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Preprint ARTICLE | doi:10.20944/preprints202207.0013.v1

Inorganic Powders Prepared from Fish Scales

Tatiana V. Safronova, Viktor I. Vorobyov, Natalia R. Kildeeva, Tatiana B. Shatalova, Otabek U. Toshev, Yaroslav Yu. Filippov, Artem O. Dmitrienko, Olga Т. Gavlina, Olga P. Chernega, Elena V. Nizhnikova, Marat M. Akhmedov, Konstantin A. Lysenko

Subject: Chemistry And Materials Science, Biomaterials Keywords: fish scale powder; high-speed grinding; heat treatment; hydroxyapatite; magnesium whitlockite; nanosized grain

Online: 1 July 2022 (10:05:25 CEST)

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Preprint REVIEW | doi:10.20944/preprints201810.0329.v1

Modeling of Protein Structural Flexibility and Large-Scale Dynamics: Coarse-grained Simulations and Elastic Network Models

Sebastian Kmiecik, Maksim Kouza, Aleksandra Elzbieta Badaczewska-Dawid, Andrzej Kloczkowski, Andrzej Kolinski

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: protein dynamics; coarse-grained simulation; Monte-Carlo dynamics; structural flexibility; large-scale dynamics; elastic network model;

Online: 15 October 2018 (17:10:57 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/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/preprints202008.0207.v1

The Prevalence and Sociodemographic Correlates of Social phobia in Oman: Online National Survey

Aamal Ambusaidi, Salim Al Huseini, Hiba Alshaqsi, Manal AlGhafri, Moon-Fai Chan, Nasser Al-Sibani, Samir Al-Adawi

Subject: Medicine And Pharmacology, Psychiatry And Mental Health Keywords: Social Anxiety Disorder; Social Phobia, Online Survey; Adult, Oman; Liebowitz Social Anxiety Scale

Online: 8 August 2020 (09:39:49 CEST)

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Preprint REVIEW | doi:10.20944/preprints202210.0034.v1

Current Scenario of Exogenously Induced RNAi for Lepidopteran Agricultural Pest Control: From dsRNA Design to Topical Application

Vívian Lucena-Leandro, Emanuel Abreu, Leonardo Vidal, Caroline Torres, Camila Junqueira, Juliana Almeida, Érika Albuquerque

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: insect; genome; biopesticide; silencing; topical; gene target; validation

Online: 5 October 2022 (10:57:47 CEST)

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Global crop yields are estimated to be reduced by 30–40% per year on account of plant pests and pathogens. Agricultural insect pests raise concerns about constraining global food security and climate changes contributing to the rise of infestation. The current management relies on plant breeding, associated or not with transgenes and chemical pesticides. Both approaches face serious technology obsolescence on the field due to resistance breakdown or development of insecticide resistance. The need for new Modes of Action (MoA) approaches in managing crop health grows each year, driven by market demands to reduce economic losses and phytosanitary requirements to meet the consumer perception. Disabling pest genes by sequence-specific expression silencing is considered a promising tool in the development of environment and health respectful biopesticides. The specificity conferred by long dsRNA-base solutions give support to minimizing effects on off-targeted genes in the insect pest genome and the target gene in non-target organisms (NTOs). In this review, we summarize the current status of gene silencing by RNA interference (RNAi) for agricultural control. More specifically, we focus on the engineering, development and application of gene silencing to control Lepidoptera by the employment of non-transforming dsRNA technologies. Despite some delivery and stability drawbacks of topical applications, we reviewed works showing convincing proof-of-concept results that point to imminent innovative solutions. Considerations about the regulamentation of the ongoing research on dsRNA-based pesticides to produce commercialized products for exogenous application are discussed. Academic and industry initiatives reveal a worthy effort to accomplish controlling Lepidoptera pests with this new mode of action to provide more sustainable and reliable technologies to field management. New data on genomics of this taxon encourage the increment of a customized target genes portfolio. As a case of study, we illustrate how dsRNA and associated methodologies could be applied to control an important Lepidopteran coffee pest.

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/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 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/preprints201910.0147.v1

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

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

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

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

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Preprint ARTICLE | doi:10.20944/preprints201810.0054.v1

Draft Genome of a Bovine Enterovirus recovered from Sewage in Nigeria

Temitope Faleye, Moses Olubusuyi Adewumi, Moses Olubusuyi Adewumi, Olayinka Oluseyi Adebowale, Emmanuel Donbraye, Bolaji Oluremi, Uwem George, Oluwadamilola A Arowolo, Ewean Chukwuma Omoruyi , Maryjoy Ijeoma Ifeorah , Adefunke Oyewumi Oyero, Johnson Adekunle Adeniji

Subject: Biology And Life Sciences, Virology Keywords: Bovine enterovirus, EV-E, Nigeria, Sewage, Complete Genome

Online: 3 October 2018 (14:24:49 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/preprints202107.0197.v1

A Study on Circular Economy Material Using Fish Scales as Natural Flame Retardant and the Properties of Its Composite Materials

Shang-Hao Liu, Ming-Yuan Shen, Cheng-You Yang, Chin-Lung Chiang

Subject: Chemistry And Materials Science, Biomaterials Keywords: fishery waste; epoxy; fish scale; ammonium polyphosphate; flame retardant

Online: 8 July 2021 (11:04:10 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201905.0002.v1

Why the Monophyly of Nymphaeaceae Currently Remains Indeterminate: An Assessment Based on Gene-Wise Plastid Phylogenomics

Michael Gruenstaeudl

Subject: Biology And Life Sciences, Plant Sciences Keywords: codon position; complete chloroplast; early-diverging angiosperms; monophyly; Nymphaeaceae; Nymphaeales; plastid genome; phylogenomics; repeatability

Online: 3 May 2019 (14:03:46 CEST)

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The monophyly of Nymphaeaceae (water lilies) represents a critical question in understanding the evolutionary history of early-diverging angiosperms. A recent plastid phylogenomic investigation claimed new evidence for the monophyly of Nymphaeaceae, but its results could not be verified from the available data. Moreover, preliminary gene-wise analyses of the same dataset provided partial support for the paraphyly of the family. The present investigation aims to re-assess the previous conclusion of the monophyly of Nymphaeaceae under the same dataset and to determine the congruence of the phylogenetic signal across different plastome genes and data partition strategies. To that end, phylogenetic tree inference is conducted on each of 78 protein-coding plastome genes, both individually and upon concatenation, and under four data partitioning schemes. Moreover, the possible effects of various sequence variability and homoplasy metrics on the inference of specific phylogenetic relationships are tested using multiple logistic regression. Differences in the variability of polymorphic sites across codon positions are assessed using parametric and non-parametric analysis of variance. The results of the phylogenetic reconstructions indicate considerable incongruence among the different gene trees as well as the data partitioning schemes. The results of the multiple logistic regression tests indicate that the fraction of polymorphic sites of codon position 3 has a significant effect on the recovery of the monophyly of Nymphaeaceae. Taken together, these results indicate that the monophyly of Nymphaeaceae currently remains indeterminate, and that specific phylogenetic conclusions are strongly dependent on the precise plastome gene, data partitioning scheme, and codon position evaluated. In closing, I discuss the importance of archiving all data of an investigation in publicly accessible data repositories, along with sufficient details to replicate the published results, and provide recommendations on future plastid phylogenomic investigations of Nymphaeales.

Preprint COMMUNICATION | doi:10.20944/preprints202004.0253.v1

Optimizing Open Data to Support One Health: Best Practices to Ensure Interoperability of Genomic Data from Microbial Pathogens

Ruth E. Timme, William J. Wolfgang, Maria Balkey, Sai Laxmi Gubbala Venkata, Robyn Randolph, Marc Allard, Errol Strain

Subject: Biology And Life Sciences, Virology Keywords: Genomic Epidemiology; GenomeTrakr; microbial pathogen surveillance, NCBI submission; whole genome sequencing; QA/QC; One Health

Online: 16 April 2020 (05:26:42 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/preprints201806.0266.v1

Improved Collecting Line Current Protection Scheme against Large-scale Wind Generators Tripping off

Wei Jin, Yuping Lu, Tao Huang

Subject: Engineering, Electrical And Electronic Engineering Keywords: Collecting line current protection (CLPC); coordination protection; large-scale WGs trip-off; risk indicator

Online: 18 June 2018 (13:48:38 CEST)

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There have been several cases of large-scale wind generators (WGs) tripping off caused by untimely fault removing in recent years. Currently, the discoordination between the box-type transformer fuse protection (BTFP) and two-section collecting line current protection (CLCP) brings a security risk to wind farm. In order to ensure the selectivity, the first section (Sec-I) CLCP should be set a enough interval that is longer than the fuse melting time, and another interval is set for the Sec-II CLCP, which weakens the speed of the CLCP. When a fault occurs on the collecting line, there is no doubt that WGs cannot work too long in abnormal operation, which may cause WGs to be placed off the grid. For a power system with high penetration of wind power, large-scale WGs tripping off will cause a great power shortage, and affect the stability of the power system. The selectivity and sensitivity of the CLCP is analyzed in detail to make the CLCP speed better. Considering the fault ride-through ability of WGs, the fault clear time is an important factor to lead to large-scale WGs tripping off. Two main works are done in this paper. The first is to accelerate the speed of the Sec-I CLCP though reducing the protection zone. Another one is introduce the risk assessment module into the CLCP, which not only improve the speed of the CLCP but also ensure the safety of the wind farm during faults. According to the deference in trip-off causes of WGs, the matching functions are created to assess the trip-off risk of WGs on the spot. In the case of fault, the trip-off risk indicators of WGs are timely updated to data sharing center and open to the CLCPs. The set of risk indicators is divided into several subsets according to the risk range. The dynamic changes of the subsets during fault help to improved CLCP scheme. This scheme can accelerate protection speed based on the increasing risk of large-scale WGs tripping off in wind farms. Compared with traditional CLCP, this approach can make the CLCP combines selectivity and speed better based on the analysis of the ride- through ability of WGs.

Working Paper ARTICLE

Structural Entropy Constrains Dynamics in Directed Networks

Blai Vidiella, Salva Duran-Nebreda, Sergi Valverde

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: structural entropy; dimensionality; flow dynamics; spin; directed network; scale-free

Online: 27 January 2021 (15:35:38 CET)

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Preprint REVIEW | doi:10.20944/preprints202005.0058.v1

Towards Engineering Biosystems with Emergent Collective Functions

Thomas E. Gorochowski, Sabine Hauert, Jan-Ulrich Kreft, Lucia Marucci, Namid R. Stillman, T-Y. Dora Tang, Lucia Bandiera, Vittorio Bartoli, Daniel O. R. Dixon, Alex J. H. Fedorec, Harold Fellermann, Alexander G. Fletcher, Tim Foster, Luca Giuggioli, Antoni Matyjaszkiewicz, Scott McCormick, Sandra Montes Olivas, Jonathan Naylor, Ana Rubio Denniss, Daniel Ward

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: synthetic biology; multi-agent modelling; individual-based modelling; agent-based modelling; systems biology; emergence; multi-scale; bioengineering; consortia; collectives

Online: 5 May 2020 (03:45:16 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/preprints202209.0252.v1

Fundamentally Good Alternative to Normal Distribution

Kabir Bindawa Abdullahi

Subject: Computer Science And Mathematics, Probability And Statistics Keywords: alternative parameterization; normal distribution; dispersion estimators; location-invariance; scale-invariance; scale-and-location-invariance

Online: 19 September 2022 (02:06:09 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202111.0557.v1

Naming the Unnamed: Over 45,000 Candidatus Names for Unnamed Archaea and Bacteria in the Genome Taxonomy Database

Mark Pallen, Nabil-Fareed Alikhan

Subject: Biology And Life Sciences, Virology Keywords: Bacterial nomenclature; archaeal nomenclature; genome taxonomy; shotgun metagenomics; Candidatus names

Online: 30 November 2021 (10:53:50 CET)

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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 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 REVIEW | doi:10.20944/preprints202006.0110.v1

An Exploratory Data Analysis on Certified Perovskite Devices Efficiency and I-V Metrics: Insights into Materials Engineering and Process Scaling Up

Jialiu Ma, Da Guo

Subject: Chemistry And Materials Science, Materials Science And Technology Keywords: Perovskite; Solar cell; scale up; efficiency; certification; process

Online: 7 June 2020 (16:42:16 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201906.0132.v1

Economical and Environmental Friendly Methods for Separation of Oil from Mill Scale

Muhammad Shoukat Hussain, Asra Shoukat, Hafiz Syed Umer Nasir, Ammara Shoukat

Subject: Environmental And Earth Sciences, Waste Management And Disposal Keywords: scale; by-product; economical method; environment friendly; zero waste

Online: 14 June 2019 (10:09:59 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201811.0534.v1

Saint Venant and Navier-Stokes Models for Tsunami Simulations

Camille Journeau, Kévin Pons, Richard Marcer

Subject: Engineering, Marine Engineering Keywords: tsunami; CFD; Saint Venant (SV) model; Adaptive Mesh Refinement (AMR); large scale propagation; 3D Navier-Stokes (NS) model; coastal impact

Online: 22 November 2018 (04:43:54 CET)

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Preprint ARTICLE | doi:10.20944/preprints201807.0397.v2

Genome-Wide Association Study and Selection Signatures Detect Genomic Regions Associated with Seed Yield and Oil Quality in Flax

Frank You, Jin Xiao, Pingchuan Li, ZHEN YAO, Gaofeng Jia, Liqiang He, Santosh Kumar, Braulio Soto-Cerda, Scott Duguid, Helen Booker, Khalid Rashid, Sylvie Cloutier

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: flax; genome-wide association study (GWAS); selective sweep; genotyping by sequencing (GBS); bi-parental population; single nucleotide polymorphism (SNP); seed yield; plant height; maturity; fatty acid composition

Online: 3 August 2018 (15:34:24 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202009.0295.v1

Streamline-Based Simulation of Nanoparticle Transport in Field-Scale Heterogeneous Subsurface Systems

Bin Wang, Yin Feng, John Blears, Karsten Thompson, Richard Hughes

Subject: Engineering, Energy And Fuel Technology Keywords: Streamline-based simulation; Nanoparticle transport; Reservoir simulation; Field-scale simulation

Online: 13 September 2020 (16:03:33 CEST)

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Nanoparticle (NP) transport is increasingly relevant to subsurface engineering applications such as aquifer characterization, fracture electromagnetic imaging and environmental remediation. An efficient field-scale simulation framework is critical for predicting NP performance and designing subsurface applications. In this work, for the first time, a streamline-based model is presented to simulate NP transport in field-scale subsurface systems. It considers a series of behaviors exhibited by engineered nanoparticles (NPs), including time-triggered encapsulation, retention, formation damage effects and variable nanofluid viscosity. The key methods employed by the algorithm are streamline-based simulation (SLS) and an operator-splitting (OS) technique for modeling NP transport. SLS has proven to be efficient for solving transport in large and heterogeneous systems, where the pressure and velocity fields are firstly solved on underlying grids using finite-difference (FD) methods. After tracing streamlines, one-dimensional (1D) NP transport is solved independently along each streamline. The adoption of OS enhances flexibility for the entire solution procedure by allowing different numerical schemes to solve different governing equations efficiently and accurately. For the NP transport model, an explicit FD scheme is used to solve the advection term, an implicit FD scheme is used for the diffusion term and an adaptive numerical integration is used to solve the retention terms. The model is implemented in an in-house streamline-based code, which is verified against analytical solutions, a commercial FD reservoir simulator (ECLIPSE) and an academic FD colloid transport code (MNMs). For a 1D homogeneous case, the effluent breakthrough curves (BTC) produced by the in-house simulator are in good agreement with the analytical solution and MNMs, respectively. For a two-dimensional (2D) heterogeneous case, the BTC and concentration pattern of the in-house simulator all match well with the solution produced by commercial simulator. Simulations on a synthetic three-dimensional (3D) nanocapsule application engineering design case, are performed to investigate the effect of fluid and NP properties on the displacement pattern of an existing subsurface fluid.

Preprint ARTICLE | doi:10.20944/preprints202007.0138.v1

Cavitation in Pharmaceutical Manufacturing

Donn Sederstrom, Rafael Valotta Rodrigues, Corinne Lengsfeld

Subject: Medicine And Pharmacology, Medicine And Pharmacology Keywords: hydrodynamic cavitation; cavitation number; turbulence; critical pressure; Kolmogorov length scale

Online: 7 July 2020 (17:37:58 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202201.0006.v1

The differences between the Connor–Davidson Resilience Scale and the Brief Resilience Scale When Assessing Resilience: Confirmatory Factor Analysis and Predictive Effects

Yun-Ci Ye, Chia-Huei Wu, Cheng-Ta Yang

Subject: Social Sciences, Psychology Keywords: resilience; Connor-Davidson Resilience Scale; Brief Resilience Scale; depression; life satisfaction; confirmatory factor analysis

Online: 4 January 2022 (12:34:37 CET)

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Preprint ARTICLE | doi:10.20944/preprints202005.0463.v3

Trends of Mutation Accumulation Across Global SARS-CoV-2 Genomes: Implications for the Evolution of the Novel Coronavirus

Chayan Roy, Santi M Mandal, Suresh K Mondol, Shriparna Mukherjee, Wriddhiman Ghosh, Ranadhir Chakraborty

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: SARS-CoV-2; genome-wide mutations; transition; transversion; nonsynonymous and synonymous mutations; microevolution

Online: 5 October 2020 (10:56:36 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201808.0456.v1

A Multi-Scale Modeling Approach for Simulating Crack Sensing in Polymer Fibrous Composites Using Electrically Conductive Carbon Nanotube Networks. Part II: Meso- and Macro-Scale Analyses

Konstantinos Tserpes, Christos Kora

Subject: Chemistry And Materials Science, Nanotechnology Keywords: Carbon nanotubes; Polymer nanocomposites; Electrical conductivity; Crack sensing; Multi-scale modeling

Online: 27 August 2018 (11:25:23 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201806.0424.v4

A Scale-Invariant, Machian Theory of Gravitation and Electrodynamics Unified

Ram Gopal Vishwakarma

Subject: Physical Sciences, Astronomy And Astrophysics Keywords: Gravitation - Fundamental Problems and General Formalism; Electrodynamics; Scale Invariance; Mach Principle; Dark Energy

Online: 3 October 2018 (15:35:51 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201905.0357.v1

Collision Space-Time. Unified Quantum Gravity. Gravity is Lorentz Symmetry Break Down at the Planck Scale

Espen Haug

Subject: Physical Sciences, Quantum Science And Technology Keywords: Quantum gravity, granular matter, Lorentz symmetry break down at the Planck scale, Heisen- berg uncertainty break down at the Planck scale, indivisible particles, gravity and Lorentz symmetry break down.

Online: 29 May 2019 (16:31:56 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201809.0378.v1

Characterization of Gene Families Encoding Beta-Lactamases of Gram-Negative Rods Isolated from Ready-to-Eat Vegetables in Mexico City

Rosalino Vázquez-López, Sandra Solano-Gálvez, Bertha Aliacia León-Chávez, María del Rocío Thompson-Bonilla, Tayde Guerrero-González, Eduardo Gómez-Conde, Daniel Martínez-Fong, Juan-Antonio González-Barrios

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: enterobacteriaceae; antibiotics; beta-lactamases; beta-lactam resistome; whole genome sequencing

Online: 19 September 2018 (09:47:42 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201808.0539.v1

Genotype Fingerprints Enable Fast and Private Comparison of Genetic Testing Results for Research and Direct-to-Consumer Applications

Max Robinson, Gustavo Glusman

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: computational genomics; genome comparison; algorithms; genetic testing; privacy; direct-to-consumer; study design; population genetics

Online: 31 August 2018 (04:59:28 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 CONCEPT PAPER | doi:10.20944/preprints202010.0160.v1

The Next Million Names for Archaea and Bacteria

Mark J. Pallen, Andrea Telatin, Aharon Oren

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: nomenclature; Candidatus; metagenome-assembled genomes; genome-based taxonomy

Online: 7 October 2020 (15:08:01 CEST)

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Working Paper ARTICLE

Effect of Interlayer Cooling Time, Constraint and Tool Path Strategy on Deformation of Large Components made by Laser Metal Deposition with Wire

Yousub Lee, Yashwanth Bandari, Peeyush Nandwana, Brian Gibson, Brad Richardson, Srdjan Simunovic

Subject: Engineering, Mechanical Engineering Keywords: large-scale additive manufacturing; interlayer cooling time; tool path optimization; part deformation; Ti-6Al-4V

Online: 10 November 2019 (09:04:24 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 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/preprints201906.0106.v2

Cheating in the Viral World

Asher Leeks, Stuart A. West, Melanie Ghoul

Subject: Biology And Life Sciences, Virology Keywords: virus evolution; cheat; cooperation; social evolution; defective interfering genome; satellite virus

Online: 22 April 2020 (06:02:05 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/preprints201807.0402.v1

Adaptive Multi-Scale Entropy Fusion De-hazing based on Fractional Order

Uche A. Nnolim

Subject: Engineering, Electrical And Electronic Engineering Keywords: fractional order calculus-based multi-scale contrast operator; hybrid local-global contrast enhancement; underwater image enhancement processing; hazy image contrast enhancement; entropy guided fusion

Online: 22 July 2018 (11:30:40 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201807.0460.v1

Removal Characteristics of N-Nitrosamines and Their Precursorsby Pilot-Scale Integrated Membrane Systems for Water Reuse

Haruka Takeuchi, Naoyuki Yamashita, Norihide Nakada, Hiroaki Tanaka

Subject: Engineering, Chemical Engineering Keywords: N-nitrosamines; formation potential; membrane treatment; reverse osmosis; membrane fouling; pilot-scale

Online: 24 July 2018 (15:46:34 CEST)

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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 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 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 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 TECHNICAL NOTE | doi:10.20944/preprints202311.1130.v1

VarChat: The Generative AI Assistant for the Interpretation of Human Genomic Variations

Federica De Paoli, Silvia Berardelli, Ettore Rizzo, Ivan Limongelli, Susanna Zucca

Subject: Computer Science And Mathematics, Software Keywords: Genomics; Variant Interpretation; Generative AI; Genome analysis; Rare Diseases; Bioinformatics

Online: 17 November 2023 (05:24:56 CET)

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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 REVIEW | doi:10.20944/preprints201911.0076.v3

Exploring Mammalian Genome within Phase-Separated Nuclear Bodies: Experimental Methods and Implications for Gene Expression

Annick Lesne, Marie-Odile Baudement, Cosette Rebouissou, Thierry Forné

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: phase separation; nuclear bodies; self-assembly; genome organization; gene expression

Online: 11 December 2019 (11:17:34 CET)

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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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Preprint ARTICLE | doi:10.20944/preprints201806.0272.v1

Assessing Cognitive and Social Attitudes Toward Environmental Conservation in Coral Reef Social-Ecological Systems

Kostas Alexandridis

Subject: Social Sciences, Cognitive Science Keywords: environmental attitudes; social-ecological systems; coral reef; scale development; item-response theory; reliability; generalized structural equation model

Online: 18 June 2018 (15:26:36 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/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 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.

Preprint HYPOTHESIS | doi:10.20944/preprints202211.0211.v1

An Oncospace for Human Cancers

Guim Aguadé-Gorgorió, José Costa, Ricard Solé

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: cancer morphospace; microenvironmental complexity; genome instability; developmental abnormalities

Online: 11 November 2022 (03:18:06 CET)

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Working Paper ARTICLE

Transcriptomic Analysis for Prognostic Value in Head and Neck Squamous Cell Carcinoma

Li-Hsing Chi, Alexander TH Wu, Michael Hsiao, Yu-Chuan (Jack) Li

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Head and Neck Squamous Cell Carcinoma (HNSCC); the Cancer Genome Atlas (TCGA); Survival Analysis; Optimal Cutoff; Surgical Margin; Holistic Cancer Care; Therapeutic Relationship; Mindfulness Meditation; Transcriptomic Analysis; Effect Size; CAMK2N1; CALML5; FCGBP

Online: 7 July 2021 (08:48:26 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202010.0335.v1

Reflection Symmetry Axes Localization Framework for Object Intelligent Perception based on Salient Symmetry Feature

Kaichao Wu, Yuan Qi, Yuanju Ma, Cheng Liu, Dazhi Jiang

Subject: Computer Science And Mathematics, Computer Science Keywords: Object perception; Reflection symmetry; Saliency Symmetry Model; Isotropic symmetry operator; Multi-scale implementation

Online: 15 October 2020 (16:32:18 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/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/preprints202008.0285.v1

Sequence Analysis of Egyptian Foot-And-Mouth Disease Virus Field and Vaccine Strains: Intertypic Recombination and Evidence for Accidental Release of Virulent Virus

Sahar Abd El Rahman, Bernd Hoffmann, Reham Karam, Mohamed El-Beskawy, Mohammed F. Hamed, Leonie F. Forth, Dirk Höper, Michael Eschbaumer

Subject: Biology And Life Sciences, Virology Keywords: FMDV; Egypt; full-genome sequencing; interserotypic recombination; vaccine composition analysis; frozen evolution

Online: 12 August 2020 (11:56:33 CEST)

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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/preprints201907.0268.v1

Development of Technology of Release of Iron and Its Oxidic Connections from Dump Steel-Smelting Slag

Sokhibjon Turdaliyevich Matkarimov, Anvar Abdullayevich Yusupkhodjayev, Bakhriddin Berdiyarov Berdiyarov

Subject: Chemistry And Materials Science, Metals, Alloys And Metallurgy Keywords: slag; metallurgical dust; rolling scale; tails of dressing-works; iron; magnetite; fusion mixture; melting; arc steel-smelting furnace; production efficiency

Online: 24 July 2019 (09:06:41 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/preprints202009.0273.v1

Integrated into Environmental Biofilm Chromobacterium Vaccinii Survives Winter with Support of Bacterial Community

Daria A. Egorova, Olga L. Voronina, Andrey I. Solovyev, Marina S. Kunda, Ekaterina I. Aksenova, Natalia N. Ryzhova, Ksenya V. Danilova, Valentina S. Rykova, Anastasya A. Scherbakova, Andrey N. Semenov, Nikita B. Polyakov, Daniil A. Grumov, Natalia V. Shevlyagina, Inna V. Dolzhikova, Yulia M. Romanova, Alexander L. Gintsburg

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Chromobacterium vaccinii; biofilm; sharing goods; social cheater; bog microbiome; bacterial genome, violacein, cold adaptation, IDBac, QS mutant

Online: 12 September 2020 (12:04:38 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202208.0176.v1

Psychometric Evaluation of the Depression Anxiety Stress Scale 8-items (DASS-8)/DASS-12/DASS-21 among Italian and Swiss Family Caregivers of Patients with Dementia

Amira Ali, Rana Ali Alameri, Amin Omar Hendawy, Rasmieh Al-Amer, Ghada Shahrour, Esraa M. Ali, Abdulmajeed A. Alkhamees, Nashwa Ibrahim, Bothaina Hussein Hassan

Subject: Social Sciences, Psychology Keywords: psychological distress/anxiety/depression; dementia; Alzheimer’s disease; Parkinson’s disease; short form of the Depression Anxiety Stress Scale 21; Depression Anxiety Stress Scale 8-items; factor structure; psychometric properties; structural validity; validation; measurement invariance; old age/elders/elderly; informal; family caregivers; spouse; adult children

Online: 9 August 2022 (08:44:11 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201811.0183.v2

Integrating Molecular Biology and Bioinformatics Education

Boas Pucker, Hanna Marie Schilbert, Sina Franziska Schumacher

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: sequencing technologies; NGS; genome research; genome assembly; variant calling; RNA-Seq; transcriptome assembly; bioinformatics; molecular biology; education

Online: 13 November 2018 (10:22:06 CET)

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Preprint ARTICLE | doi:10.20944/preprints202007.0345.v1

Foetal Music Perception: A Comparison Study between Heart Rate and Motor Responses Assessed by APIB Scale in Ultrasound Exam

Rosana Maria Tristao, Jose Alfredo Lacerda de Jesus, Mônica de Lima Lemos, Ricardo Dourado Freire

Subject: Social Sciences, Psychology Keywords: foetus; music perception; tempo; heart rate variability; ultrasound exam; APIB scale; habituation; sensitization

Online: 16 July 2020 (07:49:50 CEST)

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Music perception in foetuses has been explored under different theoretical paradigms such as habituation, categorical perception, sound preferences and recall. This study investigated the temporal dimension of music perception through the habituation and sensitization paradigm. Foetuses of 41 pregnant women, mean gestational age of 34.7 weeks (±2.4), were observed during ultrasound exams. Foetuses’ reaction to two different tempos (Allegro vs Adagio) and sources (internal vs external) of music stimuli was registered by heart rate variability (HR) and motor response according to the Assessment of Preterm Infants Behaviour scale (APIB) by its factors of movement (MOV) and organization (ORG). A folkloric lullaby, sung and played live with a stringed instrument by a musician, was presented in three stages that were compared to baseline: 1) slow tempo (Adagio), 2) fast tempo (Allegro); and 3) now sung by mother at slow tempo (Adagio). Exploratory analyses showed that all factors increased from baseline to first stage. HR and ORG varied significantly among stages, with HR being the strongest factor. MOV merely detected change from baseline to first stage. ORG decreased for Allegro but increased for maternal Adagio, while HR decreased to near baseline values. ANOVA-repeated measures with gestational age as covariate showed that all measures were sensitive to first music presentation (Adagio), although only HR and ORG differed among stages. Considering estimated marginal means, adjusted for gestational age, HR presented a sensitization pattern throughout stages, but ORG kept habituating to external source and increased to maternal Adagio, suggesting foetal discrimination by sound source. We conclude that foetuses showed different behavioural and physiological responses to external versus internal sound source and musical tempo. The combined use of a behavioural scale (APIB) and HR in foetuses proved to be a valid multidimensional instrument.

Preprint ARTICLE | doi:10.20944/preprints202005.0140.v1

Plasmids Shape the Diverse Accessory Resistomes of Escherichia coli ST131

Arun G. Decano, Nghia Tran, Hawriya Al-Foori, Buthaina Al-Awadi, Leigh Campbell, Kevin Ellison, Louisse P. Mirabueno, Maddy Nelson, Shane Power, Genevieve Smith, Cian Smyth, Zoe Vance, Caitriona Woods, Alexander Rahm, Tim Downing

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Genome; fimbrial; plasmid; ST131; Escherichia coli; evolution; infection

Online: 8 May 2020 (09:39:35 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/preprints201804.0138.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/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/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/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/preprints202207.0404.v1

Genome Editing for Sustainable Crop Improvement and Mitigation of Biotic and Abiotic Stresses

Mohd Fadhli Hamdan, Chou Khai Soong Karlson, Ee Yang Teoh, Su-Ee Lau, Boon Chin Tan

Subject: Biology And Life Sciences, Plant Sciences Keywords: Abiotic stress; biotic stress; biotechnology; climate change; CRISPR; crop improvement; genome editing

Online: 26 July 2022 (10:44:22 CEST)

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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/preprints201808.0426.v2

Cities, from Information to Interaction

Vinicius M. Netto, Edgardo Brigatti, João Meirelles, Fabiano L. Ribeiro, Bruno Pace, Caio Cacholas, Patricia Sanches

Subject: Social Sciences, Urban Studies And Planning Keywords: information; cities; interaction; environmental information; entropy; scale; enaction

Online: 10 October 2018 (05:32:09 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202104.0674.v1

Numerical Investigation of the Full-Scale Resistance of a Zero-Emission Fast Catamaran in Shallow Water

Guangyu Shi, Alexandros Priftis, Yan Xing-Kaeding, Evangelos Boulougouris, Apostolos Papanikolaou, Haibin Wang, Geoff Symonds

Subject: Engineering, Automotive Engineering Keywords: fast catamaran; shallow water resistance; full-scale CFD

Online: 26 April 2021 (13:25:12 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 REVIEW | doi:10.20944/preprints202104.0602.v2

Biochemistry, Not Oncogenes, may Demystify and Defeat Cancer

Jay Kulsh

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: cancer; DNA sequencing; DNA synthesis; enzyme; free-radicals; genome; HPV; oncogenes; retinoblastoma; ribonucleotide reductase; RnR; SMT; TCGA

Online: 6 July 2021 (11:32:47 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 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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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 ARTICLE | doi:10.20944/preprints201910.0271.v1

First Draft Genome of the Trypanosomatid Herpetomonas muscarum ingenoplastis through MinION Oxford Nanopore Technology and Illumina Sequencing

Claudia M. d’Avila-Levy, Bertrand Bearzatto, Jérome Ambroise, Raphaël Helaers, Anzhelika Butenko, Vyacheslav Yurchenko, Karina A. Morelli, Helena L. C. Santos, Pascal Brouillard, Philippe Grellier, Jean-Luc Gala, Miikka Vikkula

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: genome assembly; monoxenous trypanosomatids; insect trypanosomatids; trypanosomatidae; whole genome

Online: 24 October 2019 (05:20:52 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/preprints202004.0302.v1

From Local to Global: A Transfer Learning-Based Approach for Mapping Poplar Plantations at Large Scale

Yousra Hamrouni, Éric Paillassa, Véronique Chéret, Claude Monteil, David Sheeren

Subject: Environmental And Earth Sciences, Environmental Science Keywords: active learning; poplar plantations; spatial transfer; sentinel-2; large scale; image classification; random forest

Online: 17 April 2020 (15:05:54 CEST)

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Reliable estimates of poplar plantations area are not available at the French national scale due to the unsuitability and low update rate of existing forest databases for this short-rotation species. While supervised classification methods have been shown to be highly accurate in mapping forest cover from remotely sensed images, their performance depends to a great extent on the labelled samples used to build the models. In addition to their high acquisition cost, such samples are often scarce and not fully representative of the variability in class distributions. Consequently, when classification models are applied to large areas with high intra-class variance, they generally yield poor accuracies. In this paper, we propose the use of active learning (AL) to efficiently adapt a classifier trained on a source image to spatially distinct target images with minimal labelling effort and without sacrificing classification performance. The adaptation consists in actively adding to the initial local model, new relevant training samples from other areas, in a cascade that iteratively improves the generalisation capabilities of the classifier, leading to a global model tailored to different areas. This active selection relies on uncertainty sampling to directly focus on the most informative pixels for which the algorithm is the least certain of their class labels. Experiments conducted on Sentinel-2 time series showed that when the same number of training samples was used, active learning outperformed passive learning (random sampling) by up to 5% of overall accuracy and up to 12% of class F-score. In addition, and depending on the class considered, the random sampling required up to 50% more samples to achieve the same performance of an active learning-based model. Moreover, the results demonstrate the suitability of the derived global model to accurately map poplar plantations among other tree species with overall accuracy values up to 14% higher than those obtained with local models. The proposed approach paves the way for national-scale mapping in an operational context.

Preprint REVIEW | doi:10.20944/preprints201910.0329.v1

Prospects for hermetic sealing of scaled-up photoelectrochemical hydrogen generators for reliable and risk free operation

Sonya Calnan, Stefan Aschbrenner, Fuxi Bao, Erno Kemppainen, Iris Dorbandt, Rutger Schaltmann

Subject: Engineering, Energy And Fuel Technology Keywords: photoelectrochemical; solar hydrogen generator; hermetic sealing, reliability, safety, scale- up

Online: 29 October 2019 (10:19:46 CET)

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Preprint ARTICLE | doi:10.20944/preprints202202.0166.v1

Characterization of Bifidobacterium asteroides Isolates

Alessandra Pino, Bachir Benkaddour, Rosanna Inturri, Pietro Amico, Susanna Vaccaro, Nunziatina Russo, Amanda Vaccalluzzo, Gianluigi Agolino, Cinzia Caggia, Cinzia L. Randazzo

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: microbiological characterization; safety; VanZ; isolation; vancomycin resistant gene; genome; bee; honey

Online: 11 February 2022 (21:17:45 CET)

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Preprint ARTICLE | doi:10.20944/preprints202012.0697.v1

Repeat-Induced Point Mutations (RIP) Drives the Formation of Distinct Sub-Genomic Compartments in Fusarium Circinatum

Stephanie van Wyk, Brenda D. Wingfield, Nicolaas A. van der Merwe, Lieschen De Vos, Mkhululi Maphosa, Lizel Potgieter, Emma T. Steenkamp

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Repeat-Induced Point Mutations; RIP; Accessory Chromosome; Genome Compartmentalization; GC Content; Genetic Variation; Fusarium circinatum; Transposable Elements; Interstitial Telomeric Repeats; Effector Genes.

Online: 28 December 2020 (12:18:11 CET)

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

Unbiasing in the Genome Analysis of Iconic Shark Species

Kazuaki Yamaguchi, Shigehiro Kuraku

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

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

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Preprint 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/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/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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Preprint ARTICLE | doi:10.20944/preprints202212.0226.v1

Parameterization of Eddy Mass Transport in the Arctic Seas based on the Sensitivity Analysis of Large-scale Flows

Gennady Platov, Dina Iakshina, Elena Golubeva

Subject: Environmental And Earth Sciences, Oceanography Keywords: eddy mass transport; subgrid-scale processes; parametrization; Arctic ocean; sensitivity study; clustering

Online: 13 December 2022 (04:19:37 CET)

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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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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/preprints202211.0169.v1

Resistance and Tolerance to Viroid Infection

Takashi Naoi, Shifang Li, Teruo Sano

Subject: Biology And Life Sciences, Virology Keywords: viroid; resistance; tolerance; RNA silencing; plant hormone; spray-induced gene silencing; genome editing

Online: 9 November 2022 (03:10:00 CET)

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