scholarly journals Diversity of SARS-CoV-2 isolates driven by pressure and health index

2021 ◽  
Vol 149 ◽  
Author(s):  
R. K. Sanayaima Singh ◽  
Md. Zubbair Malik ◽  
R. K. Brojen Singh
Keyword(s):  
Fractal Dimension ◽  
Severe Acute Respiratory Syndrome ◽  
Mutation Rate ◽  
Hurst Exponent ◽  
Viral Genome ◽  
Critical Pressure ◽  
Genome Organisation ◽  
Health Index ◽  
Genome Diversity ◽  
Fast Spreading

Abstract One of the main concerns about the fast spreading coronavirus disease 2019 (Covid-19) pandemic is how to intervene. We analysed severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) isolates data using the multifractal approach and found a rich in viral genome diversity, which could be one of the root causes of the fast Covid-19 pandemic and is strongly affected by pressure and health index of the hosts inhabited regions. The calculated mutation rate (mr) is observed to be maximum at a particular pressure, beyond which mr maintains diversity. Hurst exponent and fractal dimension are found to be optimal at a critical pressure (Pm), whereas, for P > Pm and P < Pm, we found rich genome diversity relating to complicated genome organisation and virulence of the virus. The values of these complexity measurement parameters are found to be increased linearly with health index values.

scholarly journals Capital Markets Efficiency: Fractal Dimension, Hurst Exponent and Entropy

2012 ◽  
Vol 60 (2) ◽  
pp. 208-221 ◽  
Author(s):  
Ladislav Krištoufek ◽  
Miloslav Vošvrda
Keyword(s):  
Fractal Dimension ◽  
Capital Markets ◽  
Hurst Exponent

scholarly journals Papain-Like Proteases as Coronaviral Drug Targets: Current Inhibitors, Opportunities, and Limitations

2020 ◽  
Vol 13 (10) ◽  
pp. 277 ◽  
Author(s):  
Anastasiia I. Petushkova ◽  
Andrey A. Zamyatnin
Keyword(s):  
Immune Response ◽  
Immune System ◽  
Severe Acute Respiratory Syndrome ◽  
Viral Genome ◽  
Drug Targets ◽  
Structural Features ◽  
The Third ◽  
Frequent Mutations ◽  
Near Future ◽  
Viral Reproduction

Papain-like proteases (PLpro) of coronaviruses (CoVs) support viral reproduction and suppress the immune response of the host, which makes CoV PLpro perspective pharmaceutical targets. Their inhibition could both prevent viral replication and boost the immune system of the host, leading to the speedy recovery of the patient. Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the third CoV outbreak in the last 20 years. Frequent mutations of the viral genome likely lead to the emergence of more CoVs. Inhibitors for CoV PLpro can be broad-spectrum and can diminish present and prevent future CoV outbreaks as PLpro from different CoVs have conservative structures. Several inhibitors have been developed to withstand SARS-CoV and Middle East respiratory syndrome CoV (MERS-CoV). This review summarizes the structural features of CoV PLpro, the inhibitors that have been identified over the last 20 years, and the compounds that have the potential to become novel effective therapeutics against CoVs in the near future.

Determining Fractal Dimension of Umbilical Artery Doppler Signals Using Hurst Exponent

2007 ◽  
Vol 31 (6) ◽  
pp. 529-536 ◽  
Author(s):  
Fatma Latifoğlu ◽  
Sadık Kara ◽  
Mehmet Güney
Keyword(s):  
Fractal Dimension ◽  
Hurst Exponent ◽  
Umbilical Artery ◽  
Doppler Signals ◽  
Umbilical Artery Doppler

Schramm–Loewner evolution of the accessible perimeter of isoheight lines of correlated landscapes

2018 ◽  
Vol 29 (01) ◽  
pp. 1850008 ◽  
Author(s):  
N. Posé ◽  
K. J. Schrenk ◽  
N. A. M. Araújo ◽  
H. J. Herrmann
Keyword(s):  
Fractal Dimension ◽  
Random Walk ◽  
Long Range ◽  
Hurst Exponent ◽  
Diffusion Constant ◽  
Strongly Correlated ◽  
Loewner Evolution ◽  
Positive Formula ◽  
Practical Implications ◽  
Negative Formula

Real landscapes exhibit long-range height–height correlations, which are quantified by the Hurst exponent [Formula: see text]. We give evidence that for negative [Formula: see text], in spite of the long-range nature of correlations, the statistics of the accessible perimeter of isoheight lines is compatible with Schramm–Loewner evolution curves and therefore can be mapped to random walks, their fractal dimension determining the diffusion constant. Analytic results are recovered for [Formula: see text] and [Formula: see text] and a conjecture is proposed for the values in between. By contrast, for positive [Formula: see text], we find that the random walk is not Markovian but strongly correlated in time. Theoretical and practical implications are discussed.

scholarly journals Fractal analysis of muscle activity patterns during locomotion: pitfalls and how to avoid them

2020 ◽  
Author(s):  
Alessandro Santuz ◽  
Turgay Akay
Keyword(s):  
Time Series ◽  
Fractal Dimension ◽  
Fractal Analysis ◽  
Hurst Exponent ◽  
Activity Patterns ◽  
Surrogate Data ◽  
Time Dependent ◽  
Physiological Data ◽  
Adult Mice

AbstractTime-dependent physiological data, such as electromyogram (EMG) recordings from multiple muscles, is often difficult to interpret objectively. Here, we used EMG data gathered during mouse locomotion to investigate the effects of calculation parameters and data quality on two metrics for fractal analysis: the Higuchi’s fractal dimension (HFD) and the Hurst exponent (H). A curve is fractal if it repeats itself at every scale or, in other words, if its shape remains unchanged when zooming in the curve at every zoom level. Many linear and nonlinear analysis methods are available, each of them aiming at the explanation of different data features. In recent years, fractal analysis has become a powerful nonlinear tool to extract information from physiological data not visible to the naked eye. It can present, however, some dangerous pitfalls that can lead to misleading interpretations. To calculate the HFD and the H, we have extracted muscle synergies from normal and mechanically perturbed treadmill locomotion from the hindlimb of adult mice. Then, we used one set per condition (normal and perturbed walking) of the obtained time-dependent coefficients to create surrogate data with different fluctuations over the original mean signal. Our analysis shows that HFD and H are exceptionally sensitive to the presence or absence of perturbations to locomotion. However, both metrics suffer from variations in their value depending on the parameters used for calculations and the presence of quasi-periodic elements in the time series. We discuss those issues giving some simple suggestions to reduce the chance of misinterpreting the outcomes.New & NoteworthyDespite the lack of consensus on how to perform fractal analysis of physiological time series, many studies rely on this technique. Here, we shed light on the potential pitfalls of using the Higuchi’s fractal dimension and the Hurst exponent. We expose and suggest how to solve the drawbacks of such methods when applied to data from normal and perturbed locomotion by combining in vivo recordings and computational approaches.

scholarly journals Molecular dynamics analysis of fast-spreading severe acute respiratory syndrome coronavirus 2 variants and their effects in the interaction with human angiotensin-converting enzyme 2

2021 ◽  
Author(s):  
Anacleto Silva de Souza ◽  
Vitor Martins de Freitas Amorim ◽  
Gabriela D. A. Guardia ◽  
Felipe R C dos Santos ◽  
Filipe F dos Santos ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Severe Acute Respiratory Syndrome ◽  
Host Cell ◽  
Proteolytic Enzymes ◽  
Severe Disease ◽  
Host Cells ◽  
Angiotensin Converting Enzyme 2 ◽  
Fast Spreading ◽  
Host Cell Factors ◽  
Dynamics Simulations

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is evolving with mutations in the Spike protein, especially in the receptor-binding domain (RBD). The failure of public health measures to contain the spread of the disease in many countries has given rise to novel viral variants with increased transmissibility. However, key questions about how quickly the variants can spread and whether they can cause a more severe disease remain unclear. Herein, we performed a structural investigation using molecular dynamics simulations and determined dissociation constant (KD) values using surface plasmon resonance (SPR) assays of three fast-spreading SARS-CoV-2 variants, Alpha, Beta and Gamma ones, as well as genetic factors in the host cells that may be related to the viral infection. Our results suggest that the SARS-CoV-2 variants facilitate their entry into the host cell by moderately increased binding affinities to the human ACE2 receptor, different torsions in hACE2 mediated by RBD variants, and an increased Spike exposure time to proteolytic enzymes. We also found that other host cell aspects, such as gene and isoform expression of key genes for the infection (ACE2, FURIN and TMPRSS2), may have few contributions to the SARS-CoV-2 variants infectivity. In summary, we concluded that a combination of viral and host cell factors allows SARS-CoV-2 variants to increase their abilities to spread faster than wild-type.

scholarly journals Assessment of the risk of SARS-CoV-2 reinfection in an intense re-exposure setting

2020 ◽  
Author(s):  
Laith J Abu-Raddad ◽  
Hiam Chemaitelly ◽  
Joel A Malek ◽  
Ayeda A Ahmed ◽  
Yasmin A Mohamoud ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Incidence Rate ◽  
Genome Sequencing ◽  
Viral Genome ◽  
Primary Infection ◽  
Protective Immunity ◽  
Good Evidence ◽  
Contact Tracing ◽  
Random Testing ◽  
Exposure Setting

Background: Reinfection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is debated. We assessed risk and incidence rate of documented SARS-CoV-2 reinfection in a large cohort of laboratory-confirmed cases in Qatar. Methods: All SARS-CoV-2 laboratory-confirmed cases with at least one PCR positive swab that is ≥45 days after a first-positive swab were individually investigated for evidence of reinfection, and classified as showing strong, good, some, or weak/no evidence for reinfection. Viral genome sequencing of the paired first-positive and reinfection viral specimens was conducted to confirm reinfection. Risk and incidence rate of reinfection were estimated. Results: Out of 133,266 laboratory-confirmed SARS-CoV-2 cases, 243 persons (0.18%) had at least one subsequent positive swab ≥45 days after the first-positive swab. Of these, 54 cases (22.2%) had strong or good evidence for reinfection. Median time between first and reinfection swab was 64.5 days (range: 45-129). Twenty-three of the 54 cases (42.6%) were diagnosed at a health facility suggesting presence of symptoms, while 31 (57.4%) were identified incidentally through random testing campaigns/surveys or contact tracing. Only one person was hospitalized at time of reinfection, but still with mild infection. No deaths were recorded. Viral genome sequencing confirmed four out of 12 cases with available genetic evidence. Risk of reinfection was estimated at 0.01% (95% CI: 0.01-0.02%) and incidence rate of reinfection was estimated at 0.36 (95% CI: 0.28-0.47) per 10,000 person-weeks. Conclusions: SARS-CoV-2 reinfection can occur but is a rare phenomenon suggestive of a strong protective immunity against reinfection that lasts for at least a few months post primary infection.

Transition on the relationship between fractal dimension and Hurst exponent in the long-range connective sandpile models

2011 ◽  
Vol 375 (3) ◽  
pp. 324-328 ◽  
Author(s):  
Chien-chih Chen ◽  
Ya-Ting Lee ◽  
Tomohiro Hasumi ◽  
Han-Lun Hsu
Keyword(s):  
Fractal Dimension ◽  
Long Range ◽  
Hurst Exponent ◽  
Sandpile Models ◽  
The Relationship

GENERALIZED WEIERSTRASS–MANDELBROT FUNCTION MODEL FOR ACTUAL STOCKS MARKETS INDEXES WITH NONLINEAR CHARACTERISTICS

Fractals ◽  
2015 ◽  
Vol 23 (02) ◽  
pp. 1550006 ◽  
Author(s):  
L. ZHANG ◽  
C. YU ◽  
J. Q. SUN
Keyword(s):  
Fractal Dimension ◽  
Stock Market ◽  
Financial Markets ◽  
Hurst Exponent ◽  
Dimensional Space ◽  
Dynamical Behavior ◽  
Three Dimensional ◽  
Nonlinear Characteristics ◽  
Market Indexes ◽  
Three Dimensional Space

It is difficult to simulate the dynamical behavior of actual financial markets indexes effectively, especially when they have nonlinear characteristics. So it is significant to propose a mathematical model with these characteristics. In this paper, we investigate a generalized Weierstrass–Mandelbrot function (WMF) model with two nonlinear characteristics: fractal dimension D where 2 > D > 1.5 and Hurst exponent (H) where 1 > H > 0.5 firstly. And then we study the dynamical behavior of H for WMF as D and the spectrum of the time series γ change in three-dimensional space, respectively. Because WMF and the actual stock market indexes have two common features: fractal behavior using fractal dimension and long memory effect by Hurst exponent, we study the relationship between WMF and the actual stock market indexes. We choose a random value of γ and fixed value of D for WMF to simulate the S&P 500 indexes at different time ranges. As shown in the simulation results of three-dimensional space, we find that γ is important in WMF model and different γ may have the same effect for the nonlinearity of WMF. Then we calculate the skewness and kurtosis of actual Daily S&P 500 index in different time ranges which can be used to choose the value of γ. Based on these results, we choose appropriate γ, D and initial value into WMF to simulate Daily S&P 500 indexes. Using the fit line method in two-dimensional space for the simulated values, we find that the generalized WMF model is effective for simulating different actual stock market indexes in different time ranges. It may be useful for understanding the dynamical behavior of many different financial markets.

scholarly journals Point-of-Care RNA-Based Diagnostic Device for COVID-19

Diagnostics ◽  
2020 ◽  
Vol 10 (3) ◽  
pp. 165 ◽  
Author(s):  
Ting Yang ◽  
Yung-Chih Wang ◽  
Ching-Fen Shen ◽  
Chao-Min Cheng
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Respiratory Disease ◽  
Point Of Care ◽  
The Novel ◽  
Diagnostic Device ◽  
Fast Spreading ◽  
Novel Coronavirus

At the end of 2019, the novel coronavirus disease (COVID-19), a fast-spreading respiratory disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was reported in Wuhan, China and has now affected over 123 countries globally [...]

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