online: 8 April 2021 (14:25:31 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201904.0304.v1

Fatigue Assessment of Prestressed Concrete Slab-between-Girder Bridges

Eva O.L. Lantsoght, Rutger Koekkoek, Cor van der Veen, Henk Sliedrecht

Subject: Engineering, Civil Engineering Keywords: assessment; bridge evaluation; compressive membrane action; concrete bridges; fatigue; fatigue assessment; live loads; prestressed concrete; punching shear; scale model

Online: 28 April 2019 (08:38:27 CEST)

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Preprint REVIEW | doi:10.20944/preprints202101.0212.v1

Future Approaches for Treating Chronic Myeloid Leukemia: CRISPR Therapy

Elena Vuelta, Ignacio García-Tuñón, Patricia Hernández-Carabias, Lucía Méndez, Manuel Sanchez-Martin

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: CML; CRISPR/Cas9; BCR/ABL1; genome editing

Online: 12 January 2021 (10:14:46 CET)

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Preprint HYPOTHESIS | doi:10.20944/preprints202206.0409.v1

Evolutionary Honing in and Mutational Replacement: How Long-Term Directed Mutational Responses to Specific Environmental Pressures Are Possible

Adi Livnat, Daniel Melamed

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Non random mutation; interaction-based evolution; hemoglobin S; directed mutation; parallelism; genome organization

Online: 29 June 2022 (14:56:32 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202012.0473.v1

TEfinder: A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data

Vista Sohrab, Cristina López-Díaz, Antonio Di Pietro, Li-Jun Ma, Dilay Hazal Ayhan

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: transposable elements; mobile element insertion events; next generation sequencing (NGS); genome evolution

Online: 18 December 2020 (14:53:44 CET)

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Preprint ARTICLE | doi:10.20944/preprints202101.0303.v1

Controlling Nutritional Status (CONUT) Score is a Prognostic Indicator for Patients with Hemorrhagic Stroke: Results from a 3-month Follow-up Study

Bei-lei Zhu, Yan-zhi Wu, Zhong-ming Cai, Cheng-wei Liao, Le-qiu Sun, Zhi-peng Liu, Hao-man Chen, Xue-rong Huang, Ren-qian Feng, Sheng-lie Ye, Qun-li Lin, Xu-dong Zhou, Man-man Zhang, Bo Yang

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: Controlling Nutritional Status Score; Hemorrhagic stroke; Nutrition screening; Prognosis; Modified Rankin Scale

Online: 15 January 2021 (16:08:15 CET)

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Preprint DATA DESCRIPTOR | doi:10.20944/preprints202208.0349.v1

First Draft Genome Assembly of the Peruvian Creole Cattle Breed (Bos taurus) and its Comparative Genomics among the Bovinae Subfamily

Richard Estrada, Flor-Anita Corredor, Deyanira Figueroa, Wilian Salazar, Carlos Quilcate, Héctor V. Vásquez, Jorge L. Maicelo, Jhony Gonzales, Carlos I. Arbizu

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: NGS; Andean; neglected breed; genome

Online: 18 August 2022 (11:12:25 CEST)

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Working Paper ARTICLE

Chromosome-Level Genome Assembly of The Humpback Puffer, Tetraodon palembangensis

Rui Zhang, Chang Li, Mengjun Yu, Xiaoyun Huang, Mengqi Zhang, Shanshan Liu, Shanshan Pan, Weizhen Xue, Congyan Wang, Chunyan Mao, He Zhang, Guangyi Fan

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: tetraodon palembangensis; chromosome-level genome; genomic annotation; gene family

Online: 31 August 2020 (04:28:47 CEST)

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Preprint REVIEW | doi:10.20944/preprints202401.0789.v1

Microbiome Modeling: A Beginner’s Guide

Emanuel Lange, Lena Kranert, Jacob Krüger, Dirk Benndorf, Robert Heyer

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: systems microbiology; microbial ecology; omics data integration; metaproteomics; genome-scale modeling; constraint-based modeling; boolean modeling, bioinformatics

Online: 10 January 2024 (09:57:55 CET)

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Preprint DATA DESCRIPTOR | doi:10.20944/preprints202106.0368.v1

Mash Sketched Reference Dataset for Genome-Based Taxonomy and Comparative Genomics

Ayixon Sánchez-Reyes, Maikel Gilberto Fernández-López

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Microbial Mash database, Mash distance, Genome containment, Type material, Microbial taxonomy

Online: 14 June 2021 (14:54:32 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201806.0175.v1

Antineutrino Star Model of the Big Bang and Dark Energy

Tom F. Neiser

Subject: Physical Sciences, Particle And Field Physics Keywords: cosmology: theory; gravitation; early universe; dark energy; large-scale structure of universe; cosmic background radiation; neutrinos

Online: 12 June 2018 (08:43:45 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201810.0386.v1

Effects of Residual Stress Distribution on Interfacial Adhesion of Magnetron Sputtered AlN and AlN/Al Nanostructured Coatings on (100) Silicon Substrate

Rashid Ali, Marco Renzelli, Muhammad Imran Khan, Marco Sebastiani, Edoardo Bemporad

Subject: Chemistry And Materials Science, Surfaces, Coatings And Films Keywords: physical vapor deposition; magnetron-sputtering; AlN/Al coating; silicon substrate; residual stresses; wafer curvature method; Nano-scale residual stress profiling; indentation failure modes; nanoindentation adhesion

Online: 17 October 2018 (12:36:39 CEST)

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Compressive residual stresses in thin films can inhibit crack propagation under normal or sliding contact loading, with associated enhancement of the coating apparent toughness, load bearing capacity and wear resistance. This study investigates the influence of residual stress distributions on the thin film/substrate adhesion using a nanoindenter coupled with scanning electron microscope (SEM) investigations of indentation induced failure modes. Reactive and un-reactive magnetron sputtering with ion plating was used to coat a (100) silicon substrate with aluminum nitride (AlN) with and without an aluminum (Al) adhesion layer. The presence of an Al bond layer gives additional interfacial tensile stress because of the difference in thermal expansion coefficient. Additionally, a different magnitude of residual stresses in the AlN coating was achieved by changing the applied bias voltage onto the substrate. Wafer curvature method and incremental focused ion beam (FIB) milling, combined with high-resolution in situ scanning electron microscopy (SEM) imaging and full field strain analysis by digital image correlation (DIC), were used to measure the average and in-depth stress residual stress distribution in the produced coatings. The adhesion energy was then quantified by using a nanoindentation based model. Results demonstrate that the additional tensile residual stress in the aluminum adhesion layer decrease significantly the coating adhesion, even in presence of a higher compressive stress state in the AlN top-layer. Therefore, the coatings without Al-layer showed better adhesion because of a more homogeneous compressive residual stress in comparison with the coating having Al layer, even though both groups of coatings are produced under same bias voltage. Results are discussed, and some general suggestions are made on the correlation between coating/substrate property combination and the adhesion energy of multilayer stacks. The results suggested that Al bond-layer and inhomogeneous residual stresses affected the adhesion of AlN negatively to a substrate like silicon.

Preprint ARTICLE | doi:10.20944/preprints201904.0246.v2

Mathematical Models for Possible Roles of Oxytocin and Oxytocin Receptors in Autism

Mark Gottlieb

Subject: Medicine And Pharmacology, Neuroscience And Neurology Keywords: Oxytocin, Oxytocin Receptor, Autism, Nepsys Scale, MAST Immune System Disease, Dendritic Spines, Magnocellular Neurons, Desensitization, Labor, Down Regulation

Online: 23 April 2019 (11:12:19 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202010.0298.v2

Cosmic Ray Extremely Distributed Observatory

Piotr Homola, Dmitriy Beznosko, Gopal Bhatta, Łukasz Bibrzycki, Łukasz Bratek, Michalina Borczyńska, Nikolay M. Budnev, Dariusz Burakowski, David Edwin Alvarez-Castillo, Kevin Almeida Cheminant, Aleksander Ćwikła, Punsiri Dam-o, Niraj Dhital, Alan Duffy, Piotr Głownia, Krzysztof Gorzkiewicz, Dariusz Góra, Alok C. Gupta, Zuzana Hlávková, Martin Homola, Joanna Jałocha, Robert Kamiński, Michał Karbowiak, Marcin Kasztelan, Renata Kierepko, Marek Knap, Péter Kovács, Szymon Kuliński, Bartosz Łozowski, Marek Magryś, Mikhail V. Medvedev, Justyna Mędrala, Jerzy W. Mietelski, Justyna Miszczyk, Alona Mozgova, Antonio Napolitano, Vahab Nazari, Y. Jack Ng, Michał Niedźwiecki, Cristina Oancea, Bogusław Ogan, Gabriela Opiła, Krzysztof Oziomek, Maciej Pawlik, Marcin Piekarczyk, Bożena Poncyljusz, Jerzy Pryga, Matías Rosas, Krzysztof Rzecki, Jilberto Zamora-Saa, Katarzyna Smelcerz, Karel Smolek, Weronika Stanek, Jarosław Stasielak, Slawomir Stuglik, Jolanta Sulma, Oleksandr Sushchov, Manana Svanidze, Kyle Tam, Arman Tursunov, José-M. Vaquero, Tadeusz Wibig, Krzysztof W. Woźniak

Subject: Physical Sciences, Nuclear And High Energy Physics Keywords: cosmic rays; cosmic ray ensembles; extensive air showers; large scale cosmic ray correlations; CREDO Collaboration

Online: 15 October 2020 (16:13:43 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/preprints201803.0010.v1

The Effect of Propeller Scaling Methodology on the Performance Prediction

Stephan Helma, Heinrich Streckwall, Jan Richter

Subject: Engineering, Marine Engineering Keywords: propeller scale effects; propeller open-water efficiency; surface roughness; equivalent profile; strip method; betai method

Online: 1 March 2018 (15:58:14 CET)

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Preprint ARTICLE | doi:10.20944/preprints202107.0275.v1

Sequencing and Chromosome-Scale Assembly of Plant Genomes, Brassica rapa as a Use Case

Benjamin Istace, Caroline Belser, Cyril Falentin, Karine Labadie, Franz Boideau, Gwenaëlle Deniot, Loeiz Maillet, Corinne Cruaud, Laurie Bertrand, Anne-Marie Chèvre, Patrick Wincker, Mathieu Rousseau-Gueutin, Jean-Marc Aury

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: Genome sequencing; de novo Assembly; Scaffolding; Chromosome-scale; Nanopore sequencing; Long reads; Optical maps; Bionano Genomics; Hi-C; Omni-C; Pore-C; Plant genomes

Online: 12 July 2021 (22:55:37 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202007.0664.v1

Assessment of the Psychological Impact and Perceived Stress Due to COVID-19 Lockdown in Young Adult Population of India.

Sreelakshmi M, Irfanul Haque, Sarita Jangra Bhyan, Ankit Gaur, Aashi Jain, Amrita Kumari, Besty Thomas, Nancy Goel, Rashi Chauhan

Subject: Social Sciences, Psychology Keywords: COVID-19 lockdown; psychological impact; perceived stresses-R scale; PSS scale; young adults

Online: 28 July 2020 (04:39:39 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202005.0400.v1

What is the Real Shape of the Hubble Diagram, z = H₀*D or z+1= e^H0*t? Analysis of the SN1a Supernovae and Gamma Ray Burst Redshift/Magnitude Data including the High Redshift Range up to z = 8.1

Laszlo Marosi

Subject: Physical Sciences, Astronomy And Astrophysics Keywords: galaxies; distances and redshift; high redshift; stars; Gamma ray bursts; individual; supernovae; individual; cosmology; distance scale; observations

Online: 24 May 2020 (19:07:56 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201811.0448.v1

Ultra Low Temperature Process Effects on Micro-Scale Abrasion of Tool Steel AISI D2

Sílvio José Gobbi, Vagner João Gobbi, Gustavo Reinke

Subject: Engineering, Mechanical Engineering Keywords: Micro-Scale Abrasion; Ultra Low Temperature Process (ULTP) Tool Steel AISI D2;

Online: 19 November 2018 (10:32:44 CET)

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Preprint ARTICLE | doi:10.20944/preprints201809.0272.v1

A Genome Model to Explain Major Features of Neurodevelopmental Disorders

Bernard Friedenson

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Keywords: 1; genome 2; epigenetics 3; neurodevelopmental disorders; 4; chromosome anomalies; 5; retrotransposon; 6; chromosome rearrangement; 7; neurologic disease; 8; birth defects; 9; development 10; infection

Online: 15 September 2018 (18:07:03 CEST)

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Abstract: The purpose of this study was to understand the role of infection in the origin of chromosomal anomalies linked to neurodevelopmental disorders. In patients with neurodevelopmental disorders, DNA’s from viruses and bacteria including known teratogens were tested against chromosome anomalies known to cause the disorders. Results support a theory that parental infections disrupt elaborate multi-system gene coordination needed for neurodevelopment. Genes essential for neurons, lymphatic drainage, immunity, circulation, angiogenesis, barriers, structure, and chromatin activity were all found close together in polyfunctional clusters that were deleted in neurodevelopmental disorders. These deletions account for immune, circulatory, and structural deficits that accompany neurologic deficits. In deleted clusters, specific and repetitive human DNA matched infections and passed rigorous artifact tests. In some patients, epigenetic driver mutations were found and may be functionally equivalent to deleting a cluster or changing topologic chromatin interactions because they change access to large chromosome segments. In three families, deleted DNA sequences were associated with intellectual deficits and were not included in any database of genomic variants. These sequences were thousands of bp and unequivocally matched foreign DNAs. Analogous homologies were also found in chromosome anomalies of a recurrent neurodevelopmental disorder. Viral and bacterial DNAs that match repetitive or specific human DNA segments are thus proposed to interfere with highly active break repair during meiosis, and sometimes delete polyfunctional clusters, and disable epigenetic drivers. Mis-repaired gametes produce zygotes containing rare chromosome anomalies which cause neurologic disorders and accompanying non-neurologic signs. Neurodevelopmental disorders may be examples of assault on the human genome by foreign DNA with some infections more likely tolerated because they resemble human DNA segments. Further tests of this model await new technology.

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 ARTICLE | doi:10.20944/preprints202104.0353.v1

The Clampdown Effect: On The Expulsion of Super-Intelligence

Deep Bhattacharjee

Subject: Computer Science And Mathematics, Artificial Intelligence And Machine Learning Keywords: WEAK Clampdown Effect, STRONG Clampdown Effect, KARDASHEV Scale, ERROR Processing, EXTRAVAGENT Curiosity, SOFT Singularity, HARD Singularity, ERROR Approximation

Online: 13 April 2021 (12:58:00 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201907.0169.v1

Genomic Analysis of the Polyvalent Bacteriophage FP01

Ignacio Vasquez, Julio Retamales, Barbara Parra, James Robeson, Javier Santander

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: polyvalent bacteriophage FP01, Escherichia coli, Salmonella, genome

Online: 12 July 2019 (13:07:09 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/preprints201908.0116.v1

Matchmr: Exploring the Effects of Scale and Color Differences on Users’ Perception in Mixed Reality Devices

Kwang-seong Shin, Howon Kim, Dongsik Jo

Subject: Computer Science And Mathematics, Hardware And Architecture Keywords: mixed-reality; perception; scale; color; HMD

Online: 9 August 2019 (04:25:07 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/preprints201804.0138.v1

An Assessment of Wind Power Generation Potential of Built Environment Wind Turbine (BEWT) Systems in Fort Beaufort, South Africa

Terrence Manyeredzi, Golden Makaka

Subject: Engineering, Energy And Fuel Technology Keywords: distributed system; power density; renewable energy; sustainability; utility scale; wind resource

Online: 11 April 2018 (06:07:49 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202012.0421.v1

Detection of Whole Genome Selection Signatures of Pakistani Teddy Goat

Rashid Saif, Jan Henkel, Tania Mahmood, Aniqa Ejaz, Fraz Ahmed, Saeeda Zia

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: Whole genome pooled-seq; Pakistani Teddy goat; Genomic selection signatures

Online: 17 December 2020 (09:13:29 CET)

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Preprint REVIEW | doi:10.20944/preprints202111.0170.v3

A Deep Dive into Genome Assemblies of Non-vertebrate Animals

Nadège Guiglielmoni, Ramón Rivera-Vicéns, Romain Koszul, Jean-François Flot

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: genome assembly; sequencing; non-vertebrate animals

Online: 5 May 2022 (10:38:09 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202101.0526.v1

Genome Features of Asaia sp. W12 Isolated from the Mosquito Anopheles stephensi Reveal Symbiotic Traits

Shicheng Chen, Ting Yu, Nicolas Terrapon, Bernard Henrissat, Edward Walker

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: Asaia; paratransgenesis; symbiotic traits; Anopheles stephensi; genome features

Online: 26 January 2021 (08:19:00 CET)

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Preprint REVIEW | doi:10.20944/preprints202012.0044.v1

Integrins Within the Tumor Microenvironment: Biological Functions and Advances in Therapeutic Targeting

Kevin Dzobo

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: Integrins; Tumor Microenvironment; Drug Resistance; Migration; Metastasis; Solid Tumors; The Cancer Genome Atlas; Gene Expression; Computational Biology; Therapeutic Targeting

Online: 1 December 2020 (18:26:11 CET)

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Many cellular functions important for tumor initiation and progression are mediated by members of the integrin family, a diverse family of cell adhesion receptors. With recent studies emphasising on the role of the tumor microenvironment (TME) in tumor initiation and progression, it is not surprising that a lot of attention is being given to integrins. Several integrins are under trial with many demonstrating appealing activity in patients with different cancers. A deeper knowledge of the functions of integrins within the tumor microenvironment is still required, and might lead to better inhibitors being discovered. Integrin expression is commonly dysregulated in many tumors with integrins playing key roles in signaling as well as promotion of tumor cell invasion and migration. This review report new data on the differential expression of integrins within solid tumors using two publicly available resources: The Cancer Genomic Atlas (TCGA) and Gene Expression Profiling Interactive Analysis (GEPIA). In this analysis, I investigated the expression of integrin alpha 2 (ITGα2), ITGα3, ITGβ4 and ITGβ6 in tumor tissues versus adjacent normal tissues. This analysis showed that integrins were differentially expressed in cervical squamous cell carcinoma (CESC), head and neck squamous cell carcinoma (HNSC), esophageal carcinoma (ESCA) and lung adenocarcinoma (LUAD). This analysis showed that ITGα2 and ITGβ6 expression are upregulated in CESC and ESCA, ITGα3 is upregulated in HNSC and ESCA whilst ITGβ4 is highly expressed in CESC, HNSC, ESCA and LUAD tumor tissues compared to adjacent normal tissues. Integrins also play a major role in adhesion of circulating tumor cells to new sites and the resulting formation of secondary tumors. Furthermore, integrins have demonstrated the ability to promoting stem cell-like properties in tumor cells as well as drug resistance. Anti-integrin therapies rely heavily on the doses or concentrations used as these determine whether the drugs act as antagonists or as integrin agonists. This review offers the latest synthesis in terms of current knowledge of integrins functions within the tumor microenvironment and potential targets for different cancers.

Preprint REVIEW | doi:10.20944/preprints201807.0029.v1

Mapping Agricultural Ecosystem Services across Scales

Shubhechchha Sharma, Jennifer Hodbod, Emma Tebbs, Kristofer Chan

Subject: Social Sciences, Geography, Planning And Development Keywords: ecosystem services; agricultural systems; mapping; values; cross-scale; participatory; local

Online: 3 July 2018 (08:16:24 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202002.0281.v1

Extracellular Oncosomes Rich in Moonlighting Metalloproteinase (MMP3) Are Transmissive, Pro-Tumorigenic, and Induces Cellular Communication Network Factor 2 (CCN2/CTGF): CRISPR against Cancer

Yuka Okusha, Takanori Eguchi, Manh Tien Tran, Chiharu Sogawa, Kaya Yoshida, Mami Itagaki, Eman Ahmed Taha, Kisho Ono, Eriko Aoyama, Hirohiko Okamura, Ken-ichi Kozaki, Stuart K. Calderwood, Masaharu Takigawa, Kuniaki Okamoto

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: matrix metalloproteinase (MMP); moonlighting metalloproteinase; extracellular vesicles; oncosome; genome editing; cell communication network factor 2 (CCN2/CTGF); transcription factor; cancer

Online: 19 February 2020 (11:52:42 CET)

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Preprint ARTICLE | doi:10.20944/preprints202204.0005.v1

Metabolomic Comparison Using Streptomyces spp as a Factory of Secondary Metabolites

Rene Flores Clavo, Alana Kelyene Pereira, Nataly Ruiz Quiñones, Jonas Henrique Costa, Taícia Pacheco Fill, Fabiana Fantinatti Garboggini

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: genome mining; marine environments; molecular networking; bacterial extremophiles; secondary metabolites

Online: 1 April 2022 (10:21:11 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201810.0638.v1

Whole Chloroplast Genome Characterization and Comparison of Two Sympatric Species in Genus Hippophae (Elaeagnaceae)

Luoyun Wang, Jing Wang, Caiyun He, Jianguo Zhang, Yanfei Zeng

Subject: Biology And Life Sciences, Plant Sciences Keywords: Chloroplast genome; H. gyantsensis; H. rhamnoides subsp. yunnanensis; Ka/ks; Optimal codons

Online: 26 October 2018 (15:40:04 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201804.0296.v1

Study on the Construction of Landscape Ecological Classification System for Large-Scale Coal-Power Base in Semi-Arid Steppe Region

Zhenhua Wu, Shaogang Lei, Zhengfu Bian

Subject: Environmental And Earth Sciences, Environmental Science Keywords: semi-arid steppe region; large-scale coal-power base; landscape ecological classification

Online: 23 April 2018 (12:48:59 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202003.0181.v1

Comparative Plastomics of Ashwagandha (Withania, Solanaceae) and Identification of Mutational Hotspots for Barcoding Medicinal Plants

Furrukh Mehmood, Abdullah ., Zartasha Ubaid, Yiming Bao, Peter Poczai, Bushra Mirza

Subject: Biology And Life Sciences, Plant Sciences Keywords: Ashwagandha; Chloroplast Genome; InDels; Medicinal plants; Mutational hotspots; Phylogenomics; Solanaceae; Substitutions; Withania

Online: 11 March 2020 (10:21:56 CET)

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Working Paper REVIEW

Machine Learning of Spatial Data

Behnam Nikparvar, Jean-Claude Thill

Subject: Social Sciences, Geography, Planning And Development Keywords: spatial machine learning; spatial dependence; spatial heterogeneity; scale; spatial observation matrix; learning algorithm; deep learning

Online: 6 August 2021 (14:18:55 CEST)

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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/preprints202104.0788.v1

Genome-Scale Metabolic Model of Infection with SARS-CoV-2 Mutants Confirms Guanylate Kinase as Robust Potential Antiviral Target

Alina Renz, Lina Widerspick, Andreas Dräger

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: SARS-CoV-2; COVID-19; Flux Balance Analysis (FBA); Genome-Scale Metabolic Models; Target Identification; Reaction Knock-Out; Structural Proteins; Purine Metabolism; Pyrimidine Metabolism; B.1.1.7; B.1.351

Online: 30 April 2021 (15:14:06 CEST)

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Working Paper REVIEW

Discoveries and Biological Implications of Mammalian 45S rDNA Variants and Non-Structural rRNAs

Yih-Horng Shiao

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Ribosomal DNA; ribosomal RNA; mammalian genome; intra- and inter-individual variations; development; diseases.

Online: 26 February 2021 (11:35:55 CET)

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Preprint ARTICLE | doi:10.20944/preprints201904.0085.v2

Meta-Analysis of Cancer Triploidy: Whole-Genome Rearrangements in Male Human Tumours Are Characterised by XXY Karyotypes

Ninel M. Vainshelbaum, Pawel Zayakin, Regina Kleina, Alessandro Giuliani, Jekaterina Erenpreisa

Subject: Biology And Life Sciences, Cell And Developmental Biology Keywords: cancer near-triploidy; male tumours; karyotype meta-analysis; XXY; whole genome rearrangements; digyny

Online: 14 July 2019 (09:25:18 CEST)

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Preprint REVIEW | doi:10.20944/preprints201912.0128.v1

Comparative Analysis of Risk Management Techniques for Large-Scale Systems

Mehreen Sirshar, Aliya Shahid, Zoya Alam

Subject: Engineering, Control And Systems Engineering Keywords: large scale systems; risk assessment; risk management techniques; risk mitigation

Online: 10 December 2019 (07:14:12 CET)

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Preprint ARTICLE | doi:10.20944/preprints201905.0331.v1

On the Role of Electric Vehicles towards Low-Carbon Energy Systems: Italy and Germany in Comparison

Sara Bellocchi, Kai Klöckner, Michele Manno, Michel Noussan, Michela Vellini

Subject: Engineering, Energy And Fuel Technology Keywords: large-scale RES; curtailments; electric vehicles; EnergyPLAN; integrated energy systems analysis; CO2 emissions

Online: 28 May 2019 (10:33:27 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202201.0273.v1

What Makes Small-Scale Fishers Resilient? Lessons from the Coping Strategies under COVID-19 Outbreak Observed in Trang Province, Thailand

Yuki Arai, Maneewan Sanlee, Misato Uehara, Shimpei Iwasaki

Subject: Biology And Life Sciences, Aquatic Science Keywords: small-scale fishers; resilience; Adaptive Cycle Model; Sustainable Livelihood Framework; COVID-19; coping strategy; alternative livelihood; Trang Province; Thailand

Online: 19 January 2022 (14:20:19 CET)

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Preprint ARTICLE | doi:10.20944/preprints202001.0336.v1

The effect of Autonomy-Supportive Patient-Centered Communication on Health Literacy: Exploring the Mediating Role of the Patient Health Engagement Model

Serena Barello, Lorenzo Palamenghi, Guendalina Graffigna

Subject: Social Sciences, Psychology Keywords: health literacy; patient health engagement model; Health Care Climate Questionnaire; patient autonomy; PHE-s; Patient Health Engagement Scale; health communication; patient centered communication; patient engagement

Online: 28 January 2020 (10:29:43 CET)

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Preprint ARTICLE | doi:10.20944/preprints202109.0051.v1

Genetic Knockouts Indicate That the ABCC2 Gene in the Bollworm Helicoverpa Zea Is Not a Major Receptor for the Cry1Ac Insecticidal Protein.

Omaththage P. Perera, Nathan S LIttle, Heba Abdelgaffar, Juan Luis Jurat-Fuentes, Gadi V. P. Reddy

Subject: Biology And Life Sciences, Insect Science Keywords: Helicoverpa zea; Bollworm; CRISPR; Cry1A; Bt Toxin; Genome Editing; Knockout; Functional Genomics; Resistance

Online: 3 September 2021 (08:19:44 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202007.0144.v1

Molecular Tracing of SARS-CoV-2 in Italy in the First Three Months of the Epidemic

Alessia Lai, Annalisa Bergna, Sara Caucci, Nicola Clementi, Ilaria Vicenti, Filippo Dragoni, Anna Maria Cattelan, Stefano Menzo, Angelo Pan, Annapaola Callegaro, Adriano Tagliabracci, Arnaldo Caruso, Francesca Caccuri, Silvia Ronchiadin, Claudia Balotta, Maurizio Zazzi, Emanuela Vaccher, Massimo Clementi, Massimo Galli, Gianguglielmo Zehender

Subject: Biology And Life Sciences, Virology Keywords: phylodynamic analyses; SARS-CoV2 circulation in Italy; molecular tracing; Whole Genome Sequencing

Online: 8 July 2020 (11:00:19 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201808.0243.v1

Validation of the SM-GIBED Scale: Attitudes of Emergency and Mental Health Nurses about Alcoholics and other Drug-Dependent Patients

Jesús Molina-Mula, Antonio González-Trujillo

Subject: Social Sciences, Sociology Keywords: alcoholism; health professionals’ attitudes; social perception; Seaman-Mannello scale; validation

Online: 14 August 2018 (05:42:32 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202012.0311.v1

Resource Interaction in Smallholder Farms is Linked to Farm Sustainability: Evidence from Indian Sundarbans

Rupak Goswami, Sonja Brodt, Sangita Patra, Purnabha Dasgupta, Biswanath Mukherjee, Somen Nandi

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: resource integration; network analysis; sustainability; small-scale farm

Online: 14 December 2020 (09:26:08 CET)

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Preprint REVIEW | doi:10.20944/preprints202311.0461.v1

Ten Quick Tips for Accurate Reconstruction of Prokaryotic and Eukaryotic Genome-Scale Metabolic Models

Gabriela Canto-Encalada, Jenna Armstrong, Carlos Focil-Espinosa4, Ademikanra Adekunle-Fiyin, Ila Peeler, William R. Gebbie, Julio Nunez-Garcia, Alexis Saldivar, Diego Martinez, Cristal Zuniga

Subject: Biology And Life Sciences, Other Keywords: Genome-scale metabolic model reconstruction; manual curation; quick tips; systems biology

Online: 7 November 2023 (14:59:34 CET)

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Preprint ARTICLE | doi:10.20944/preprints201809.0094.v1

Marketing Arrangements Used by Small Scale Bean Farmers in Kenya: What Needs to Change for Sustainable Trade Volumes?

Simon Wanjala P.O., David Karanja, scholastica Wambua, George Otiep, Collins Odhiambo, Eliud Birachi

Subject: Business, Economics And Management, Marketing Keywords: Small-scale bean farmers, marketing arrangements, formal and informal marketing, intensification models

Online: 5 September 2018 (11:30:25 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201811.0508.v1

Muller’s Ratchet and Ribosome Degeneration in the Obligate Intracellular Parasites Microsporidia

Sergey Melnikov, Kasidet Manakongtreecheep, Keith Rivera, Arthur Makarenko, Darryl Pappin, Dieter Söll

Subject: Biology And Life Sciences, Parasitology Keywords: Muller's ratchet; genome decay; ribosome; protein synthesis, rudiment

Online: 20 November 2018 (16:30:43 CET)

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Preprint ARTICLE | doi:10.20944/preprints202108.0312.v1

Characterization of Komagataeibacter Isolate Reveals New Prospects on Waste Stream Valorization for Bacterial Cellulose Production

Pietro Cannazza, Antti Rissanen, Dieval Guizelini, Pauli Losoi, Essi Sarlin, Diego Romano, Ville Santala, Rahul Mangayil

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Komagataeibacter rhaeticus; Bacterial cellulose; Crude glycerol; Minimal medium; Whole-genome analysis; Acetate

Online: 16 August 2021 (08:32:19 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201810.0635.v1

Improving the Accuracy of Open Source Digital Elevation Models with Multi-scale Fusion and Slope Position-Based Linear Regression Method

Yu Tian, Shaogang Lei, Zhegnfu Bian, Jie Lu, Shubi Zhang, Jie Fang

Subject: Environmental And Earth Sciences, Remote Sensing Keywords: DEM fusion; multi-scale analysis; WT; BEMD; N-AMD

Online: 26 October 2018 (15:26:12 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201810.0542.v1

Emergent Scale Invariance and Climate Sensitivity

Rypdal Martin, Hege-Beate Fredriksen, Eirik Myrvoll-Nilsen, Sigrunn H. Sørbye, Kristoffer Rypdal

Subject: Environmental And Earth Sciences, Geophysics And Geology Keywords: Climate sensitivity; scale invariance; long-range persistence; climate variability; emergent constrains

Online: 23 October 2018 (15:59:17 CEST)

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Working Paper REVIEW

Advances in Engineering CRISPR-Cas9 as a Molecular Swiss Army Knife

Grace A. Meaker, Emma J. Hair, Thomas E. Gorochowski

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: synthetic biology; CRISPR; Cas9; biotechnology; biodesign; nickase; base editing; prime editing; genome editing; ethics; responsible innovation

Online: 1 October 2020 (08:38:22 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201808.0464.v1

Post-partum Depression in Mothers of Children under 2 years in Military Barracks in Lagos, Nigeria

Alero Ann Roberts, Chisa Mariam Nworka, Esther Oluwakemi Oluwole, Ezekiel Sofela Oridota

Subject: Medicine And Pharmacology, Psychiatry And Mental Health Keywords: Postpartum depression, Edinburgh Postpartum Depression Scale, general help-seeking, mothers, military barracks

Online: 27 August 2018 (14:59:46 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201811.0297.v1

Development of a Transformation Method for Metschnikowia borealis and Other CUG-Serine Yeasts

Zachary Gordon, Maximillian P. M. Soltysiak, Christopher Leichthammer, Jasmine A. Therrien, Rebecca S. Meaney, Carolyn Lauzon, Matthew Adams, Dong Kyung Lee, Preetam Janakirama, Marc-Andre Lachance, Bogumil J. Karas

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: genome engineering; synthetic biology; yeasts; Metschnikowia; genetic tools; DNA delivery; CUG-Ser

Online: 13 November 2018 (05:17:45 CET)

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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 REVIEW | doi:10.20944/preprints202101.0110.v2

Induced Polyploidy: A Tool for Forage Species Improvement

Saeed Rauf, Rodomiro Ortiz, Dariusz Malinowski, Wellington Clarindo, Wardah Kainat, Muhammad Shehzad, Ummara Waheed, Syed Wasim Hassan

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: Amphiploidy; Disomic Polyploidy; Plant Genome Evolution; Neo-polyploidy; Polysomic Polyploidy

Online: 23 February 2021 (14:25:28 CET)

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Preprint ARTICLE | doi:10.20944/preprints202104.0607.v1

A Dual-Color Tyr-FISH Method for Visualizing Genes/Markers on Plant Chromosomes to Create Integrated Genetic and Cytogenetic Maps

Natalya Kudryavtseva, Aleksey Ermolaev, Gennady Karlov, Ilya Kirov, Masayoshi Shigyo, Shusei Sato, Ludmila Khrustaleva

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Tyr-FISH; plant chromosome preparation; recombinant and cytogenetic maps; transcript-based markers; genome assembly; Allium cepa

Online: 22 April 2021 (12:19:32 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201910.0096.v1

Test of a Modified Rainfall-runoff Model in Large-scale River Basins

Spyros Giakoumakis, Dimitris Tigkas

Subject: Environmental And Earth Sciences, Water Science And Technology Keywords: Rainfall-runoff model; large-scale river basins; calibration; validation

Online: 9 October 2019 (10:16:32 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201906.0310.v1

Insights into the Diversity of Secondary Metabolites of Planktothrix Using a Biphasic Approach Combining Global Genomics and Metabolomics

Sanrda Kim Tiam, Muriel Gugger, Justine Demay, Severine Le Manach, Charlotte Duval, Cecile Bernard, Benjamin Marie

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: cyanobacteria; secondary metabolite; genome mining; molecular networking

Online: 30 June 2019 (10:42:22 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201910.0154.v1

Whole Genome Sequencing of Familial Non-Medullary Thyroid Cancer Identifies Germline Alterations in MAPK/ERK and PI3K/AKT Signaling Pathways

Aayushi Srivastava, Abhishek Kumar, Sara Giangiobbe, Elena Bonora, Kari Hemminki, Asta Försti, Obul Reddy Bandapalli

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: papillary thyroid cancer; germline mutations; whole genome sequencing; predisposition markers; pathway analysis

Online: 13 October 2019 (17:07:34 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202107.0094.v1

Chloroplast Genome of Phyllanthus Emblica and Leptopus Cordifolius: Comparative Analysis and Phylogenetic within Family Phyllanthaceae

Umar Rehman, Nighat Sultana, Abdullah ., Abbas Jamal, Maryam Muzaffar, Peter Poczai

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Phyllanthaceae; Phyllanthus; Leptopus; transition and transversion substitutions; chloroplast genome; phylogenetic; polymorphic loci; rps16 loss; atpF intron loss

Online: 5 July 2021 (12:03:13 CEST)

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Family Phyllanthaceae is one of the largest segregates of the eudicot order Malpighiales and its species are herb, shrub, and tree, which are mostly distributed in tropical regions. Certain taxonomic discrepancies exist at genus and family level. Here, we report chloroplast genomes of three Phyllanthaceae species—Phyllanthus emblica, Flueggea virosa, and Leptopus cordifolius— and compare them with six others previously reported Phyllanthaceae chloroplast genomes. The species of Phyllanthaceae displayed quadripartite structure, comprising inverted repeat regions (IRa and IRb) that separate large single copy (LSC) and small single copy (SSC) regions. The length of complete chloroplast genome ranged from 154,707 bp to 161,093 bp; LSC from 83,627 bp to 89,932 bp; IRs from 23,921 bp to 27,128 bp; and SSC from 17,424 bp to 19,441 bp. Chloroplast genomes contained 111 to 112 unique genes, including 77 to 78 protein-coding, 30 transfer RNA (tRNA), and 4 ribosomal RNA (rRNA) that showed similarities in arrangement. The number of protein-coding genes varied due to deletion/pseudogenization of rps16 genes in Baccaurea ramiflora and Leptopus cordifolius. High variability was seen in number of oligonucleotide repeats while analysis of guanine-cytosine (GC) content, codon usage, amino acid frequency, simple sequence repeats analysis, synonymous and non-synonymous substitutions, and transition and transversion substitutions showed similarities in all Phyllanthaceae species. We detected a higher number of transition substitutions in the coding sequences than non-coding sequences. Moreover, the high number of transition substitutions was determined among the distantly related species in comparison to closely related species. Phylogenetic analysis shows the polyphyletic nature of the genus Phyllanthus which requires further verification. We also determined suitable polymorphic coding genes, including rpl22, ycf1, matK, ndhF, and rps15 which may be helpful for the reconstruction of the high-resolution phylogenetic tree of the family Phyllanthaceae using a large number of species in the future. Overall, the current study provides insight into chloroplast genome evolution in Phyllanthaceae.

Preprint ARTICLE | doi:10.20944/preprints202107.0311.v1

Genome-Wide Identification and Expression Analysis of Sucrose Nonfermenting-1-Related Protein Kinase (SnRK) Genes in Triticum aestivum in Response to Abiotic Stress

Shefali Mishra, Pradeep Sharma, Rajender Singh, ratan Tiwari, Gyanendra Pratap Singh

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: Genome-wide; SnRK and abiotic stress.; wheat

Online: 13 July 2021 (15:11:54 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202103.0682.v1

Modelling Small-scale Storage Interventions in Semi-Arid India at the Basin Scale

Robyn Horan, Pawan Wable, Veena Srinivasan, Helen Baron, Virginie D. J. Keller, Kaushal K. Garg, Nathan Rickards, Mike Simpson, Helen Houghton-Carr, Gwyn Rees

Subject: Environmental And Earth Sciences, Environmental Science Keywords: semi-arid hydrology, small-scale storage, checkdams, tanks, farm bunds, Cauvery, GWAVA

Online: 29 March 2021 (11:22:07 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201805.0415.v1

The Use of Colors as an Alternative to Size in Mold Growth Studies

Edgar Cambaza, Shigenobu Koseki, Shuso Kawamura

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Fusarium graminearum, mycelial growth, RGB, gray scale.

Online: 28 May 2018 (16:31:22 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201903.0117.v1

An Accelerating and Rotating Planck-Hubble Universe (A Very Simple Model of Quantum Cosmology)

U. V. S. Seshavatharam, S. Lakshminarayana

Subject: Physical Sciences, Nuclear And High Energy Physics Keywords: planck scale; quantum cosmology; critical density; ordinary matter; dark matter; expansion velocity; angular velocity; Hubble’s law;

Online: 11 March 2019 (08:01:28 CET)

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Preprint ARTICLE | doi:10.20944/preprints202103.0520.v1

New Image Recognition Technique for Intuitive Understanding in Class of the Dynamic Response of High-Rise Buildings

Rocío Porras Soriano, Behnam Mobaraki, José Antonio Lozano-Galant, Santos Sanchez-Cambronero, Federico Prieto Muñoz, Juan José Gutierrez

Subject: Engineering, Automotive Engineering Keywords: Intuitive learning; Dynamic response; Small-scale model; Image-recognition; Shaking table

Online: 22 March 2021 (11:21:47 CET)

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Preprint ARTICLE | doi:10.20944/preprints202004.0472.v1

Open Source Digitally Replicable Lab-Grade Scales

Benjamin R. Hubbard, Joshua M. Pearce

Subject: Chemistry And Materials Science, Analytical Chemistry Keywords: 3-D printing; additive manufacturing; distributed manufacturing; laboratory equipment; open hardware; open source; open source hardware; scale; balance; mass

Online: 27 April 2020 (02:59:34 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/preprints201808.0187.v1

Possibility of Gene Rearrangement between Porcine Rotavirus H and Porcine Rotavirus C in Nonstructural Protein 3

Tohru Suzuki, Daisuke Inoue

Subject: Medicine And Pharmacology, Veterinary Medicine Keywords: Porcine rotavirus H; Porcine rotavirus C; Full genome; Classification; Genotype; Non-structural protein 3; Gene rearrangement

Online: 9 August 2018 (11:38:44 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202103.0403.v1

Glucose-limited Fed-batch Cultivation Strategy to Mimic Large-scale Effects in Escherichia coli Linked to Accumulation of Non-Canonical Branched-Chain Amino Acids by Combination of Pyruvate Pulses and Dissolved Oxygen Limitation

Ángel Córcoles García, Peter Hauptmann, Peter Neubauer

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: non-canonical branched chain amino acids; scale-down; strain screening; mixed-acid fermentation; pyruvate pulse; norvaline; norleucine; fed-batch cultivation; bioreactor; Enpresso; Enbase

Online: 16 March 2021 (09:11:34 CET)

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Working Paper ARTICLE

A New 3D Geological Modeling Method Based On Remote Sensing and Its Application in Ya 'an Area Sichuan Province

Zhaoyang Ma, Lihai Zhang, Yan Wang, Guifan Zhu, Yinping Liang

Subject: Environmental And Earth Sciences, Atmospheric Science And Meteorology Keywords: Multi-source heterogeneity; remote sensing; large-scale high-precision modeling; grid division; geostatistics; spatial interpolation

Online: 20 January 2021 (16:19:34 CET)

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Preprint ARTICLE | doi:10.20944/preprints201806.0459.v1

Fractal Structure and Non Extensive Statistics

Airton Deppman, Eugenio Megias, Debora P. Menezes, Tobias Frederico

Subject: Physical Sciences, Thermodynamics Keywords: fractal structure; non extensive statistics; Tsallis statistics; self-similarity; scale invariance

Online: 28 June 2018 (05:30:41 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201810.0629.v1

Multiscale Hydro-Meteorological Factors Variations and Its Links to Large-Scale Atmospheric Circulation Systems in the Source Region of Yangtze River

Jian Tang, Hui-Qun Cao

Subject: Environmental And Earth Sciences, Atmospheric Science And Meteorology Keywords: hydro-meteorological factors; large-scale atmospheric circulation systems; South Asia monsoon; streamflows; source region of the Yangtze River

Online: 26 October 2018 (11:52:13 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202105.0333.v1

Functional Validation of cas9/guideRNA Constructs for Site-directed Mutagenesis of Triticale ABA8’OH1 loci

Krzysztof Michalski, Christian Hertig, Dariusz Mańkowski, Jochen Kumlehn, Janusz Zimny, Anna M. Linkiewicz

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: genome editing; CRISPR; protoplast; , targeted mutagenesis; TREX2; construct validation; transi-ent expression

Online: 14 May 2021 (13:44:26 CEST)

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Preprint REVIEW | doi:10.20944/preprints202210.0313.v1

The Complex World of Emaraviruses – Challenges, Insights and Prospects

Marius Rehanek, David G. Karlin, Martina Bandte, Rim Al Kubrusli, Shaheen Nourinejhad Zarghani, Thierry Candresse, Carmen Büttner, Susanne Von Bargen

Subject: Biology And Life Sciences, Virology Keywords: diagnosis; distribution; emaraviruses; forest trees; Fimoviridae; genome organization; phylogenetic relations; protein domains; symptomatology; transmission

Online: 20 October 2022 (14:09:37 CEST)

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Preprint REVIEW | doi:10.20944/preprints202402.0461.v1

A Guide for the Bioinformatic Analysis of Metabolomics Data

Guillem Santamaria, Francisco R Pinto

Subject: Biology And Life Sciences, Other Keywords: metabolomics; bioinformatics; workflow; biostatistics; genome-scale metabolic modelling.

Online: 8 February 2024 (09:15:31 CET)

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Preprint ARTICLE | doi:10.20944/preprints202004.0235.v1

Sensitivity of Stomate Size in Red Maple (Acer rubrum L.) Trees in Deciduous Forests to Urban Conditions

Covel R. McDermot, Vince D'Amico, Tara Trammell

Subject: Environmental And Earth Sciences, Environmental Science Keywords: abiotic stress; metro-scale; physiological acclimation; urban leaf morphology; red maple trees; stomate size; urban forests

Online: 15 April 2020 (09:32:30 CEST)

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Preprint ESSAY | doi:10.20944/preprints201910.0354.v1

A Perceptive Scale Toolkit for Navigating Across Length Scales

Ipsa Jain, Minhaj Sirajuddin

Subject: Biology And Life Sciences, Biophysics Keywords: science communication; scale; education; toolkit

Online: 30 October 2019 (09:31:14 CET)

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Preprint REVIEW | doi:10.20944/preprints201912.0385.v1

Genome Editing for the Understanding and Treatment of Cardiomyopathies

Quynh Nguyen, Kenji Rowel Q. Lim, Toshifumi Yokota

Subject: Medicine And Pharmacology, Cardiac And Cardiovascular Systems Keywords: dilated cardiomyopathy (DCM); hypertrophic cardiomyopathy (HCM); restrictive cardiomyopathy (RCM); arrhythmogenic right ventricular cardiomyopathy (ARVC); left ventricular non-compaction cardiomyopathy (LVNC); Duchenne muscular dystrophy; dystrophin; genome editing; CRISPR/Cas9; Cpf1 (Cas12a)

Online: 29 December 2019 (13:41:48 CET)

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Preprint ARTICLE | doi:10.20944/preprints201806.0062.v1

Optimization of Planting Structure for Irrigation Area with Biannual Cropping Patterns in Xinjiang Oasis in China

Bing Liu, Zhenhua Wang

Subject: Environmental And Earth Sciences, Environmental Science Keywords: optimization of planting structure; biannual cropping pattern; arid oasis irrigation area; moderate scale; benefit of unilateral water use

Online: 5 June 2018 (11:08:42 CEST)

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Light and heat resources are ample in Xinjiang plain oasis region. Planting structure is single in irrigation area, which leads to severe seasonal water shortages due to high concentration of water utilization. Therefore, how to make full use of light and heat resources to develop oasis agriculture without expanding planting scale has become the focus of research. The biannual cropping patterns are possible solutions to the problem. Manas River Irrigation area, which is located on the northern slope of Tianshan Mountain in Xinjiang in China is regarded as a typical case study to analyze the suitable planting structure and planting scale for biannual cropping pattern. The effects of optimizing planting patterns on alleviating the contradiction between water supply and water need，and the efficiency of water resources utilization was also studied. The results of the study show that：(1) the suitable planting scales of Manas River irrigation area in wet year (P = 25%), normal year (P = 50%), and low flow year (P = 75%) are about 72.66%, 78.73% and 83.91% of the current planting scale. (2) After the planting structure was optimized, the water use process in the irrigation area extends from May to August at present to April to November. The water use ratio at the peak period of water use decreased from 0.847 to 0.601, and the water use peak was significantly dispersed. (3) Economic benefits per cubic metre of water of the biannual cropping patterns increased from 8.65 yuan·m⁻³ at present to 9.45 yuan·m⁻³, 10.31 yuan·m⁻³and 11.43 yuan·m⁻³in wet year (P = 25%), in normal year (P = 50%) and low flow year (P = 75%) respectively, which proved that replanting crops could improve the efficiency of water resources utilization in irrigated areas. Therefore, the optimal planting pattern can be implemented to improve the utilization efficiency of soil and water resources in irrigation area in the arid oasis with single planting pattern with excessive concentration of water use peak and serious water shortage.

Preprint ARTICLE | doi:10.20944/preprints202101.0544.v2

Gravitation with Cosmological Term, Expansion of the Universe as Uniform Acceleration in Clifford Coordinates

Alexander Kritov

Subject: Physical Sciences, Mathematical Physics Keywords: Clifford algebras Cl(3,0) and Cl(0,3); center of Cl(3); two dimensional spacetime of time-volume; constant uniform acceleration; Rindler coordinates; FLRW metric; scale factor; AdS and de Sitter models

Online: 5 February 2021 (10:13:00 CET)

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Preprint ARTICLE | doi:10.20944/preprints202205.0225.v1

Revealing the Complete Chloroplast Genome of an Andean Horticultural Crop, Sweet Cucumber (Solanum muricatum), and Its Comparative Analysis with Other Solanaceae Species

Carla L. Saldaña, Julio C. Chávez-Galarza, Germán De la Cruz, Jorge H. Jhoncon, Juan C. Guerrero-Abad, Héctor V. Vásquez, Jorge L. Maicelo, Carlos I. Arbizu

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: chloroplast; genome; sweet cucumber; Solanaceae; next-generation sequencing

Online: 17 May 2022 (08:38:03 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202105.0770.v1

Prediction of Peak Friction Angle using Photogrammetry and Comparison to Shear Test Results of Metric Scale Rock Fractures

Lauri Uotinen, Masoud Torkan, Alireza Baghbanan, Enrique Caballero Hernández, Mikael Rinne

Subject: Engineering, Automotive Engineering Keywords: shear test; scale effect; roughness; photogrammetry; friction angle

Online: 31 May 2021 (12:35:04 CEST)

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Preprint REVIEW | doi:10.20944/preprints202107.0045.v1

Insights Gained from Genomic Studies on the Role of Sex Steroids in the Aetiology of Endometriosis

Philippa TK Saunders

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: genome wide association studies (GWAS); single nucleotide polymorphism (SNP); oestrogen; ESR1; HOXA10

Online: 2 July 2021 (09:59:27 CEST)

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Endometriosis is a chronic neuro-inflammatory disorder the defining feature of which is the growth of tissue (lesions) that resembles the endometrium in sites outside the uterus. Estimates of prevalence typically quote rates of ~10% of women of reproductive age, equating to ~190 million women world-wide. Three subtypes of endometriosis are usually considered when discussing the aetiology of the disorder - superficial peritoneal, ovarian (endometrioma cysts), and deep (infiltrating). Genetic, hormonal and immunological factors have all been proposed as contributing to risk factors associated with the development of lesions. Twin studies report the heritable component of endometriosis as ~50%. Genome wide association studies (GWAS) have been conducted allowing unbiased scanning of the genome for single nucleotide polymorphisms (SNPs) in many thousands of individuals. These studies have identified SNPs that appear over-represented in patients with endometriosis, particularly those with more extensive disease (stage III/IV). Amongst the larger scale GWAS there has been replication of SNPs near genes involved in oestrogen and other signalling pathways including ESR1 (oestrogen receptor alpha), GREB1, HOXA10, WNT4 and MAPK kinase signalling. The results from patients with endometriosis have also provided an opportunity to make comparisons with GWAS conducted on other patient cohorts including those with reproductive traits (age at menarche) and disorders (fibroids, endometrial and ovarian cancer) and conditions that are reported by women with endometriosis (migraine, depression). These comparative studies have highlighted some shared genetically-controlled biological mechanisms, including hormone-regulated pathways which might explain the co-occurrence of endometriosis with these disorders. In summary, unbiased genetic analysis has provided new insights into the genetic factors that may contribute to increased risk of developing endometriosis. New studies are needed to broaden the range of patients contributing to these datasets and to improve integration with non-genomic and tissue expression data before their full potential for diagnosis and improvements in patient care can be fully realised.

Preprint REVIEW | doi:10.20944/preprints202011.0603.v1

Current Capabilities, Precision, and Risks of Genome Editing Techniques in Agricultural Systems

Morgan Carter

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: genome editing, agriculture, crispr, talen, specificity, off-target

Online: 24 November 2020 (08:35:00 CET)

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