Abstract:

Nepeta cyrenaica Quézel & Zaffran (Lamiaceae), an endemic species of Libyan flora, is here characterized for the first time for its phytochemical composition and biological activities. Phenolic composition, antioxidant and enzyme inhibiting effects of extracts, prepared from five-week-old in vitro propagated N. cyrenaica shoots, were evaluated. Extraction was performed using dichloromethane, methanol, 96% ethanol or hot distilled water. LC-MS analysis showed that the methanol extract contained the highest amount of phenolic components, especially ferulic and rosmarinic acids (1300.73 mg/kg and 528.88 mg/kg, respectively), and epigallocatechin gallate (719.05 mg/kg). The strongest antioxidant activity was recorded for aqueous extract in DPPH assay (66.91%) and dichloromethane extract in β-carotene bleaching assay (81.06%), both tested at the concentration of 2 mg/mL. Concerning α-glucosidase inhibition, dichloromethane extract was shown to possess a higher inhibition capacity than acarbose at the concentration of 2 mg/mL (95.33% vs. 88.29%). The aqueous extract exhibited higher acetylcholinesterase inhibition than the other tested extracts, which was lower compared to the positive control, galantamine. Although methanol extract contained the highest amount of polyphenolics, dichloromethane and aqueous extracts were shown to be more suitable for the extraction of bioactive components. In conclusion, endemic N. cyrenaica could be efficiently propagated through in vitro propagation protocols as a polyphenolic-rich plant with valuable medicinal potential.

Keywords: biological activities; extracts; in vitro propagation; Nepeta cyrenaica

Exact string-matching algorithms have become very supreme in many bioinformatics tools. Despite the abundance and diversity of such algorithms, exposing them to real-time experimental analysis has been critical. This study was conducted to evaluate the efficiency of ten exact-string matching algorithms on large-scale genomic sequences from a runtime perspective. To define the most efficient algorithms are qualified to handle the short alphabet used for nucleic acid coding. The methodology promoted for this study was the factorial experiment with Randomized Complete Block Design (FRCBD). Under influence of four independent parameters, four levels of pattern lengths, four levels of pattern indices, two levels of programming languages, and ten levels of algorithmic architecture. The yield of the tested algorithms was calculated in nanoseconds. One-way ANOVA and Two-way ANOVA tests with post-hoc Games-Howell test were used separately for statistical analysis. In this study two widely accepted programming languages, C# and JAVA were used to speculate the possible effect of programing language on algorithm performance.

One of the unique combinations in the mammalian genome, that revolutionized concepts in the fields of genetics and molecular

pathology is what is termed the CpG islands. However, the accurate and rapid determination of CpG islands for DNA sequences remains

experimentally and computationally challenging. The main goal of this project is to design an offline, cross-platform CpG islands detection

tool. The Algorithm implemented in this study was the traditional sliding window algorithm by using the C++ programming language.

Three datasets were used for evaluating the performance of the application. The ANK1 gene, SPTB gene, and RET gene sequence files

were obtained from NCBI. In this study, the highest CGIs were reported in ANK1 (ankyrin 1) Gene which scored 13 successive islands

whereas the lowest score was reported in RET (ret proto-oncogene) Gene which shows only 6 islands. Generally, the program fulfills the

boundary limits as expected. We strongly recommend for further work, the implementation of other algorithms in addition to the sliding

window algorithm such as the Hidden Markov Model (HMM).

Abstract

Abstract

Introduction:

Coronavirus Disease 2019 (COVID-19) is an infectious res-

piratory disease caused by SARS-CoV-2. The disease was first broke out in

Wuhan City, Hubei Province, China and subsequently spread to all countries

and was considered by WHO as a worldwide pandemic. This study is aimed

to determine the epidemiology of SARS-CoV-2 and the presence of UK va-

riants in Zintan city of Libya taking some risk factors into account. Me-

thods: In a cross-sectional retrospective study, a total of 15486 nasopha-

ryngeal swabs were collected from COVID-19 suspected patients, travelers

and people need disease-free certificates for hospital admission, etc. The

samples were collected during the period from August 2020 to June 2021

and tested using real-time RT -PCR (rRT-PCR) kits for SARS-CoV-2 and

UK variants. Age groups, sex, and monthly weather were considered as risk

factors. Results: The positivity rate of COVID-19 in Zintan city was esti-

mated to be (3891; 25.12%) for the period from August 2020 to June 2021.

Females showed significantly (p < 0.05) higher positivity rate (2100; 54%) as

compared to males (1791; 46%). Out of the 3891 positive cases, 52 were de-

ceased. The Case Fatality Rate (CFR) was 1.33 recorded significantly in cas-

es aged ≥ 65 years which was higher in males (56.66%) than females (43.33%).

The peak of the first wave of infection was recorded in October 2020 (590;

15.15%) whereas the peak of the second wave of infection was recorded in

April 2021 (727; 18.71%). The positivity rate was decreased as the tempera-

ture increased. UK variant is detected firstly in May 2021 with the percen-

tage of 6.2% of tested samples. Conclusions: Health Authorities are en-

crease phase of infection to stop transmission of the virus in the next wave.

Early detection of new variants and studying their genetic characteristics

play a valuable role in prevention and control.

Keywords

SARS

-

CoV

-

2, UK Variant, Epidemiology, Zintan,

Libya, rRT

-

PCR.

Lithostratigraphically, the Sidi As sid Formation (Upper Cretaceous) in the El Zintan section (JabalNafusah, NW Libya) consists of three units: upper marl, middle marl with intercalations of dolostone, and lower dolostone. Based on crystal size and shape, three types of dolomite have been classified. Fine crystalline dolomite (D1) consists of nonplanar dolomites, fine to medium crystalline dolomite (D2), and very coarse, consisting of mostly planar dolomites (D-3). The Cathodoluminescence technique also showed that most of these dolomites have bright yellow to red and dull orange luminescence and zoning. Based on X-ray diffraction (XRD), all dolomites are relatively well ordered and non to nearly stoichiometric dolomite. The stable isotopic studies and element analysis show that the major elements such as sodium (D1: 412.166 ppm; D2: 175 ppm; D3: 420 ppm), strontium (D1: 107 ppm; D2: 85 ppm; D3: 81.2 ppm), manganese (D1: 271 ppm; D2: 91 ppm; V3: 242 ppm), and iron (D1: 4856.66 ppm; D2: 373 ppm; D3: 3287 ppm) and the values of the stable isotope of oxygen (D1:-2.202‰; D2:-2.131; D3:-4.359‰) and carbon (D1: 2.080; D2: 2.076‰; D3: 1.581‰). The values of major elements and depletion of the carbon and oxygen isotopes can be related to the effects of temperature diagenetic, and mesosaline reflux of dolomitizing fluids during the early diagenesis. These dolomites originated in a tidal environment in this Formation. The major sources of magnesium for the dolomites are seawater and hypersaline fluids.

In this study, we present the new generalized derivative and integral operators which are based on the newly constructed new generalized Caputo fractal–fractional derivatives (NGCFFDs). Based on these operators, a numerical method is developed to solve the fractal–fractional differential equations (FFDEs). We approximate the solution of the FFDEs as basis vectors of shifted Legendre polynomials (SLPs). We also extend the derivative operational matrix of SLPs to the generalized derivative operational matrix in the sense of NGCFFDs. The efficiency of the developed numerical method is tested by taking various test examples. We also compare the results of our proposed method with the methods existed in the literature In this paper, we specified the fractal–fractional differential operator of new generalized Caputo in three categories: (i) different values in  and fractal parameters, (ii) different values in fractional parameter while fractal and  parameters are fixed, and (iii) different values in fractal parameter controlling fractional and  parameters.

Exact string-matching algorithms have become very supreme in many bioinformatics tools. Despite the abundance and diversity of such algorithms, exposing them to real-time experimental analysis has been critical. This study was conducted to evaluate the efficiency of ten exact-string matching algorithms on large-scale genomic sequences from a runtime perspective. To define the most efficient algorithms are qualified to handle the short alphabet used for nucleic acid coding. The methodology promoted for this study was the factorial experiment with Randomized Complete Block Design (FRCBD). Under influence of four independent parameters, four levels of pattern lengths, four levels of pattern indices, two levels of programming languages, and ten levels of algorithmic architecture. The yield of the tested algorithms was calculated in nanoseconds. One-way ANOVA and Two-way ANOVA tests with post-hoc Games-Howell test were used separately for statistical analysis. In this study two widely accepted programming languages, C# and JAVA were used to speculate the possible effect of programing language on algorithm performance. The One-way ANOVA results revealed that the Backward-Oracle-Matching (BOM), Zhu-Takaoka (ZT), and Horspool's (HP) algorithms exhibited the highest final performance correspondingly. These algorithms have demonstrated an efficiency of up to 250% higher than other algorithms. The results of two-way ANOVA revealed a significant interaction between programing language adopted and execution time with the absence of pattern lengths and pattern index effect. The combination of the C# programing language and the Backward-Oracle-Matching algorithm produced the most effective performance on genomic sequences. 

Short Tandem Repeats (STRs) are one of the utmost mutable provinces in the human genome. They comprise tandem repeating DNA sequences ranging in length from two to six base pairs. Owing to their significant mutation rate, they exhibit considerable variation in pattern among populations and the capacity to be passed on from generation to generation. These loci are broadly employed in medicine, biology, and criminal investigation. They are pivotal in the genesis of a variety of genetic illnesses and have been intensively investigated in forensics, population genetics, and genetic genealogy. Although many implementations that manage STR loci are offered, the overwhelming majority of them rely primarily on the Command-Line Interface (CLI) inputs, which frequently necessitate the implementation of tools carried out in various scripting languages. Installing and launching programs through the Command Line (CL) is timeconsuming and/or unprofitable for many students and scholars. The fundamental intention of this project is to develop a cross-platform Graphical User Interface (GUI) package directed to the Combined DNA Index System (CODIS) STR analysis. Zenobia is a Java-based application considered as a step in consistently making CL-only programs available to more apprentices and researchers. In general, Zenobia's application outcomes satisfy the evaluation metrics for efficiency and time consumption. However, more genetic markers should be introduced to increase productivity of the application.