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Preprint REVIEW | doi:10.20944/preprints202403.0881.v1

Concerns regarding Transfusions of Blood Products Derived from Genetic Vaccine Recipients and Proposals for Specific Measures

Jun Ueda, Hideyuki Motohashi, Yuriko Hirai, Kenji Yamamoto, Yasufumi Murakami, Masanori Fukushima, Akinori Fujisawa

Subject: Medicine And Pharmacology, Transplantation Keywords: COVID-19 vaccine; genetic vaccine; blood product; blood transfusion; spike protein; post-vaccination syndrome; harm–benefit assessment; prion; spikeopathy; inspection standard; diagnostic criteria

Online: 15 March 2024 (08:54:06 CET)

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Preprint REVIEW | doi:10.20944/preprints202303.0140.v1

Autoimmune Inflammatory Reactions Triggered by the COVID-19 Genetic Vaccines in Terminally Differentiated Tissues

Panagis Polykretis, Alberto Donzelli, Janci C. Lindsay, David Wiseman, Anthony M. Kyriakopoulos, Michael Mörz, Paolo Bellavite, Masanori Fukushima, Stephanie Seneff, Peter A. McCullough

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: COVID-19; genetic vaccines; adverse reactions; autoimmunity; immunohistochemistry; spike protein

Online: 8 March 2023 (02:57:33 CET)

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Preprint REVIEW | doi:10.20944/preprints202206.0284.v1

Building Consensus around the Assessment and Interpretation of Symbiodiniaceae Diversity

Sarah Davies, Matthew H. Gamache, Lauren I. Howe-Kerr, Nicola G. Kriefall, Andrew C. Baker, Anastazia T. Banaszak, Line K. Bay, Anthony J. Bellantuono, Debashish Bhattacharya, Cheong Xin Chan, Danielle C. Claar, Mary Alice Coffroth, Ross Cunning, Simon K. Davy, Javier del Campo, Erika M. Diaz-Almeyda, Jorg C. Frommlet, Lauren E. Fuess, Raul A. Gonzalez-Pech, Tamar L. Goulet, Kenneth D. Hoadley, Emily J. Howells, Benjamin C. C. Hume, Dustin W. Kemp, Carly, D. Kenkel, Sheila A. Kitchen, Todd C. LaJeunesse, Senjie Lin, Shelby McIlroy, Ryan McMinds, Matthew R. Nitschke, Clinton A. Oakley, Raquel S. Peixoto, Carlos Prada, Hollie M. Putnam, Kate Quigley, Hannah G. Reich, James Davis Reimer, Mauricio Rodriguez-Lanetty, Stephanie Rosalas, Osama S. Saad, Eugenia M. Sampayo, Scott Santos, Eiichi Shoguchi, Edward G. Smith, Michael Stat, Timothy G. Stephens, Marie E. Strader, David J. Suggett, Timothy D. Swain, Cawa Tran, Nikki Traylor-Knowles, Christian R. Voolstra, Mark E. Warner, Virginia M. Weis, Rachel Wright, Tingting Xiang, Hiroshi Yamashita, Maren Ziegler, Adrienne M.S. Correa, John Everett Parkinson

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: Symbiodinaceae; genetic diversity; coral symbiosis

Online: 21 June 2022 (04:49:04 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201806.0201.v1

The Critical Needs and Challenges for Genetic Architecture Studies in Africa

Alicia R. Martin, Solomon Teferra, Marlo Möller, Eileen G. Hoal, Mark J. Daly

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: genetic architecture; Africa; GWAS; health disparities

Online: 13 June 2018 (11:17:04 CEST)

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Preprint REVIEW | doi:10.20944/preprints201712.0170.v1

Life Emerged from [GADV]-Protein World, but Not from RNA World!?

Kenji Ikehara

Subject: Biology And Life Sciences, Life Sciences Keywords: RNA world; [GADV]-protein world; GADV hypothesis; origin of life; protein 0th-order structure; origin of protein; origin of genetic code; origin of gene

Online: 25 December 2017 (08:08:37 CET)

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Preprint ARTICLE | doi:10.20944/preprints202104.0770.v1

Representation of Non-Western Cultural Knowledge on Wikipedia: The Case of the Visual Arts

Martin Poulter, Waqās Ahmed

Subject: Social Sciences, Library And Information Sciences Keywords: Wikipedia, knowledge equity, Wikimedia, open culture, visual arts, cultural bias

Online: 29 April 2021 (09:16:07 CEST)

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Preprint REVIEW | doi:10.20944/preprints202004.0359.v1

Genomic Diversity and Evolution, Diagnosis, Prevention, and Therapeutics of the Pandemic COVID-19 Disease

M. Nazmul Hoque, Abed Chaudhury, Md. Abdul Mannan Akanda, M. Anwar Hossain, Md Tofazzal Islam

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: SARS-CoV-2; genetic diversity; genome evolution; diagnostics; therapeutics; vaccines

Online: 20 April 2020 (02:33:15 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201608.0046.v1

Visual Symmetry: From Geometry to Sensation and Preference

Birgitta Dresp-Langley

Subject: Social Sciences, Cognitive Science Keywords: visual symmetry; affine projection; fractals; visual sensation; aesthetics; preference

Online: 5 August 2016 (05:15:32 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201607.0015.v1

Design and analysis of the redundancy allocation problem using a greedy technique

Souradeep Nanda, SIDDHARTH SHARMA, Kundnani Piyush, ANAND SHANKER DEB, C. Vijayalakshmi

Subject: Computer Science And Mathematics, Data Structures, Algorithms And Complexity Keywords: Redundancy Allocation Problem, Genetic Algorithm, Simulated Annealing, Greedy Algorithm

Online: 9 July 2016 (05:13:42 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201609.0126.v2

Visual Motion Onset Brain–Computer Interface

Jair Pereira Junior, Caio Teixeira, Tomasz Rutkowski

Subject: Computer Science And Mathematics, Computer Science Keywords: Brain-computer interface (BCI); visual motion perception; neurotechnology application; EEG; realtime brain signal decoding

Online: 4 October 2016 (14:43:48 CEST)

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Preprint CONCEPT PAPER | doi:10.20944/preprints201705.0121.v1

Frozen Accident Pushing 50: Stereochemistry, Expansion and Chance in the Evolution of the Genetic Code

Eugene Koonin

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Genetic code evolution; frozen accident; error minimization; stereochemcial theory; evolution of translation

Online: 16 May 2017 (12:52:10 CEST)

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Preprint REVIEW | doi:10.20944/preprints202006.0120.v1

Why Children Are Less Affected by COVID-19 Than Adults: Potential Immunological Factors and the Renin-Angiotensin System Associated Mechanisms

Olga Krogh-Jensen, Irina Nikitina, Andrew Donnikov, Anna Lenyushkina, Nataliya Degtyareva, Anna Degtyareva

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: SARS-CoV-2; COVID-19; pathogenesis; children; neonates; immune response; secondary hemophagocytic lymphohistiocytosis; renin-angiotensin system; genetic polymorphisms; ACE2; AGTR2; AGTR1; NOS; lung injury

Online: 9 June 2020 (08:07:40 CEST)

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The spread of the infection caused by the new coronavirus SARS-CoV-2 (COVID-19) became pandemic on March 11, 2020. From the time of the first cases (in November 2019, Wuhan, China), to date, a large number of COVID-19 observations have been accumulated in different age groups of patients both in China and abroad. Published scientific data allows us to conclude that children suffer from COVID-19 much less often than adults and tolerate the disease in a milder form, often appear to be asymptomatic. There is currently no final answer why children are less susceptible to this virus; however, scientists are increasingly inclined to consider a complex effect of the immune response and components of the renin-angiotensin system (RAS), which according to recent studies affects not only the cardiovascular system, but is also responsible for the activation of inflammatory reactions. A hypothesis of genetic predisposition to the development of severe forms of COVID-19 has recently been made. We conducted a search for publications in the databases and showed current scientific ideas about COVID-19 pathogenesis and factors influencing the disease development in childhood. Childhood immunity may have several protective features against SARS-CoV-2: immaturity of particular elements of the innate immune response, constitutional lymphocytosis with a shift towards anti-inflammatory Th2-response, as well as "trained" immunity. The influence of renin-angiotensin system reactions in this review is shown from two perspectives: expression of ACE2 receptors and polymorphisms of certain genes of this system. It was established that ACE2 transmembrane protein is not only the entry point for the virus but also plays a regulatory role, turning the pro-inflammatory vasoconstrictor angiotensin II into anti-inflammatory angiotensin (1-7), which has vasodilating properties. Higher ACE2 content in children compared with adults helps maintain balance in the renin-angiotensin system and prevents the development of complications. It was also shown that the presence of certain genetic polymorphisms (AGTR1, AGTR2, ACE2, ACE) could determine the imbalance inside the RAS, leading to more pronounced reactions of alveolocytes, vascular endothelium and smooth muscle fibers in response to SARS-CoV-2 infection due to a shift towards vasoconstrictor, proliferative and profibrotic mechanisms.

Preprint HYPOTHESIS | doi:10.20944/preprints202003.0419.v9

The ATP Hypothesis Discovers the Missing “Matchmaker” between Proteins and Nucleic Acids

Ping Xie

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: ATP hypothesis; origin of genetic code; life’s building block; probiotic “soup”; coevolution; biochemical system; missing “matchmaker”; energy transformation; informatization; structuralization; precellular selection; photo- chemical origin of life; virus; anti-life form; 2019-nCoV

Online: 11 September 2020 (08:39:39 CEST)

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A plenty of theories on the origin of genetic codes have been proposed so far, yet all ignored the energetic driving force, its relation to the biochemical system, and most importantly, the missing “matchmaker” between proteins and nucleic acids. Here, a new hypothesis is proposed, according to which ATP is at the origin of the primordial genetic code by driving the coevolution of the genetic code with the pristine biochemical system. This hypothesis aims to show how the genetic code was produced e.g. by photochemical reactions in a protocell that derived from a lipid vesicle enclosing various life’s building blocks (e.g. nucleotides and peptides). At extant cell, ATP is the only energetic product of photosynthesis, and is at the energetic heart of the biochemical systems. ATP could energetically form and elongate chains of both polynucleotides and polypeptides, thus acting a “matchmaker” between these two bio-polymers and eventually mediating precellular biochemical innovation from energy transformation to informatization. ATP was not the only one that could drive the formation of polynucleotides and polypeptides, but favored by precellular selection. The protocell innovated a photosynthesis system to produce ATP efficiently and regularly with the aids of proteins and RNA/DNA. The completion of permanently recording the genetic information by DNA marked the dawn of cellular life operated by Darwinian evolution. The ATP hypothesis assumes or supports the photochemical origin of life, shedding light on the origins of both photosynthetic and biochemical systems, which remains largely unknown thus far. Based on ATP hypothesis, virus (like the new coronavirus) could not be the earliest life on Earth, as it has neither biochemical systems nor lipid bilayer membrane that provided relatively isolated environment for the development of protobiochemical reactions, although it owns the genetic code of a cellular life. Virus could not be a bridge between life and non-life, but is an anti-life substance, as it depletes cellular material for its own replication, and then spreads by destroying the host cells. It can be imagined that if cellular life are completely wiped out by the virus, the complete destruction of life on Earth would be inevitable.

Preprint REVIEW | doi:10.20944/preprints202001.0276.v1

Genetic Variation of Traits in Natural Enemies Relevant for Biological Control: A Systematic Review

Kim B. Ferguson, Sophie R. Chattington, Wouter N. Plouvier, Bart A. Pannebakker

Subject: Biology And Life Sciences, Insect Science Keywords: genetic improvement; genetic variation; heritability; systematic review; biocontrol agent; life history traits

Online: 24 January 2020 (10:39:55 CET)

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Preprint REVIEW | doi:10.20944/preprints202109.0234.v1

How Biological Concepts and Evolutionary Theories Are Inspiring Advances in Machine Intelligence

Abigail R. Gutai, Thomas E. Gorochowski

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: artificial intelligence; artificial neural networks; genetic algorithms; evolution; neuroevolution; machine learning

Online: 14 September 2021 (10:40:01 CEST)

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Preprint CASE REPORT | doi:10.20944/preprints202403.1661.v2

A Case Report of Acute Lymphoblastic Leukaemia (ALL)/Lymphoblastic Lymphoma (LBL) Following the Second Dose of Comirnaty®: An Analysis of the Potential Pathogenic Mechanism Based on of the Existing Literature

Patrizia Gentilini, Janci C. Lindsay, Nafuko Konishi, Masanori Fukushima, Panagis Polykretis

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: COVID-19 genetic vaccines; mRNA vaccines; adverse effects; lymphoblastic leukemia; lymphoblastic lymphoma

Online: 1 April 2024 (13:21:50 CEST)

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In this report we describe the case of a healthy, young, athletic woman who developed acute lymphoblastic leukaemia (ALL)/lymphoblastic lymphoma (LBL) after receiving the second dose of the Pfizer/BioNTech modified mRNA (modRNA) COVID-19 genetic vaccine (marketed as Comirnaty^®). The first dose of the genetic vaccine did not appear to illicit any noticeable side effects, but within 24 hours of the second dose the patient suffered widespread and intensifying bone pain, fever, vomiting, and general malaise. Due to the persistence of the symptoms, the patient underwent a series of tests and examinations including a full laboratory workup, a consult with a clinical immunologist and rheumatologist, a Positron Emission Tomography (PET) imaging, as well as an osteomedullary biopsy. These together led to a definitive diagnosis of ALL. A time interval of 16 weeks from the second vaccination to the diagnosis of cancer was noted. Several similar cases with identical pathology which developed after the modRNA COVID-19 vaccination, are described in case reports in the scientific literature. The massive and indiscriminate use of genetic vaccines to fight COVID-19 is raising serious concerns about their safety and about the technology platform as a whole for this purpose. Growing evidence is accumulating regarding the biodistribution and persistence of the modRNA which can reach, thanks to the lipid nanoparticles, a multitude of tissues and organs of the body, including the bone marrow and other blood-forming organs and tissues. Moreover, there is evidence that the modRNA vaccines display a particular tropism for the bone marrow, influencing the immune system at multiple levels and being able to trigger not only autoimmune-based pathologies, but also neoplastic mechanisms. The aim of this article is to assess, on the basis of the available scientific literature, the risk of developing haematopoietic cancers after modRNA vaccination, and to investigate the potential genetic mechanisms involved in the pathogenesis of disease.

Preprint ARTICLE | doi:10.20944/preprints201704.0030.v1

Automatic Localization Algorithm for Ultrasound Breast Tumors Based on Human Visual Mechanism

Yuting Xie, Ke Chen, Jiangli Lin

Subject: Computer Science And Mathematics, Data Structures, Algorithms And Complexity Keywords: Automatic localization; human visual mechanism; superpixel contrast feature; ultrasound breast tumor.

Online: 5 April 2017 (15:50:40 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201611.0033.v1

Construct Linear Polynomial Complementary Transformation for NP-Completeness Using Parallel Genetic Algorithm

Tarik Eltaeib, Julius Dichter

Subject: Computer Science And Mathematics, Information Systems Keywords: genetic algorithms; parallel computation; computational complexity; algorithms; optimization techniques; traveling salesman problem; NP-Hard problems; Berlin-52 data set; machine learning; linear regression

Online: 7 November 2016 (04:57:46 CET)

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Preprint ARTICLE | doi:10.20944/preprints201704.0148.v1

Multi-objective Optimization of Draft Tube in Francis Turbine Using DOE, RBF and NSGA-II

Chol Nam Mun, De Chun Ba, Xiang Ji Yue, Myong Il Kim

Subject: Engineering, Energy And Fuel Technology Keywords: francis turbine; draft tube; optimization design; experiment of design; non–dominated sorting genetic algorithm

Online: 24 April 2017 (10:52:28 CEST)

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Preprint REVIEW | doi:10.20944/preprints202004.0333.v1

Visiting Bitter Gourd (Momordica charantia) from a Breeding Perspective: A Review

Hari Kesh, Prashant Kaushik

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: bitter gourd; breeding; genetic diversity; genomics; heterosis; molecular breeding; mutation breeding

Online: 19 April 2020 (06:00:00 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201703.0015.v1

Evolutionary Optimization of Colebrook’s Turbulent Flow Friction Approximations

Dejan Brkić, Žarko Ćojbašić

Subject: Physical Sciences, Fluids And Plasmas Physics Keywords: colebrook equation; colebrook-white; moody diagram; turbulent flow; hydraulic resistance; darcy friction; pipes; genetic algorithms; optimization techniques; error analysis

Online: 2 March 2017 (07:57:54 CET)

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Preprint ARTICLE | doi:10.20944/preprints201803.0199.v1

Optimisation of Multipurpose Reservoir Operation by coupling SWAT and Genetic Algorithm for Optimal Operating Policy (Case Study: Ganga River basin)

Jatin Anand, A K Gosain, R Khosa

Subject: Engineering, Civil Engineering Keywords: Reservoir operation; SWAT; Genetic Algorithm; Urbanisation; Ganga River

Online: 23 March 2018 (15:07:22 CET)

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Reservoirs are recognized as one of the most efficient infrastructure components in integrated water resources management and development. At present, with the ongoing advancement of social economy and requirement of water, the water resources shortage problem has worsened, and the operation of reservoirs, in terms of consumption of flood water, has become significantly important. Reservoirs perform both regulation of flood and integrated water resources management, in which the flood limited water level is considered as the most important parameter for trade-off between regulation of flood and conservation. To achieve optimal operating policies for reservoirs, large numbers of simulation and optimization models have been developed in the course of recent decades, which vary notably in their applications and working. Since each model has their own limitations, the determination of fitting model for derivation of reservoir operating policies is challenging and most often there is always a scope for further improvement as the selection of model depends on availability of data. Subsequently, assessment and evaluation associated with the operation of reservoir stays conventional. In the present study, the Soil and Water Assessment Tool (SWAT) models and a Genetic Algorithm model has been developed and applied to two reservoirs in Ganga River basin, India to derive the optimal operational policies. The objective function is set to minimize the annual sum of squared deviation form desired irrigation release and desired storage volume. The decision variables are release for irrigation and other demands (industrial and municipal demands), from the reservoir. As a result, a simulation-based optimization model was recommended for optimal reservoir operation, such as allocation of water, flood regulation, hydropower generation, irrigation demands and navigation and e-flows using a definite combination of decision variables. Since the rule curves are derived through random search it is found that the releases are same as that of demand requirements. Hence based on simulated result, in the present case study it is concluded that GA-derived policies are promising and competitive and can be effectively used operation of the reservoir.

Preprint ARTICLE | doi:10.20944/preprints201804.0157.v1

Topological Information Data Analysis: Poincare-Shannon Machine and Statistical Physic of Finite Heterogeneous Systems

Pierre Baudot, Monica Tapia, Jean-Marc Goaillard

Subject: Computer Science And Mathematics, Probability And Statistics Keywords: information theory; cohomology; algebraic topology; topological data analysis; genetic expression; epigenetics; machine learning; statistical physic; multivariate mutual-information; complex systems; biodiversity

Online: 12 April 2018 (05:35:26 CEST)

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This paper establishes methods that quantify the structure of statistical interactions within a given data set using the characterization of information theory in cohomology by finite methods, and provides their expression in terms of statistical physic and machine learning. Following [1–3], we show directly that k multivariate mutual-informations (I_k) are k-coboundaries. The k-cocycles are given by I_k = 0, which generalize statistical independence to arbitrary dimension k. The topological approach allows to investigate Shannon’s information in the multivariate case without the assumptions of independent identically distributed variables. We develop the computationally tractable subcase of simplicial information cohomology represented by entropy H_k and information I_k landscapes. The I₁ component defines a self-internal energy functional U_k, and (−1)^k I_k_,k≥2 components define the contribution to a free energy functional G_k of the k-body interactions. The set of information paths in simplicial structures is in bijection with the symmetric group and random processes, provides a topological expression of the 2nd law and points toward a discrete Noether theorem (1st law). The local minima of free-energy, related to conditional information negativity and the non-Shannonian cone of Yeung [4], characterize a minimum free energy complex. This complex formalizes the minimum free-energy principle in topology, provides a definition of a complex system, and characterizes a multiplicity of local minima that quantifies the diversity observed in biology. Finite data size effects and estimation bias severely constrain the effective computation of the information topology on data, and we provide simple statistical tests for the undersampling bias and for the k-dependences following [5]. We give an example of application of these methods to genetic expression and cell-type classification. The maximal positive I_k identifies the variables that co-vary the most in the population, whereas the minimal negative I_k identifies clusters and the variables that differentiate-segregate the most. The methods unravel biologically relevant I₁₀ with a sample size of 41. It establishes generic methods to quantify the epigenetic information storage and a unified epigenetic unsupervised learning formalism.

Preprint ARTICLE | doi:10.20944/preprints201903.0244.v1

Studying a Light Sensor with Light: Multiphoton Imaging in the Retina

Thomas Euler, Katrin Franke, Tom Baden

Subject: Biology And Life Sciences, Neuroscience And Neurology Keywords: vertebrate retina, mouse, zebrafish, two-photon microscopy, biosensor, activity probes, visual stimulus-evoked activity, laser-evoked retinal activity

Online: 26 March 2019 (14:01:49 CET)

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Preprint ARTICLE | doi:10.20944/preprints201705.0109.v1

The Genetic Structure of Turnip mosaic Virus Population Reveals the Rapid Expansion of a New Emergent Lineage in China

Xiangdong Li, Tiansheng Zhu, Xiao Yin, Chengling Zhang, Jia Chen, Yanping Tian, Jinliang Liu

Subject: Biology And Life Sciences, Plant Sciences Keywords: Turnip mosaic virus; Potyvirus; Genetic structure; Population; China

Online: 15 May 2017 (11:38:11 CEST)

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Preprint REVIEW | doi:10.20944/preprints201703.0031.v2

Self-Referential Encoding on Modules of Anticodon Pairs—Roots of the Biological Flow System

Romeu Cardoso Guimarães

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: genetic code; tRNA dimers; self-reference; modularity; error-compensation; metabolism chronology; protein stability; punctuation system

Online: 17 March 2017 (04:55:46 CET)

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Preprint REVIEW | doi:10.20944/preprints202009.0162.v2

Chaos, Order and Systematics in Evolution of the Genetic Code

Lei Lei, Zachary F. Burton

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: amyloids; frozen accident; genetic code; hydrogels; liquid-liquid phase separation; mRNA; polyglycine; rRNA; ribosomes; translational fidelity; tRNA

Online: 21 October 2020 (10:48:18 CEST)

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Preprint REVIEW | doi:10.20944/preprints202106.0018.v1

The Crustacean Model Parhyale hawaiensis

Mathilde Paris, Carsten Wolff, Nipam Patel, Michalis Averof

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: emerging model organism; evo-devo; development; evolution; regeneration; genetic tools; live imaging

Online: 1 June 2021 (10:37:04 CEST)

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Preprint REVIEW | doi:10.20944/preprints202010.0149.v1

Advances in Melon Breeding (Cucumis melo L.): An Update

Hari Kesh, Prashant Kaushik

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: breeding; diversity; genetic engineering; genomics; male sterility; melon; QTLs

Online: 7 October 2020 (09:22:33 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202109.0090.v1

A Metaheuristic Algorithm for Flexible Energy Storage Management in Residential Electricity Distribution Grids

Ovidiu Ivanov, Bogdan-Constantin Neagu, Gheorghe Grigoraș, Florina Scarlatache, Mihai Gavrilaș

Subject: Engineering, Electrical And Electronic Engineering Keywords: residential electricity distribution networks; renewable generation sources; energy storage; optimization; multipurpose algorithm; genetic algorithms

Online: 6 September 2021 (12:10:22 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202003.0298.v1

A Composite Hybrid Feature Selection Learning-Based Optimization of Genetic Algorithm For Breast Cancer Detection

Ahmed Abdullah Farid, Gamal Selim, Hatem Khater

Subject: Computer Science And Mathematics, Information Systems Keywords: Data Mining; Breast Cancer; Hybrid Feature Selection; Machine learning; Support Vector Machine; Optimize Genetic Algorithm; boosting algorithms

Online: 19 March 2020 (11:13:15 CET)

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Preprint ARTICLE | doi:10.20944/preprints202201.0465.v1

Genetic Algorithm-based Optimal Deep Neural Network for Detecting Network Intrusions

Sourav Adhikary, Md. Musfique Anwar, Mohammad Jabed Morshed Chowdhury, Iqbal H. Sarker

Subject: Computer Science And Mathematics, Data Structures, Algorithms And Complexity Keywords: genetic algorithm; deep neural network; hidden layer; optimal architecture; intrusion detection

Online: 31 January 2022 (13:26:18 CET)

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Preprint ARTICLE | doi:10.20944/preprints201704.0088.v1

Hierarchical Gradient Similarity Based Video Quality Assessment Metric

Jie Yang, Jian Xiong, Guan Gui, Rongfang Song, Wang Luo, Xianzhong Long

Subject: Engineering, Other Keywords: hierarchical video quality assessment; human visual systems; primate visual cortex; full reference

Online: 14 April 2017 (11:52:44 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201712.0184.v1

Multivariable Static Output Feedback Control of a Binary Distillation Column using Linear Matrix Inequalities and Genetic Algorithm

Kalpana R., Harikumar Kandath, Senthilkumar J., Balasubramanian G., Abhay S. Gour

Subject: Engineering, Control And Systems Engineering Keywords: distillation column; disturbance rejection; genetic algorithm; H∞ control; linear matrix inequalities; static output feedback

Online: 26 December 2017 (05:22:09 CET)

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Preprint ARTICLE | doi:10.20944/preprints201807.0243.v1

Determination of the Visual Preferences of Different Habitat Types

Engin Eroğlu, Sertaç Kaya, Tuba Gul Dogan, Alperen Meral, Sena Demirci, Nermin Başaran, Omer Lutfu Corbaci

Subject: Biology And Life Sciences, Forestry Keywords: Habitat types, visual differences, landscape characteristics.

Online: 13 July 2018 (17:07:05 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202306.1230.v1

Revealing the Genetic Code Symmetries through Computations Involving Fibonacci-like Sequences and Their Properties

Tidjani Négadi

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: genetic code; symmetries; Fibonacci-like sequences; amino acids; ribonucleotides; patterns; hydrogen; atom; molecular mass

Online: 16 June 2023 (11:02:55 CEST)

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In this work, we present a new way to study the genetic code mathematical and chemical structure, based on the use of mathematical computations involving some few recently designed Fibonacci-like sequences, the “seeds” (“initial conditions”) of which are chosen according to the chemical and physical data of the three amino acids serine, arginine and leucine, playing a prominent role in a recent symmetry classification scheme of the genetic code. It appears that these mathematical sequences, of the same kind as the famous Fibonacci series, apart from their usual recurrence relations, are highly interwinned by many useful linear relationships. Using these sequences and also various sums or linear combinations of them, we derive several physical and chemical quantities of interest, as the number of total coding codons, 61, obeying various degeneracy patterns, the detailed number of hydrogen atoms, the detailed number of atoms (H/CNOS) and the integer molecular mass (or nucleon number), in the side chains of the 61 “amino acids”, also in various degeneracy patterns, in agreement with those described in the literature. Also, unexpectedly but interestingly, we find, as a by-product, an accurate description of the very chemical structure of the four ribonucleotides uridine monophosphate (UMP), cytidine monophosphate (CMP), adenosine monophosphate (AMP) and guanosine monophosphate (GMP), the building blocks of RNA whose groupings, in three units, constitutes the triplet codons. In summary, we find a full mathematical and chemical connection with the “ideal sextet’s classification scheme” mentioned above as well as with several others, notably, the Findley-Findley-McGlynn symmetrical classification. We organize the content of the text in such a way that, besides the presentation of several new research results, it has also an educational dimension. The paper could therefore be read and the computations easily worked out, also by non-experts with mathematical background.

Preprint REVIEW | doi:10.20944/preprints201906.0022.v1

Pursuing the potential of heirloom cultivars to improve adaptation, nutritional and culinary features in a changing climate

Sangam Dwivedi, Irwin Goldman, Rodomiro Ortiz

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: culinary and nutritional traits; farmer-breeder-chef-consumer nexus; folk cultivars; genetic diversity; global warming; heritage seedbank; local food systems; seed savers; stress tolerance

Online: 3 June 2019 (12:34:14 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201711.0079.v1

Cryptic Species Diversity of Rice Hopper Parasitoids in Southeast Asia

Christina Sann, Franziska Wemheuer, Alexis Beaurepaire, Rolf Daniel, silvio Erler, Stefan Vidal

Subject: Biology And Life Sciences, Insect Science Keywords: DNA barcoding; genetic diversity; hymenopteran parasitoids; Nephotettix spp.; Nilaparvata lugens; rice

Online: 13 November 2017 (17:06:38 CET)

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Preprint ARTICLE | doi:10.20944/preprints201707.0005.v1

Improved Forms for Controlling the Acrobot with Motors of Atypical Size Using Artificial Intelligence Techniques

Gonzalo Mier, Javier de Lope

Subject: Engineering, Control And Systems Engineering Keywords: Acrobot; Artificial Intelligence; SARSA; PWM; Genetic Algorithm

Online: 4 July 2017 (16:12:37 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201707.0047.v1

Genetic Structure and Eco-Geographical Differentiation of Wild Sheep Fescue (Festuca ovina L.) in Xinjiang, Northwest China

Chenglin Zhang, Jianbo Zhang, Yan Fan, Ming Sun, Wendan Wu, Wenda Zhao, Xiaopeng Yang, Linkai Huang, Yan Peng, Xiao Ma, Xinquan Zhang

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Festuca ovina L.; AFLP, genetic diversity; genetic barriers; environmental factors

Online: 18 July 2017 (10:05:56 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201706.0038.v1

Minimization of Construction Costs for an All Battery-Swapping Electric-Bus Transportation System: Comparison with an All Plug-In System

Shyang-Chyuan Fang, Bwo-Ren Ke, Chen-Yuan Chung

Subject: Engineering, Energy And Fuel Technology Keywords: Public bus transportation; Battery-swapping e-bus; Battery charging; Construction costs; Particle swarm optimization (PSO); PSO-genetic algorithm (GA)

Online: 6 June 2017 (17:52:24 CEST)

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Preprint COMMUNICATION | doi:10.20944/preprints202007.0403.v2

Complete Quantum Information in the DNA Genetic Code

Michel Planat, Raymond Aschheim, Marcelo Amaral, Fang Fang, Klee Irwin

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: DNA genetic code; informationally complete characters; finite groups,; hyperelliptic curve

Online: 6 October 2020 (10:11:17 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201705.0081.v1

Electric Power Grids Distribution Generation System For Optimal Location and Sizing – An Case Study Investigation by Various Optimization Algorithms

Ahmet Ali, Sanjeevikumar Padmanaban, Bhekisipho Twala, Tshilidzi Marwala

Subject: Engineering, Electrical And Electronic Engineering Keywords: optimization; simulated annealing; genetic algorithm; power losses; power consumption

Online: 9 May 2017 (10:45:49 CEST)

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Preprint CONCEPT PAPER | doi:10.20944/preprints202011.0387.v1

Genetic Music: When Genes Code for Melodies Instead of Proteins

Marga Consortium, Blanca A. Gutierrez, Iván Aitor Lucas del-Amo, Beatriz Alejos Bermudez, Cristina Gonzalez Moran, Veronica Noval Gutierrez, Borja Sanchez

Subject: Social Sciences, Anthropology Keywords: genetic music; genetic code; music composition; steam disciplines; notch1 gene

Online: 13 November 2020 (15:34:47 CET)

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Preprint ARTICLE | doi:10.20944/preprints201804.0128.v1

The Size and Content of the Sex-Determining Region of the Y Chromosome in Dioecious Mercurialis annua, a Plant with Homomorphic Sex Chromosomes

Paris Veltsos, Guillaume Cossard, Emmanuel Beaudoing, Genséric Beydon, Camille Roux, Santiago C. González-Martínez, John R. Pannell

Subject: Biology And Life Sciences, Plant Sciences Keywords: bacterial artificial chromosomes; RNAseq; genetic map; transposable element; gene density

Online: 10 April 2018 (10:49:41 CEST)

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Preprint REVIEW | doi:10.20944/preprints202104.0105.v1

Development of Therapies for Rare Genetic Disorders of GPX4: Roadmap and Opportunities

Dorian Cheff, Alysson Muotri, Brent Stockwell, Edward Schmidt, Qitao Ran, Reena Kartha, Simon Johnson, Plavi Mittal, Elias Arnér, Kristen Wigby, Matthew Hall, Sanath Ramesh

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: Sedaghatian-type Spondylometaphyseal Dysplasia; SSMD; glutathione peroxidase 4; GPX4; rare genetic disorder; therapy development; roadmap; ultra-rare disease

Online: 5 April 2021 (11:57:03 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201807.0063.v1

A Method for Analysis and Visualization of Similar Hotspot Flow Patterns between Different Regional Groups

Haiping Zhang, Xingxing Zhou, Xin Gu, Genlin Ji, Guoan Tang

Subject: Environmental And Earth Sciences, Space And Planetary Science Keywords: regional group interaction; similar hotspot flow patterns; spatial interaction; visual analytics; Geo-Information-Tupo; GIS

Online: 4 July 2018 (09:26:18 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201806.0284.v1

Next-Generation Counseling: Noninvasive Prenatal Screening Results Disclosure and Management

Aishwarya Arjunan, Rotem Ben-Shachar, Jamie Kostialik, Katherine Johansen Taber, Gabriel Lazarin, Elizabeth Denne, Dale Muzzey, Carrie Haverty

Subject: Medicine And Pharmacology, Obstetrics And Gynaecology Keywords: cell-free DNA analysis; genetic counseling; noninvasive prenatal screening; prenatal screening; results delivery; telehealth

Online: 19 June 2018 (03:45:49 CEST)

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Background: As noninvasive prenatal screening usage grows in the general obstetrics setting, proper patient education on the screen’s benefits and limitations is needed. Objective: Describe the use of a technology platform designed for large-scale dissemination of noninvasive prenatal screening information and results. Study Design: The technology platform functioned as follows: Patients were emailed a link to an noninvasive prenatal screening general-education video upon laboratory receipt of a test requisition. Providers were then notified upon availability of patients’ results. If noninvasive prenatal screening results were negative, the patient was sent an automated email with instructions to access results through a secure portal where she could watch tailored informational videos, request “on-demand” or scheduled genetic counseling, or decline any further services. If genetic counseling was elected, a summary of the session was sent to the ordering provider and patient upon completion. If noninvasive prenatal screening results were positive, either the ordering provider or a board-certified genetic counselor contacted the patient directly to communicate test results and provide counseling. The number and type of results issued through the platform, the number and type of genetic counseling consultations completed, and factors associated with requesting laboratory-delivered genetic counseling were tracked and analyzed for a 39-month period. Results: Over the study period, 67,122 noninvasive prenatal screening results were issued through the platform, and 4,673 patients elected genetic counseling consultations; 95.2% (n=4,450) of consultations were for patients receiving negative results. Over 70% (n= 3,370) of consultations were on-demand rather than scheduled. Median consultation time was 14 minutes for positive results and six minutes for negative results. A positive screen, advanced maternal age, family history, previous history of a pregnancy with a chromosomal abnormality, and other high-risk pregnancy were associated with the greatest odds of electing laboratory-delivered genetic counseling. Conclusions: By combining web education, automated notifications, and genetic counseling, we implemented a service that effectively facilitates results disclosure for ordering providers. These data demonstrate the capability to deliver noninvasive prenatal screening results, education, and counseling—congruent with management guidelines—to a large population, which is imperative to quality care as uptake increases.

Preprint REVIEW | doi:10.20944/preprints202108.0514.v1

Advances and Milestones of Radish Breeding: An Update

Anand Kumar, Prashant Kaushik

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: radish; breeding; interspecific hybridization; molecular breeding; genomics; genetic engineering

Online: 26 August 2021 (16:46:36 CEST)

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Preprint REVIEW | doi:10.20944/preprints202105.0194.v1

Risk Factors for Recurrent Aphthous Stomatitis: A Systematic Review

César Rivera, Antonieta Muñoz, Carolina Puentes, Esteban Aguayo

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: aphthous stomatitis, risk factors, genetic polymorphisms, multivariate analysis, systematic review

Online: 10 May 2021 (13:55:48 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201710.0028.v1

Security-Constrained Optimal Dispatch of Combined Natural Gas and Electricity Networks Using Genetic Algorithms

Denis C. L. Costa, João Paulo Vieira, Marcus V. A. Nunes

Subject: Engineering, Energy And Fuel Technology Keywords: Integrated Electric Power and Natural Gas Network, Optimal Power Flow, Genetic Algorithm.

Online: 5 October 2017 (09:41:12 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202006.0028.v1

Genetic Algorithm: Reviews, Implementations, and Applications

Tanweer Alam, Shamimul Qamar, Amit Dixit, Mohamed Benaida

Subject: Computer Science And Mathematics, Data Structures, Algorithms And Complexity Keywords: genetic algorithm; search techniques; random tests; evolution; applications

Online: 4 June 2020 (07:44:03 CEST)

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Preprint REVIEW | doi:10.20944/preprints201805.0303.v1

Glial Bridge Ecology: Cellular Mechanisms that Drive Spinal Cord Regeneration in Zebrafish

Corbin J. Schuster, Robert M. Kao

Subject: Biology And Life Sciences, Cell And Developmental Biology Keywords: glial bridge; ctgfa; Fgf signaling; MAPK signaling; shh; slit2/3; Wnt signaling; genetic compensation; glial bridge cycle; spinal cord regeneration; termination signal; central nervous system; peripheral nervous system; zebrafish

Online: 22 May 2018 (12:09:09 CEST)

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Preprint REVIEW | doi:10.20944/preprints202007.0751.v2

Self-adaptive Biosystems Through Tunable Genetic Parts and Circuits

Vittorio Bartoli, Mario di Bernardo, Thomas E. Gorochowski

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: tunable; genetic part; control; adaptation; cybergenetics; synthetic biology; systems biology

Online: 6 October 2020 (13:32:00 CEST)

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Working Paper HYPOTHESIS

Human Genetic Diversity Possibly Determines Human's Compliance to COVID-19

Yiqiang Zhao, Yunchun Gu, Yongji Liu, Sa Li, Yuzhan Wang, Lina Bu, Qi Liu, Hongyi Lv, Fang Wan, Lida Wu, Zemin Ning

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: COVID-19; severe symptoms; inactivation; genetic diversity

Online: 16 April 2020 (09:15:49 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202101.0173.v1

Molecular Epidemiology Surveillance of SARS-Cov-2: Mutations and Genetic Diversity One Year After Emerging

Alejandro Flores-Alanis, Armando Cruz-Rangel, Flor Rodríguez-Gómez, James González, Carlos Alberto Torres-Guerrero, Gabriela Delgado, Alejandro Cravioto, Rosario Morales-Espinosa

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: SARS-CoV-2; genetic diversity; molecular surveillance; natural selection; non-synonymous substitution

Online: 11 January 2021 (09:50:55 CET)

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Preprint ARTICLE | doi:10.20944/preprints201808.0036.v1

An Overview of Multi-Antibiotic Resistance in Pathogenic Bacteria - From Selected Genetic and Evolutionary Aspects - A Review

András Fodor, Birhan Addisie Abate, Péter Deák, László Fodor, Michael G. Klein, László Makrai, Josephat Muvevi, Dávid Vozik

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: ESKAPE-bacteria; persistence; resistance; Intrinsic/Acquired/ Multidrug (MDR) and Pan – Resistance; genetic background; experimental evolution; collateral sensitivity; agrocin

Online: 2 August 2018 (06:29:07 CEST)

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The challenge posed by multi-drug resistance (MDR) of pathogenic organisms, spectacularly manifested in the 6 “ESKAPE” bacterium (two Gram-positive, four Gram-negative) species, should invoke new comprehensive strategies, and needs cooperation of scientists with medical, veterinary and natural science background. This review is aimed at informing newcomers, coming from the field of biology and genetics, about problems related to rapidly emerging, new multi-drug resistant, pathogenic, bacteria. Unlike persistence, the antibiotic resistance is inherited. A functioning “resistance gene” makes a susceptible organism resistant to a given antibiotic, encoding for polypeptides capable of acting either as decomposing enzymes, or acting as trans-membrane pumps, or membrane structure components capable of modifying the permeability implementing a «by pass» mechanism enabling the antibiotic molecule to reach its cellular target(s). A functioning “sensitivity gene” encode for a polypeptide, capable (directly or indirectly) of transferring toxic molecules into target cells, or of metabolizing non-transferable to transferable, or non-toxic molecules to toxic derivatives. A gene of a normal function could act as a “sensitivity” gene in the presence of antibiotics of chemical structures similar to the natural substrate of the gene product, (enzyme or binding/ trans-membrane protein). The Agrocin 84 story is a good example. Multi-drug resistance is a phenotypic consequence of the sequential accumulation of mutations, and/or up-take of plasmids or genomic islands carrying resistance genes from the environment via horizontal gene transfer, mediated by conjugative plasmid or bacteriophage carrying mobile genetic elements. Both multi-drug resistance and collateral sensitivity are evolutionary products. Some revealed evolutionary process and their Lamarckian and Darwinian interpretations are discussed. Toolkits of comparative full-genome sequencing, genomics, experimental evolution and population genetics may provide perspectives for overcoming the invincibility of multi-drug panresistance. The status of some recently emerging pathogenic bacterium species with zoonic features and of veterinary background is also discussed.

Preprint ARTICLE | doi:10.20944/preprints201904.0321.v1

Whole Genome Diversity, Population Structure and Linkage Disequilibrium Analysis of Chickpea (Cicer arietinum L.) Genotypes Using Genome-Wide DArTseq-Based SNP Markers

Somayeh Farahani, Mojdeh Maleki, Rahim Mehrabi, Homayoun Kanouni, Reza Talebi

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: chickpea; genetic diversity; linkage disequilibrium; DArTseq-SNP markers

Online: 29 April 2019 (07:56:52 CEST)

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Characterization of genetic diversity, population structure and linkage disequilibrium is prerequisite for proper management of breeding programs and conservation of genetic resources. In this study, 186 chickpea genotypes including advanced “Kabuli” breeding lines and Iranian landrace “Desi” chickpea genotypes were genotyped using DArTseq-Based SNP markers. Out of 3339 SNPs, 1152 markers with known chromosomal position were selected for genome diversity analysis. The number of mapped SNP markers varied from 52 (LG8) to 378 (LG4), with an average of 144 SNPs per linkage group. The chromosome size that covered by SNPs varied from 16236.36 kbp (LG8) to 67923.99 kbp (LG5), while LG4 showed higher number of SNPs, with an average of 6.56 SNPs per Mbp. Polymorphism information content (PIC) value of SNP markers ranged from 0.05 to 0.50, with an average of 0.32, while the markers on LG4, LG6 and LG8 showed higher mean PIC value than average. Un-weighted Neighbor Joining cluster analysis and Bayesian-based model population structure grouped chickpea genotypes into four distinct clusters. Principal component analysis (PCoA) and Discriminant Analysis of Principal Component (DAPC) results were consistent with that of the cluster and population structure analysis. Linkage disequilibrium (LD) was extensive and LD decay in chickpea germplasm was relatively low. A few markers showed r²≥0.8, while 2961 pairs of markers showed complete LD (r²=1) and a huge LD block was observed on LG4. High genetic diversity and low kinship value between pairs of genotypes suggesting the presence of a high genetic diversity among studied chickpea genotypes. This study also demonstrated the efficiency of DArTseq-based SNP genotyping for large scale genome analysis in chickpea. The genotypic markers provided in this study are useful for various association mapping studies when combined with phenotypic data of different traits such as seed yield, abiotic and biotic stresses and therefore can be efficiently used in breeding programs to improve chickpea.

Preprint COMMUNICATION | doi:10.20944/preprints202307.2035.v1

Children of AI: A Protocol for Managing the Born-Digital Ephemera Spawned by ChatGPT

Dirk H.R. Spennemann

Subject: Computer Science And Mathematics, Artificial Intelligence And Machine Learning Keywords: audio-visual archiving; ChatGPT; cultural heritage digital ephemera; publications ethics

Online: 31 July 2023 (04:15:50 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201710.0093.v1

A New Visual Attention Model Designed for SAR Images Based on Texture Saliency

Wei Xiong, Yongli Xu, Yafei Lv, Libo Yao

Subject: Engineering, Automotive Engineering Keywords: SAR image; Visual attention model; Texture Saliency; Feature map; Focus of attention

Online: 13 October 2017 (17:08:14 CEST)

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

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

Radhey S. Gupta, Bijendra Khadka

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

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

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

Preprint ARTICLE | doi:10.20944/preprints201806.0329.v1

Ethical, Legal and Social Implications of Susceptibility Genetic Testing for Late-Onset Neurodegenerative Diseases

Amaranta Manrique de Lara, Elisa Núñez-Acosta, Garbiñe Saruwatari-Zavala, Liliana Soto-Gómez, Miguel E. Rentería

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Alzheimer’s disease; Parkinson’s disease; Genetic testing; bioethics

Online: 21 June 2018 (04:38:35 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201804.0313.v1

Cross-Modal Multistep Fusion Network with Co-Attention for Visual Question Answering

Mingrui Lao, Yanming Guo, Hui Wang, Xin Zhang

Subject: Computer Science And Mathematics, Computer Networks And Communications Keywords: visual question answering; cross-modal multistep fusion network; attention mechanism

Online: 24 April 2018 (09:09:45 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201804.0131.v2

The Genetic Coding System and Unitary Matrices

Sergey Petoukhov

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: genetic code, alphabet, unitary matrix, dyadic shift, decomposition, spectral presentation, fractal, tensor product, quantum informatics

Online: 27 September 2018 (13:36:53 CEST)

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Preprint REVIEW | doi:10.20944/preprints202306.0360.v1

Behind Mouse Eyes: The Function and Control of Eye Movements in Mice

Eleonora Ambrad Giovannetti, Ede Rancz

Subject: Biology And Life Sciences, Neuroscience And Neurology Keywords: eye movements; visual system; mouse vision

Online: 6 June 2023 (02:44:55 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201809.0509.v1

Visual Inertial Odometry with Robust Initialization and Online Scale Estimation

Euntae Hong, Jongwoo Lim

Subject: Engineering, Control And Systems Engineering Keywords: visual-inertial odometry; UAV navigation; sensor fusion; optimization

Online: 26 September 2018 (13:23:48 CEST)

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

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

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

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

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

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

Preprint REVIEW | doi:10.20944/preprints202104.0177.v1

Excel VBA-Based User Defined Functions for Highly Precise Colebrook’s Pipe Flow Friction Approximations: A Comparative Overview

Dejan Brkić, Zoran Stajić

Subject: Computer Science And Mathematics, Algebra And Number Theory Keywords: Hydraulic resistance; Colebrook flow friction; Lambert W-function; Excel Macro Programming; Visual Basic for Applications (VBA); User Defined Functions (UDFs)

Online: 6 April 2021 (13:27:55 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201803.0120.v1

Molecular Diversity of The Tidal Swamp Rice (Oryza sativa L.) Germplasm of The South Kalimantan, Indonesia

Dindin H. Mursyidin, Purnomo Purnomo, Issirep Sumardi, Budi S. Daryono

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Oryza sativa; genetic diversity; tidal swamp; breeding and conservation programs

Online: 15 March 2018 (06:50:32 CET)

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Preprint ARTICLE | doi:10.20944/preprints201910.0209.v1

Agronomic Practices, Genetic Diversity and Population Structure of Moringa oleifera (Lam.) in Nigeria

Jacob Popoola, David Igwe, Opeyemi Jegede, Victoria Iwu, Adegoke Adegbite, Conrad Omonhinmin

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: agronomic practices; agrobiodiversity; aflp; climate change; cluster analysis; genetic diversity; moringa oleifera; food and nutrition security

Online: 18 October 2019 (07:34:50 CEST)

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Evaluation of agronomic practices, genetic diversity and population structure of Moringa oleifera (Lam.) is crucial to its sustainable utilization to ensure food and nutritional security. Four agronomic practices of field preparation and soil analysis, regeneration, weeding and pruning, as well as harvesting, were adopted. Genetic diversity and population structure of 20 populations were evaluated using amplified fragment length polymorphism (AFLP) primer pairs (E-ACC/M-CAC and E-ACA/M-CAG). The effects of agronomic practices on leaf quantity production were evaluated using standard procedures. The physico-chemical and morphological data were analyzed using descriptive statistics, while genetic diversity, population structure, dendrogram reconstruction, and Principal Component Analysis (PCA) were analyzed from the AFLP genetic data. Significant effects (P ≤ 0.05) of agronomic practices on the quantity of leaf production were recorded across the accessions. The two primer pairs generated a total of 80 alleles with a mean major allele frequency of 0.0250. Gene diversity and polymorphic information content (PIC) values were high with a mean of 0.98 and 0.974, respectively. The Gst value of 0.0490 indicated that 5 % of the total genetic divergence was among the population while 95 % within the population. Dendrogram reconstruction with genetic distance ranging from 0.87 to 0.96 segregated the accessions into eleven clusters while PCA generated six cluster groups. Field preparation and physico-chemical soil properties, regeneration, weeding and pruning, and stand development, as well as harvesting, influenced the leaf yield and genetic diversity observed in this study. The genetic data revealed that some accessions were clustered along eco-geographical lines while others grouped disparately. Identified potential parent genotypes with valuable and desirable genetic traits can be exploited for commercial, breeding and conservation purposes to ensure sustainable utilization of the species in Nigeria.

Preprint ARTICLE | doi:10.20944/preprints201909.0227.v1

Circadian Tuning with Metameric White Light: Visual and non-visual Aspects

Tamara Aderneuer, Oliver Stefani, Oscar Fernández, Christian Cajochen, Rolando Ferrini

Subject: Physical Sciences, Optics And Photonics Keywords: non-visual effect; metamerism; light-emitting diodes (LEDs); lighting; spectral optimization

Online: 19 September 2019 (15:43:06 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202101.0614.v1

Unlocking the Patterns of the Tunisian Durum Wheat Landraces Genetic Structure Based on Phenotypic Characterization in Relation to Farmer’s Vernacular Name

Cyrine Robbana, Zakaria Kehel, Karim Ammar, Carlos Guzmán, M’Barek Ben Naceur, Ahmed Amri

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: Durum wheat; Tunisian landraces; genetic diversity; population structure; phenotypic characterization

Online: 29 January 2021 (11:53:26 CET)

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Preprint ARTICLE | doi:10.20944/preprints201811.0603.v1

Adjuvant Potential of CD24 on Immunogenicity and Lethal Challenge Protection of a DNA vector Expressing Nucleocapsid Protein of Crimean Congo Hemorrhagic Fever Virus

Touraj Aligholipour Farzani, Alireza Hanifehnezhad, Katalin Foldes, Koray Ergunay, Erkan Yilmaz, Hiba Hashim Mohamed Ali, Aykut Ozkul

Subject: Biology And Life Sciences, Virology Keywords: CCHFV, CD24, nucleocapsid, genetic adjuvant, immunogenicity, IFNAR-/- mice

Online: 27 November 2018 (12:15:59 CET)

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Preprint ARTICLE | doi:10.20944/preprints202208.0042.v1

Serological and Oncoinformatic Analysis of HbA1c as a Prognostic Biomarker in Screening the Risks of Different Cancers among the Male T2D Patients of Bangladesh

Md. Al Hasibuzzaman, Salauddin Al Azad, Md. Abdur Rashid Mia, Samarth Islam, Sharmin Ahmed, Afsana Masud, Samiur Rahman, Arysha Alif Khan, Fahmida Hoque Rimti, Ashrak Shad Pyash, Partha Biswas, Homayra Rahman Shoshi, Fariha Hoque Rimu, Ramiza Nausheen Zaman, Md. Ataur Rahman, Bonglee Kim

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: HbA1c biomarker; type 2 diabetes; cancer risk profiling; serological diagnosis; oncoinformatic screening; genetic overexpression; promoter methylation

Online: 2 August 2022 (06:04:42 CEST)

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This research aimed to figure out the applications of HbA1c protein and HbA1 gene as the prognostic biomarkers for assessing the risks of different cancers among male T2D patients in Bangladesh considering their serological and oncoinformatic parameters. Depending on the concentrations of HbA1c (%) of the T2D patients (n=300), their individual FBS (mmol/L); THABF (mmol/L); creatinine (mg/dl); SC (mg/dl); STGs (mg/dl); HDLC (mg/dl); and LDLC (mg/dl) were estimated. The values of the patients were compared with the control (n=60) group as the serological analysis. Besides, HbA1 gene (encoding hBA1c protein) overexpression and promotor methylation responsible for BLCA, BRCA, CHOL, COAD, LUAD, LUSC, PAAD, and PRAD cancers in the male T2D patients were profiled as the oncoinformatic parameters based on the sample types; caner stages; racial footprints; gender; age; nodal metastasis; p53 methylations; pancreatitis; diabetes status; smoking behaviors; and overall/disease-free survivability. Finally, the ‘HbA1 gene strings’ responsible for genetic coexpression; endophytic vesicle regulation; antioxidant regulation; oxygen species metabolic regulation; and gene-mediated response to the reactive oxygen molecules were studied comprehensively. A strong correlation between BMI and FBS was observed in both the patients and the control (P<0.0001). Similarly, the values of FBS, THABF, and creatinine resulted in equal significance (P<0.0001) as compared to the HbA1c concentrations of all the T2D and control individuals. The SC, STGs, HDLC, and LDLC concentrations regulated ardently in both the control (P<0.0001), and patients group (P<0.0001), while HbA1c ranged from 3.8-5.8%, and 5.11-15.8% respectively. HbA1 gene is found downregulating with cancer progressed in most of the oncoinformatic parameters. According to the DA, CS, EI, CE, PC, NC, GF, H, and AT profiles; the HbA1 gene interacts with 8 other genes responsible for creating a protein cluster comprising- AHSP, HBA1, HBA2, HBB, HBD, HBE1, HBG2, RPS12, and RPS19 proteins for cancer formation. To recapitulate, HbA1c protein and HbA1 gene can be used as the prognostic serological and molecular biomarkers respectively for determining the risks of cancers among male chronic T2D patients.

Preprint ARTICLE | doi:10.20944/preprints201908.0097.v1

Evaluation of Machine Learning Techniques for Daily Reference Evapotranspiration Estimation

Ali Rashid Niaghi, Oveis Hassanijalilian, Jalal Shiri

Subject: Engineering, Civil Engineering Keywords: Evapotranspiration, Genetic programming, Support vector machine, Multiple linear regression, Random forest

Online: 7 August 2019 (11:28:34 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202103.0103.v1

Automated Capture-Based NGS Workflow: One Thousand Patients Experience in a Clinical Routine Framework

Elena Tenedini, Fabio Celestini, Pierluigi Iapicca, Marco Marino, Sara Castellano, Lucia Artuso, Fiammetta Biagiarelli, Laura Cortesi, Angela Toss, Elena Barbieri, Luca Roncucci, Monica Pedroni, Rossella Manfredini, Mario Luppi, Tommaso Trenti, Enrico Tagliafico

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: Next Generation Sequencing; Laboratory automation; Hereditary Cancer; Genetic Testing; Clinical Genomics.

Online: 2 March 2021 (16:00:24 CET)

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Preprint ARTICLE | doi:10.20944/preprints202008.0707.v1

Comparative Study of the Restorative Effects of Forest and Urban Videos during Covid-19 Lockdown: Intrinsic and Benchmark Value

Federica Zabini, Lorenzo Albanese, Francesco Riccardo Becheri, Gioele Gavazzi, Fiorenza Giganti, Fabio Giovanelli, Giorgio Gronchi, Andrea Guazzini, Marco Laurino, Qing Li, Tessa Marzi, Francesca Mastorci, Francesco Meneguzzo, Stefania Righi, Maria Pia Viggiano

Subject: Social Sciences, Cognitive Science Keywords: Anxiety; Audio-Visual stimulation; COVID-19; Environmental enrichment; Forest environments; Forest therapy; Lockdown; Mental health; Stress; Quarantine

Online: 31 August 2020 (05:20:50 CEST)

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Preprint REVIEW | doi:10.20944/preprints202107.0182.v1

CRISPR Cas9 Tip of an Iceberg: It’s Potential in Genome Editing and Many More

Jalal Ahmad, Nayyer Siddique

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: CRISPR-Cas9; Genome editing; plant editing; bacterial immune system; genetic disease

Online: 8 July 2021 (09:50:22 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201712.0129.v1

Nonlinear Modeling and Coordinate Optimization of Semi-Active Energy Regenerative Suspension with Electro-Hydraulic Actuator

Farong Kou, Jiafeng Du, Zhe Wang, Dong Li, Jianan Xu

Subject: Engineering, Automotive Engineering Keywords: semi-active suspension; feed energy; parameter optimization; genetic algorithm

Online: 19 December 2017 (06:53:01 CET)

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Preprint ARTICLE | doi:10.20944/preprints202201.0101.v1

Line × tester Study in Bread Wheat (Triticum aestivum L.) for Important Biochemical and Morphological Traits

Anand Kumar, Lokendra Singh, Prashant Kaushik

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Bread wheat; general combining ability; specific combining ability; heritability; genetic advance

Online: 10 January 2022 (11:30:43 CET)

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Preprint HYPOTHESIS | doi:10.20944/preprints202109.0372.v1

Endometriosis Etiology: Hypothesis of Maternal Microchimerism

Tanya Barad

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Endometriosis; microchimerism; maternal microchimerism; reproduction; gynaecology; etiology; auto-immune; immune response; hormonal; vascular; genetic; hereditary; male; fetal; fetus; stem cells; pregnancy; Műllerianosis; embryology; ROS; apoptosis; disease; endometrium; basalis; menstruation; post-menopausal; neurogenesis

Online: 22 September 2021 (10:27:52 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201803.0215.v1

Estimation of Genetic Parameters and Prediction of Genotypic Values in Common Beans Using Mixed Models

Jessica Delfini, Vania Moda Cirino, Claudete de Fátima Ruas, Paulo Mauricio Ruas, José dos Santos Neto, Leandro Simões Azeredo Gonçalves

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Phaseolus vulgaris L.; REML/BLUP; genetic diversity

Online: 26 March 2018 (10:35:00 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201804.0213.v2

Stuck on a Plateau? A Model-Based Approach to Fundamental Issues in Visual Temporal-Order Judgments

Jan Tünnermann, Ingrid Scharlau

Subject: Social Sciences, Cognitive Science Keywords: Temporal-order judgments; modeling; theory of visual attention; TVA; range of indecision; encoding reset

Online: 8 June 2018 (16:12:09 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202101.0131.v1

Finite Groups for the Kummer Surface: the Genetic Code and a Quantum Gravity Analogy

Michel Planat, David Chester, Raymond Aschheim, Marcelo Amaral, Fang Fang, Klee Irwin

Subject: Computer Science And Mathematics, Algebra And Number Theory Keywords: Kummer surface; DNA genetic code; hexamers and pentamers; informationally complete characters; finite groups; hyperelliptic curve

Online: 6 January 2021 (16:02:22 CET)

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Preprint ARTICLE | doi:10.20944/preprints202003.0079.v1

Performance Comparisons of Bio-micro Genetic Algorithms on Robot Locomotion

Francisco A. Chávez-Estrada, Jacobo Sandoval-Gutierrez, Juan C. Herrera-Lozada, Mauricio Olguín-Carbajal, Daniel L. Martínez-Vázquez, Miguel Hernández-Bolaños, Israel Rivera-Zárate

Subject: Engineering, Control And Systems Engineering Keywords: micro segmented genetic algorithm; multicore embedded system; parallel processing

Online: 5 March 2020 (03:23:59 CET)

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Preprint ARTICLE | doi:10.20944/preprints201808.0523.v1

The Effects of Visual Cues, Blindfold, Synesthetic Experience and Music Training on Pure-Tone Frequency Discrimination

Cho Kwan Tse, Calvin Kai-Ching Yu

Subject: Social Sciences, Cognitive Science Keywords: frequency difference limens; blindfold; visual cues; auditory-visual synesthesia; gliding frequencies; perceptual limit, common resource theory; multiple resource model

Online: 30 August 2018 (10:40:28 CEST)

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Working Paper CONCEPT PAPER

The Physics–Biology Continuum Refutes Darwinism: Evolution is Directed by the Homeostasis-Dependent Bidirectional Relation between Genome and Phenotype

Didier Auboeuf

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: evolution; darwinism; genetic code; RNA; homoestasis; physics

Online: 6 January 2021 (15:06:41 CET)

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Preprint REVIEW | doi:10.20944/preprints202109.0432.v1

Cancer: More Than a Geneticist’s Pandora’s Box

Kritika Saxena, Ayalur Raghu Subbalakshmi, Prakash Kulkarni, Mohit Kumar Jolly

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: Non-genetic heterogeneity; multistability; drug-tolerant persisters; phenotypic plasticity; biological noise; epithelial-mesenchymal plasticity; PAGE4

Online: 24 September 2021 (12:44:34 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201909.0269.v1

Contesting the Geneticization Thesis in Human Reproduction: Dealing with Spiral Shaped Processes and Technoscientific Imaginaries

Ido Alon, Jose Guimon, Rosa Urbanos-Garrido

Subject: Medicine And Pharmacology, Obstetrics And Gynaecology Keywords: assisted reproductive technologies; In-Vitro Fertilization; Delphi; geneticization; Preimplantation Genetic Diagnosis; diffusion of innovation

Online: 24 September 2019 (05:32:19 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201804.0227.v1

Converting Ensemble Clustering Problem to a Mathematical Optimization Problem and Providing an Approach to Solve Based on Optimization Toolbox

Simintaj Salehpour, Hamid Parvin

Subject: Computer Science And Mathematics, Data Structures, Algorithms And Complexity Keywords: Ensemble clustering; cluster stability; F-measure; co-association matrix; genetic algorithm

Online: 17 April 2018 (15:58:22 CEST)

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Preprint REVIEW | doi:10.20944/preprints201807.0443.v1

Can Genetic Factors Compromise the Success of Dental Implants? A Systematic Review and Meta-Analysis

Joel Ferreira Santiago Junior, Claudia Cristina Biguetti, Mariza Akemi Matsumoto, Guilherme Abu Halawa Kudo, Raquel Barroso Parra da Silva, Patrícia Pinto Saraiva, Walid D. Fakhouri

Subject: Medicine And Pharmacology, Dentistry And Oral Surgery Keywords: genetic factors; dental implants; bone quality; bone regeneration; success rate

Online: 24 July 2018 (06:01:10 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201806.0211.v1

Effects of Exogenous and Endogenous Attention on Metacontrast Masking

Sevda Agaoglu, Bruno Breitmeyer, Haluk Ogmen

Subject: Social Sciences, Cognitive Science Keywords: metacontrast; attention; exogenous attention; endogenous attention; visual masking; masking attention interactions

Online: 13 June 2018 (11:06:02 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 REVIEW | doi:10.20944/preprints201806.0191.v1

Recent Developments in Using Drosophila as a Model for Human Genetic Disease

Christine Oriel, Paul Lasko

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: rare disease; functional genomics; genetic variant validation

Online: 12 June 2018 (12:36:08 CEST)

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Preprint REVIEW | doi:10.20944/preprints201902.0090.v1

Germline Missense Variants in BRCA1: New Trends and Challenges for Clinical Annotation

Volha Golubeva, Thales Nepomuceno, Alvaro Monteiro

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: BRCA1; variants of uncertain clinical significance; VUS; germline variants; hereditary breast and ovarian cancer; breast cancer; genetic testing, ovarian cancer; variant classification; clinical annotation

Online: 11 February 2019 (16:12:03 CET)

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Preprint ARTICLE | doi:10.20944/preprints202105.0211.v1

Evaluation of SYK Gene as a Prognostic Biomarker and Suggested Aromatic Potential Phytochemicals to Halt the Colorectal Cancer

Partha Biswas, Dipta Dey, Atikur Rahman, Md. Aminul Islam, Tasmina Ferdous Susmi, Md. Abu Kaium, Md. Nazmul Hasan, MD. Hasanur Rahman, Shafi Mahmud, Md. Abu Saleh, Priyanka Paul, Md Rezanur Rahman, Md. Ataur Rahman, Han Gyeul Song, Bonglee Kim

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: Colorectal cancer; SYK; Prognostic Significance; Genetic Alteration; Molecular dynamics simulations

Online: 10 May 2021 (15:20:54 CEST)

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Background: Colorectal cancer is considered the third most fetal among all type of cancer. Spleen tyrosine kinase (SYK) is a non-receptor type tyrosine-protein that plays crucial role in signaling mediated via immune receptor. We adopted an onco-informatics analysis to evaluate the SYK expression and prognostic value of SYK in colorectal cancer, and identification of potential phytochemicals which may inhibit overexpression of SYK protein as well as minimized colorectal cancer. Materials & Methods: Differential expression of SYK gene was analyzed using the several transcriptomic databases including Oncomine, UALCAN, GENT2 and GEPIA2. The server, cBioPortal was used to analyze mutation and copy number alterations whereas GENT2, GEPIA, OncoLnc and PrognoScan were employed to examine the survival rate. A protein-protein interaction network of SYK and co-expressed genes of SYK was conducted via GeneMANIA. Considering SYK gene encoding protein as drug target, selected phytochemicals were assessed by molecular docking using PyRx 0.8 packages. YASARA molecular dynamics simulators were applied for the post validation of the molecular docking data. Results: We have observed significant overexpression of mRNA expression levels of SYK gene colorectal adenocarcinoma (COAD) samples compared with normal tissues. Significant methylation level and various genetic alterations are assembled in SYK gene which can lead to the development of colorectal cancer. As a result, lower level of SYK expression was related to the more chances of patients’ survival by which all the outcomes from the multiple bioinformatics platforms and web resources have demonstrated the significant evidences that the SYK kinsase can possess as a potential biomarker for the treatment of colorectal cancer. Here, aromatic phytochemicals namely, Kaempferol and Glabridin targeting SYK showed more stability compared to controls and may be useful for the treatment of colorectal cancer. Conclusion: Our study showed dysregulated expression of SYK in colorectal cancer and potentiality to act as a biomarker for the prognosis of CRC. Moreover, we have shown phytochemicals (Kaempferol and Glabridin) target SYK as potential treatment strategies and drug repositioning potentiality in colorectal cancer.

Preprint ARTICLE | doi:10.20944/preprints201804.0040.v1

Toxic Effects of Methanol among Illegally Dispatched Workers at Aluminum CNC cutting process in Small-scale 3rd tier Subcontractor Factories of Smartphone Manufacturers in the Republic of Korea

Chung Won Kang, Hyunjoo Kim, Kyoung Seok Shin, Jia Rhu, Kyounghee Jungchoi, Key Hwan Lim, Jin-Ha Kim

Subject: Medicine And Pharmacology, Ophthalmology Keywords: Methanol exposure; toxic effects; subcontractor manufacturing; dispatched workers; visual defect; neurobehavioral function

Online: 3 April 2018 (16:11:15 CEST)

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Preprint REVIEW | doi:10.20944/preprints202012.0738.v1

Utility of Whole-Exome Sequencing in Pediatric and Medical Diagnosis

Mohd Fareed, Varun Sharma, Hemender Singh

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Next generation sequencing; Genetic disorders; Genomic medicine; Genetic counseling; Rare diseases

Online: 29 December 2020 (16:47:01 CET)

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Preprint ARTICLE | doi:10.20944/preprints201803.0021.v2

Map Archive Mining: Visual-analytical Approaches to Explore Large Historical Map Collections

Johannes Uhl, Stefan Leyk, Yao-Yi Chiang, Weiwei Duan, Craig A. Knoblock

Subject: Environmental And Earth Sciences, Remote Sensing Keywords: map processing; retrospective landscape analysis; visual data mining, image retrieval, low-level image descriptors, color moments, t-distributed stochastic neighborhood embedding, USGS topographic maps, Sanborn fire insurance maps

Online: 17 April 2018 (09:23:37 CEST)

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Working Paper ARTICLE

Identifying Genetic Variants and Pathways Associated with Extreme Levels of Fetal Hemoglobin in Sickle Cell Disease in Tanzania

Siana Nkya, Liberata Mwita, Josephine Mgaya, Happiness Kumburu, Marco van Zwetselaar, Stephan Menzel, Gaston K. Mazandu, Raphael Z. Sangeda, Emile R. Chimusa, Julie Makani

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Sickle cell disease; genetic disorder; fetal hemoglobin; hemoglobinopathy; Tanzania

Online: 20 September 2019 (11:47:39 CEST)

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