scholarly journals A Quantitative Genomic View of the Coronaviruses: SARS-COV2

2020 ◽  
Author(s):  
Sk Sarif Hassan ◽  
Ranjeet Kumar Rout ◽  
Vipul Sharma
Keyword(s):  
Hurst Exponent ◽  
Hamming Distance ◽  
Gc Content ◽  
Large Family ◽  
Healthcare Facility ◽  
Viral Disease ◽  
Complete Sequences ◽  
Quantitative Understanding ◽  
The Common ◽  
Purine Pyrimidine

In 2020, the pandemic caused by the Coronaviruses (CoV) that are a large family of viruses that cause illness ranging from the common cold to more severe diseases such as Middle East Respiratory Syndrome (MERS-CoV) and Severe Acute Respiratory Syndrome (SARS-CoV2). The Coronavirus disease (COVID-19) is a new strain that was discovered in 2019 and has not been previously identified in humans. It is the high time to investigate the quantitative and/or qualitative genomic informations of the virus SARS-CoV2 in order to strengthen the healthcare facility to fight against this viral disease. In this article, a through quantitative understanding of the purine and pyrimidine spatial distribution/organization of all 89 complete sequences of SARS-CoV (available as on date in the NCBI virus database, is made using different parameters such as fractal dimension, Hurst exponent, Shannon entropy and GC content of the nucleotide sequences of the genome of SARS-CoV2. Also a cluster among all the the SARS-CoV sequences of nucleotide have been made based on their phylogeny made through their closeness (Hamming distance) based on respective purine-pyrimidine distribution.

scholarly journals A Quantitative Comparisons of $\beta$-Coronavirus Genomes and Their Associated Genes

2020 ◽  
Author(s):  
Sk Sarif Hassan ◽  
Ranjeet Kumar Rout
Keyword(s):  
Density Estimation ◽  
Shannon Entropy ◽  
Hurst Exponent ◽  
Gc Content ◽  
Spatial Representations ◽  
Human Coronavirus ◽  
Precise Understanding ◽  
Different Types ◽  
Purine Pyrimidine ◽  
Nucleotide Bases

A precise understanding of the genes and associated genomes of SARS-CoV2 is important for various reasons such as discovering origin of the virus and virulence and so on. A thorough descriptive understanding of the SARS-CoV2 genomes and other coronavirus of the beta-coronavirus genus is primarily important. In this article, a set of ten genomes of four CoVs and their associated genes are considered for this present study. A spatial representations of nucleotide bases including purine-pyrimidine representations of the different genes of the corresponding genomes are quantified using Hurst exponent, Shannon entropy and density estimation of different nucleotides including GC content, in order to draw a comparison and contrast among the ten genomes of different types of CoVs which include MERS, SARS-CoV, HKU1 (Human Coronavirus) and associated their genes.

scholarly journals Role of Radiologic Computed Tomography in Evaluating Coronavirus (COVID-19) Patients

2021 ◽  
pp. 39-44
Author(s):  
Mwahib Sayed Ahmed Aldosh
Keyword(s):  
Computed Tomography ◽  
Ct Scan ◽  
Ct Scanning ◽  
Viral Disease ◽  
Human Beings ◽  
Complementary Method ◽  
High Incidence ◽  
High Incidence Rate ◽  
The Common

Objective: Coronavirus (Covid 19) is a dangerous viral disease that principally targets the respiratory system of human beings. The main objective of this study is to evaluate the significant effects resulting from Covid19 using radiologic CT scanning technology. Methods: The recent study was conducted in order to evaluate covid19 among the local public. The sample size for this study consisted of two hundred and thirty (230) patients diagnosed with coronavirus and underwent a chest computed tomography scan. The study was conducted at Najran city, between the period from September to December 2020. Results: The results showed that it is possible to diagnose the complications of coronavirus that affects the respiratory tract in an accurate manner using chest CT imaging and the main results revealed that coronavirus COVID-19 affected all, but males more than female. (50-60) Age group was the big distribution while acute respiratory failure is the most common clinical etiology. The CT scan findings revealed that bilateral pneumonia was the common complication with a high incidence rate of 32% percent and blood coagulation achieved 5% percent as the minimum distribution result. Conclusion: The sensitivity of the CT scans in assessing COVID-19 was significantly high, it has the efficiency to assess complications of COVID-19 in an accurate manner, and therefore it has been proposed to use CT scan as a complementary method in covid-19 diagnosis. More studies on coronavirus disease were recommended by the author.

scholarly journals An Intelligent Optimization Algorithm for Constructing a DNA Storage Code: NOL-HHO

2020 ◽  
Vol 21 (6) ◽  
pp. 2191 ◽  
Author(s):  
Qiang Yin ◽  
Ben Cao ◽  
Xue Li ◽  
Bin Wang ◽  
Qiang Zhang ◽  
...  
Keyword(s):  
Optimization Algorithm ◽  
Dna Sequences ◽  
Learning Strategy ◽  
Hamming Distance ◽  
Experimental Testing ◽  
Gc Content ◽  
Smooth Transition ◽  
Local Optima ◽  
Dna Storage

The high density, large capacity, and long-term stability of DNA molecules make them an emerging storage medium that is especially suitable for the long-term storage of large datasets. The DNA sequences used in storage need to consider relevant constraints to avoid nonspecific hybridization reactions, such as the No-runlength constraint, GC-content, and the Hamming distance. In this work, a new nonlinear control parameter strategy and a random opposition-based learning strategy were used to improve the Harris hawks optimization algorithm (for the improved algorithm NOL-HHO) in order to prevent it from falling into local optima. Experimental testing was performed on 23 widely used benchmark functions, and the proposed algorithm was used to obtain better coding lower bounds for DNA storage. The results show that our algorithm can better maintain a smooth transition between exploration and exploitation and has stronger global exploration capabilities as compared with other algorithms. At the same time, the improvement of the lower bound directly affects the storage capacity and code rate, which promotes the further development of DNA storage technology.

scholarly journals Acute kidney injury in COVID-19; a review on current knowledge

2020 ◽  
Vol 9 (4) ◽  
pp. e31-e31 ◽  
Author(s):  
Elahe Aleebrahim-Dehkordi ◽  
Ali Reyhanian ◽  
Shirin Saberianpour ◽  
Ali Hasanpour-Dehkordi
Keyword(s):  
Genomic Sequence ◽  
Current Knowledge ◽  
Kidney Injury ◽  
Large Family ◽  
Lung Damage ◽  
Low Oxygen ◽  
Respiratory Involvement ◽  
Coronavirus Infection ◽  
The Common ◽  
Review Study

Coronaviruses are a large family of viruses that can cause a variety of diseases in humans. Some coronaviruses cause only mild illnesses like the common cold. While, some coronaviruses such as SARS-CoV (SARS-associated coronavirus) and Middle East respiratory syndrome coronavirus (MERS-CoV) have, in recent years, been able to cause severe respiratory involvement (pneumonia), leading to death in several patients. By identifying the genomic sequence of the new human coronavirus SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) it has been revealed that it belongs to the beta coronavirus genus. COVID-19 appears to be transmitted by a mechanism similar to the influenza virus via person to person, sneezing coughing, or contact with the secretions of infected patients. Early symptoms of these respiratory viruses include fever, cough, and shortness of breath, with an incubation period of 2-14 days. SARS-CoV-2 is an acute respiratory disease that initially causes lung damage. SARS-CoV-2 can affect other organs, including the kidneys. Kidney damage may be caused by alterations that occur during coronavirus infection. It seems that low-oxygen delivery to tissues like the kidney in the setting of this disease may lead to ischemic damage of the kidney. Considering the importance of the kidneys, as one, this review study aimed to investigate the effect of the new coronavirus on the kidneys and its role in the development of renal failure.

scholarly journals Middle East Respiratory Syndrome Coronavirus (MERS-CoV): State of the Science

2020 ◽  
Vol 8 (7) ◽  
pp. 991 ◽  
Author(s):  
Ahmed Mostafa ◽  
Ahmed Kandeil ◽  
Mahmoud Shehata ◽  
Rabeh El Shesheny ◽  
Abdallah M. Samy ◽  
...  
Keyword(s):  
Middle East ◽  
Severe Acute Respiratory Syndrome ◽  
Disease Outbreaks ◽  
Case Fatality ◽  
Large Family ◽  
Middle East Respiratory Syndrome ◽  
Current State ◽  
The Common ◽  
Mode Of Transmission ◽  
State Of The Science

Coronaviruses belong to a large family of viruses that can cause disease outbreaks ranging from the common cold to acute respiratory syndrome. Since 2003, three zoonotic members of this family evolved to cross species barriers infecting humans and resulting in relatively high case fatality rates (CFR). Compared to Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV, CFR = 10%) and pandemic Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2, CFR = 6%), the Middle East Respiratory Syndrome Coronavirus (MERS-CoV) has scored the highest CFR (approximately 35%). In this review, we systematically summarize the current state of scientific knowledge about MERS-CoV, including virology and origin, epidemiology, zoonotic mode of transmission, and potential therapeutic or prophylactic intervention modalities.

scholarly journals Draft Genome Sequences and Complete Sequences of Two Plasmids of Escherichia coli Strain BOq 01, a Multiple-Antibiotic-Resistant Strain Isolated from a Poultry Farm in Mexico

2018 ◽  
Vol 7 (20) ◽  
Author(s):  
Armando Hernández-Mendoza ◽  
Daniel Rivera Mendoza ◽  
Abimael Moran-Vazquez ◽  
Edgar Dantán-González
Keyword(s):  
Escherichia Coli ◽  
Draft Genome ◽  
Gc Content ◽  
Coli Strain ◽  
Poultry Farm ◽  
Genome Sequences ◽  
Antibiotic Resistant ◽  
Content Type ◽  
A Genome ◽  
Complete Sequences

We report here the draft genome sequence of Escherichia coli strain BOq 01, a bacterium isolated from a poultry farm; the genome includes two plasmids conferring antibiotic resistances. This bacterium has a GC content of 50.89% and a genome size of 4.6 Mb.

Holo-Transcriptome Sequences from the Tropical Marine Sponge Cinachyrella alloclada

2021 ◽  
Author(s):  
Yvain Desplat ◽  
Jacob F Warner ◽  
Jose V Lopez
Keyword(s):  
Marine Sponge ◽  
High Throughput Sequencing ◽  
Gc Content ◽  
Model Organism ◽  
Sequence Length ◽  
Microbial Abundance ◽  
Average Sequence Length ◽  
The Common ◽  
Transcriptome Sequences ◽  
Average Sequence

Abstract Marine sponge transcriptomes are underrepresented in current databases. Furthermore, only two sponge genomes are available for comparative studies. Here we present the assembled and annotated holo-transcriptome of the common Florida reef sponge from the species Cinachyrella alloclada. After Illumina high throughput sequencing, the data assembled using Trinity v2.5 confirmed a highly symbiotic organism, with the complexity of high microbial abundance (HMA) sponges. This dataset is enriched in poly-A selected eukaryotic, rather than microbial transcripts. Overall, 39,813 transcripts with verified sponge sequence homology coded for 8,496 unique proteins. The average sequence length was found to be 946 bp with an N50 sequence length of 1290 bp. Overall, the sponge assembly resulted in a GC content of 51.04%, which is within the range of GC bases in a eukaryotic transcriptome. BUSCO scored completeness analysis revealed a completeness of 60.3% and 60.1% based on the Eukaryota and Metazoa databases, respectively. Overall, this study points to an overarching goal of developing the Cinachyrella alloclada sponge as a useful new experimental model organism.

Historical Insight, Classification, and Common Features of Coronavirus Family

2022 ◽  
pp. 1-20
Author(s):  
Moulay Abdelmonaim El Hidan ◽  
Soraia El Baz ◽  
Mohamed Merzouki ◽  
Kholoud Kahime ◽  
Moulay Abdeljalil Ait Baamrane ◽  
...  
Keyword(s):  
Large Family ◽  
Upper Respiratory Tract ◽  
Virus Family ◽  
Respiratory Tract Illnesses ◽  
History Of ◽  
The Common ◽  
Upper Respiratory ◽  
Novel Coronavirus ◽  
Viral Surface

Coronaviruses are a large family of viruses that usually cause mild to moderate upper-respiratory tract illnesses, like the common cold. They were named according to the shape of glycoprotein spikes present on the viral surface and resembling to the solar corona. The first coronaviruses identified in human were HCoV 229E and the HCoV OC43, known also as β-coronavirus. This virus family has become increasingly important and received more attention within scientific community in the past two decades because of three new viruses that can cause serious, even fatal, disease. These are SARS coronavirus (SARS-CoV), which emerged in November 2002 and caused severe acute respiratory syndrome (SARS); Middle East respiratory syndrome (MERS) caused by the MERS coronavirus (MERS-CoV), identified in September 2012 and continues to cause sporadic and localized outbreaks. The third novel coronavirus to emerge in this century is called SARS-CoV-2. This chapter will describe the history of the coronavirus family discovery, emergence, and classification of the main coronaviruses.

The Diathesis of General Paralysis

1892 ◽  
Vol 38 (160) ◽  
pp. 30-40
Author(s):  
G. R. Wilson
Keyword(s):  
Nervous System ◽  
Large Family ◽  
Recent History ◽  
The Sun ◽  
General Paralysis ◽  
Hereditary Factor ◽  
History Of ◽  
The Common ◽  
As If

Ten years ago Mr. Jonathan Hutchinson said that the description of a fresh diathesis was almost as easy as the discovery of a new nerve centre or the revelation of a new bacterium. Yet no new diathesis, so far as I know, has since then become generally recognized in our special branch of medicine. To-day the neurotic diathesis stands as god-mother to a large family of diseases, and little has been done to differentiate their ætiology, or to trace their genealogy. On the contrary there seems to be a tendency to exaggerate the importance of environment in the ætiology of many of the diseases of the nervous system, and to ignore the hereditary factor. Especially is this the case with general paralysis. Excepting the writings of a few, a course of reading on the ætiology of general paralysis would incline one to believe that there is no evil under the sun—from syphilis to the cessation of lactation—that may not sufficiently account for the onset of that disease. It seems almost as if the observers had first tried to find an acknowledged raison d'être, and, failing in that, had adduced as “cause” anything in the recent history of the patient at all out of the common, or which had ranked as important in the estimation of his friends.

Rare earth-ruthenium-magnesium intermetallics

2017 ◽  
Vol 72 (6) ◽  
pp. 447-455
Author(s):  
Sebastian Stein ◽  
Marcel Kersting ◽  
Lukas Heletta ◽  
Rainer Pöttgen
Keyword(s):  
Rare Earth ◽  
Large Family ◽  
Structural Motif ◽  
X Ray Diffraction ◽  
Space Group ◽  
Cscl Type ◽  
Magnesium Compounds ◽  
Pauli Paramagnetism ◽  
The Common ◽  
Subgroup Scheme

AbstractEight new intermetallic rare earth-ruthenium-magnesium compounds have been synthesized from the elements in sealed niobium ampoules using different annealing sequences in muffle furnaces. The compounds have been characterized by powder and single crystal X-ray diffraction. Sm9.2Ru6Mg17.8 (a=939.6(2), c=1779(1) pm), Gd11Ru6Mg16 (a=951.9(2), c=1756.8(8) pm), and Tb10.5Ru6Mg16.5 (a=942.5(1), c=1758.3(4) pm) crystallize with the tetragonal Nd9.34Ru6Mg17.66 type structure, space group I4/mmm. This structure exhibits a complex condensation pattern of square-prisms and square-antiprisms around the magnesium and ruthenium atoms, respectively. Y2RuMg2 (a=344.0(1), c=2019(1) pm) and Tb2RuMg2 (a=341.43(6), c=2054.2(7) pm) adopt the Er2RuMg2 structure and Tm3Ru2Mg (a=337.72(9), c=1129.8(4) pm) is isotypic with Sc3Ru2Mg. Tm3Ru2Mg2 (a=337.35(9), c=2671(1) pm) and Lu3Ru2Mg2 (a=335.83(5), c=2652.2(5) pm) are the first ternary ordered variants of the Ti3Cu4 type, space group I4/mmm. These five compounds belong to a large family of intermetallics which are completely ordered superstructures of the bcc subcell. The group-subgroup scheme for Lu3Ru2Mg2 is presented. The common structural motif of all three structure types are ruthenium-centered rare earth cubes reminicent of the CsCl type. Magnetic susceptibility measurements of Y2RuMg2 and Lu3Ru2Mg2 samples revealed Pauli paramagnetism of the conduction electrons.

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