Handling DNA malfunctions by unsupervised machine learning model.

The cell cycle is a rich field for research, especially, the DNA damage. DNA damage, which happened naturally or as a result of environmental influences causes change in the chemical structure of DNA. The extent of DNA damage has a significant impact on the fate of the cell in later stages. In this paper, we introduced an Unsupervised Machine learning Model for DNA Damage Diagnosis and Analysis. Mainly, we employed K-means clustering unsupervised machine learning algorithms. Unsupervised algorithms commonly draw conclusions from datasets by solely utilizing input vectors, disregarding any known or labeled outcomes. The model provided deep insight about DNA damage and exposes the protein levels for proteins when work together in sub-network model to deal with DNA damage occurrence, the unsupervised artificial model explained the sub-network biological model activities in regard to the changing in their concentrations in several clusters, they have been grouped in such as (0 - no damage, 1 - low, 2 - medium, 3 - high, and 4 - excess) DNA damage clusters. The results provided a rational and persuasive explanation for numerous important phenomena, including the oscillation of the protein p53, in a clear and understandable manner. Which is encouraging since it demonstrates that the K-means clustering approach can be easily applied to many similar biological systems, which aids in better understanding the key dynamics of these systems.

Nigella sativa-chitosan nanoparticles: Novel intestinal mucosal immunomodulator controls and protects against Salmonella enterica serovar Enteritidis infection in broilers.

BACKGROUND: Salmonella Enteritidis (SE) propagates in chickens' gastrointestinal surfaces and is transmitted to humans, causing food poisoning. Oral supplementation with natural nanoparticles can overcome the harsh gastrointestinal conditions facing oral vaccines and requires no antibiotic administration to protect against microbial infection. This study was designed to study Nigella sativa-chitosan nanoparticles (CNP-NS) prophylactic immunomodulatory efficacy against SE infection in broiler chicks. The CNP-NS was prepared and characterized, and its in vivo immunomodulatory activities against an avian virulent-MDR SE-induced challenge in chicks were investigated. RESULT: To verify the immune-protective activities of the CNP-NS, colony forming units (CFU) in the liver and fecal droppings; intestinal histopathological alterations and immune cell recruitment; MUC-2, TLR-4, cecal cytokines, and specific IgA gene expression levels were assessed. On the 7th and 12th days after the SE challenge, the CNP-NS supplemented chicks showed complete clearance of SE CFU in livers and fecal droppings, as well as an improvement in food conversion rate compared to non-supplemented CNP-NS that revealed the presence of the challenge SE CFU on the same days. A prominent influx of antigen presenting cells and lymphoid aggregates into the intestinal wall, spleen, and liver was detected with improvements in the intestinal villi morphometry of the CNP-NS-supplemented chicks. The changes of INF-γ, IL-1ß, and IL-4 cecal cytokines, as well as TLR-4, MUC-2, and IgA mRNA expression levels, confirm CNP-NS immunomodulatory activities and provide a mechanism(s) for its protective actions against the induced SE challenge of the tested chickens. CONCLUSION: These findings suggest promising useful insights into CNP-NS supplementation as a safe food additive for poultry meat consumers' and a protective immunomodulator of the chickens' mucosal immune systems. It could be recommended for epidemiological purposes to reduce the risk of SE food poisoning and transmission to humans.

Fasudil Ameliorates Methotrexate-Induced Hepatotoxicity by Modulation of Redox-Sensitive Signals.

Methotrexate (MTX) is one of the most widely used cytotoxic chemotherapeutic agents, and it is used in the treatment of different autoimmune disorders. However, the clinical applications of MTX are limited by its hepatic toxicity. Hence, the present study was conducted to evaluate the efficacy of fasudil (Rho-Kinase inhibitor) in the amelioration of MTX hepatotoxicity and the possible underlying mechanisms. Experimentally, 32 male Sprague Dawley rats were used and divided into four groups: control, MTX (20 mg/kg, i.p., single dose), fasudil (10 mg/kg/day i.p.) for one week, and fasudil plus MTX. It was found that MTX significantly induced hepatitis and hepatocellular damage, as shown by abnormal histological findings and liver dysfunction (ALT and AST), with up-regulation of the inflammatory mediators NF-κB-p65 and IL-1ß. Moreover, MTX remarkably disrupted oxidant/antioxidant status, as evidenced by malondialdehyde (MDA) up-regulation associated with the depletion of superoxide dismutase (SOD), catalase, and reduced glutathione (GSH) levels. Moreover, MTX reduced the hepatic expression of B-cell lymphoma 2 (Bcl-2). On the contrary, the i.p. administration of fasudil significantly ameliorated MTX hepatotoxicity by histopathological improvement, restoring oxidant/antioxidant balance, preventing hepatic inflammation, and improving the hepatic anti-apoptotic capability. Furthermore, fasudil hepatic concentration was determined for the first time using the validated RP-HPLC method. In conclusion, the present study revealed that fasudil has a reliable hepatoprotective effect against MTX hepatotoxicity with underlying antioxidant, anti-inflammatory, and anti-apoptotic mechanisms. It also introduced a new method for the determination of fasudil hepatic tissue concentration using the RP-HPLC technique.

Nigella sativa Extract Potentially Inhibited Methicillin Resistant Staphylococcus aureus Induced Infection in Rabbits: Potential Immunomodulatory and Growth Promoting Properties.

Weaning is the most crucial period associated with increased stress and susceptibility to diseases in rabbits. Methicillin-resistant Staphylococcus aureus (MRSA), a historic emergent pathogen related to post weaning stressors, adversely affects rabbit's growth rate and productive cycle. Since MRSA is rapidly evolving antibiotics resistance, natural products are desperately required to tackle the public health threats posed by antimicrobial resistance. Thus, this study aimed to screen the iin vitro antibacterial activity of Nigella sativa extract (NSE) and its interactions with antibiotics against MRSA isolates. Moreover, 200 weaned rabbits were divided into 4 groups to investigate the iin vivo superiority of NSE graded levels towards growth performance, tight junction integrity, immune responsiveness and resistance against MRSA. Herein, NSE showed promising antimicrobial activities against MRSA isolates from animal (77.8%) and human (64.3%) origins. Additionally, MRSA isolates exposed to NSE became sensitive to all antimicrobials to which they were previously resistant. Our results described that the growth-promoting functions of NSE, especially at higher levels, were supported by elevated activities of digestive linked enzymes. Post-NSE feeding, rabbits' sera mediated bactericidal activities against MRSA. Notably, upregulated expression of occludin, CLDN-1, MUC-2 and JAM-2 genes was noted post NSE supplementation with maximum transcriptional levels in 500 mg/kg NSE fed group. Our data described that NSE constitutively motivated rabbits' immune responses and protected them against MRSA-induced experimental infection. Our results suggest the antimicrobial, growth stimulating and immunomodulation activities of NSE to maximize the capability of rabbits for disease response.

Nigella sativa oil extract: A natural novel specific conjugal transfer inhibitor of vancomycin resistance from vanA/B-resistant Enterococcus faecium to Staphylococcus aureus.

AIM: The emergence of vancomycin-resistant Staphylococcus aureus (VRSA) has been identified as one of the most challenging problems in healthcare settings worldwide. Specific conjugation inhibitors' development is critical in the fight against the spread of emerging VRSA. The impact of Nigella sativa oil on VR genes conjugal transfer from Enterococcus faecium (VREtfm) to vancomycin-sensitive S. aureus (VSSA) was investigated in this study. METHODS AND RESULTS: Enterococciwere isolated from retail broilers, fish, cows' milk, and human urine. VR E. faecalis and VREtfm VanA phenotypes were prevalent in retail broiler samples. The VREtfm isolates were dominant, exhibiting high levels of resistance to gentamycin and ciprofloxacin antibiotics, as well as the existence of both vanA and vanB genes and virulence traits (ESP+ , asa1+ ) as determined by PCR. Transconjugant VREtfm strains containing vanA/vabB and 20 kb plasmids (transfer frequency around 103 ) and carrying the Tn1546 transposon were identified. Tn1546 transposon transfer with its VR markers to VSSA was effectively inhibited in treated VREtfm donor strains with a sub-minimum inhibitory concentration of N. sativa oil. THE SIGNIFICANCE AND IMPACT OF THE STUDY: This work offers new insights for overcoming VR conjugal transfer utilizing natural N. sativa oil, as well as a suggestion for a novel specialized conjugation inhibitor that could effectively facilitate the difficulty of eliminating VR bacteria from healthcare settings.

Nano-Structured Lipid Carrier-Based Oral Glutathione Formulation Mediates Renoprotection against Cyclophosphamide-Induced Nephrotoxicity, and Improves Oral Bioavailability of Glutathione Confirmed through RP-HPLC Micellar Liquid Chromatography.

The study aimed to develop a new glutathione (GSH) oral formulation to enhance the delivery of GSH and counter the nephrotoxicity of the anticancer drug, cyclophosphamide (CP). A nanostructured lipid carrier glutathione formulation (GSH-NLCs) composed of glutathione (500 mg), stearic and oleic acid (300 mg, each), and Tween® 80 (2%, w/v) was prepared through the emulsification-solvent-evaporation technique, which exhibited a 452.4 ± 33.19 nm spheroidal-sized particulate material with narrow particle size distributions, -38.5 ± 1.4 mV zeta potential, and an entrapment efficiency of 79.8 ± 1.9%. The GSH formulation was orally delivered, and biologically tested to ameliorate the CP-induced renal toxicity in a rat model. Detailed renal morphology, before and after the GSH-NLCs administration, including the histopathological examinations, confirmed the ameliorating effects of the prepared glutathione formulation together with its safe oral delivery. CP-induced oxidative stress, superoxide dismutase depletion, elevation of malondialdehyde levels, depletion of Bcl-2 concentration levels, and upregulated NF-KB levels were observed and were controlled within the recommended and near normal/control levels. Additionally, the inflammatory mediator marker, IL-1ß, serum levels were marginally normalized by delivery of the GHS-NLCs formulation. Oral administration of the pure glutathione did not exhibit any ameliorating effects on the renal tissues, which suggested that the pure glutathione is reactive and is chemically transformed during the oral delivery, which affected its pharmacological action at the renal site. The protective effects of the GSH-NLCs formulation through its antioxidant and anti-inflammatory effects suggested its prominent role in containing CP-induced renal toxicity and renal tissue damage, together with the possibility of administrating higher doses of the anticancer drug, cyclophosphamide, to achieve higher and effective anticancer action in combination with the GSH-NLCs formulation.

Sage, Salvia officinalis L., Constituents, Hepatoprotective Activity, and Cytotoxicity Evaluations of the Essential Oils Obtained from Fresh and Differently Timed Dried Herbs: A Comparative Analysis.

Sage, Salvia officinalis L., is used worldwide as an aromatic herb for culinary purposes as well as a traditional medicinal agent for various ailments. Current investigations exhibited the effects of extended dryings of the herb on the yields, composition, oil quality, and hepatoprotective as well as anti-cancer biological activities of the hydrodistillation-obtained essential oils from the aerial parts of the plant. The essential oils' yields, compositions, and biological activities levels of the fresh and differently timed and room-temperature dried herbs differed significantly. The lowest yields of the essential oil were obtained from the fresh herbs (FH, 631 mg, 0.16%), while the highest yield was obtained from the two-week dried herbs (2WDH, 1102 mg, 0.28%). A notable decrease in monoterpenes, with increment in the sesquiterpene constituents, was observed for the FH-based essential oil as compared to all the other batches of the essential oils obtained from the different-timed dried herbs. Additionally, characteristic chemotypic constituents of sage, i.e., α-pinene, camphene, ß-pinene, myrcene, 1, 8-cineole, α-thujone, and camphor, were present in significantly higher proportions in all the dried herbs' essential oils as compared to the FH-based essential oil. The in vivo hepatoprotective activity demonstrated significant reductions in the levels of AST, ALT, and ALP, as well as a significant increase in the total protein (p < 0.05) contents level, as compared to the acetaminophen (AAP) administered experimental group of rats. A significant reduction (p < 0.05) in the ALT level was demonstrated by the 4WDH-based essential oil in comparison to the FH-based essential oil. The levels of creatinine, cholesterol, and triglycerides were reduced (p < 0.05) in the pre-treated rats by the essential oil batches, with non-significant differences found among them as a result of the herbs dryings based oils. A notable increase in the viability of the cells, and total antioxidant capacity (TAOxC) levels, together with the reduction in malondialdehyde (MDA) levels were observed by the essential oils obtained from all the batches as compared with the AAP-treated cell-lines, HepG-2, HeLa, and MCF-7, that indicated the in vitro hepatoprotective effects of the sage essential oils. However, significant improvements in the in vivo and in vitro hepatoprotective activities with the 4WDH-based oil, as compared to all other essential oil-batches and silymarin standard demonstrated the beneficial effects of the drying protocol for the herb for its medicinal purposes.

Chemical Profile, Antioxidant, Antimicrobial, and Anticancer Activities of the Water-Ethanol Extract of Pulicaria undulata Growing in the Oasis of Central Saudi Arabian Desert.

Pulicaria undulata (L.) C. A. Mey has multiple uses as part of the traditional medicament, and several biological activities of the plant have been corroborated in the scientific literature. The current work evaluates the phytochemical constituents and biological properties of the water-ethanol extract of the P. undulata growing in Qassim, the central arid regions of the Kingdom of Saudi Arabia. Qualitative UPLC-ESIQ-TOF analysis identified 27 compounds belonging to the phenolics, flavonoids, triterpenes, coumarins, and of fatty acids chemical classes. The quantitative analysis exhibited 33.3 mg/g GAE (Gallic Acid Equivalents), and 10.8 mg/g QE (Quercetin Equivalents) of the phenolics and flavonoids in the plant's concentrated (to dryness) water-ethanol extract. The trace elements analysis of the plant's dry powder established the presence of copper (20.13 µg/kg), and zinc (68.2 µg/kg) in the higher levels of occurrences. In terms of the antioxidant potential of the plant's extract, the ferric-reducing, and free-radicals scavenging activities were recorded at 47.11 mg/g, and 19.13 mg/g equivalents of the concentrated to dryness water-ethanol extract of the plant. The water-ethanol extract of P. undulata also exhibited antimicrobial activity against the tested Gram-positive bacteria, while no activity was observed against the tested Gram-negative bacteria, or the fungi. The MIC (minimum inhibitory concentration) values were in the range of 49 to 1563 µg/mL, whereas the MBC (minimum bactericidal concentration) values ranged from 49 to 3125 µg/mL, against the tested Gram-positive bacteria. The P. undulata water-ethanol extract also exhibited potent cytotoxic effects with the IC50 value at 519.2 µg/mL against the MCF-7 breast cancer cell-lines, followed by the anticancer activity of erythroleukemic cell-lines, K562 at 1212 µg/mL, and pancreatic cell-lines, PANC-1, at 1535 µg/mL, as compared to the normal fibroblast cells (4048 µg/mL). The Annexin-V assay demonstrated that, as the P. undulata extract's dose increased from IC50 to twice of the IC50, the percentage of the necrosis was found to be increased in the late apoptosis stage of the cancer cells. These data confirmed the P. undulata extract's ability to inhibit several human cancer cell lines' growth in comparison to other local halophytes. The antimicrobial activity of the plant was also confirmed.

Molecular Detection of New SHV ß-lactamase Variants in Clinical Escherichia coli and Klebsiella pneumoniae Isolates from Egypt.

The emergence of multidrug-resistant (MDR) pathogens was reported worldwide. Herein, SHV extended-spectrum ß-lactamase (SHV-ESBL) variants detection was investigated in MDR E. coli and K. pneumoniae isolates recovered from human subjects (n = 144), one day-old chicks (n = 36) and broiler clinical samples (n = 90). All examined samples were positive for E. coli (n = 246/270; 91.11%) and Klebsiella pneumoniae (n = 24/270; 8.89%). Antimicrobial susceptibility testing was performed on E. coli and K. pneumoniae. SHV-ESBL producing isolates were defined followed by SHV-ESBL amino acids sequence and proteins structure-function analyses. Phylogenetic analysis of 11 MDR isolates resistant to at least 6 ß-lactams was designed to determine their genetic relationship with those previously identified in Egypt. SHV-ESBL variants were detected in 28% and 16% of E. coli and K. pneumoniae isolates, respectively. Among the 11 SHV-ESBL producing isolates, one isolate displayed 100% blaSHV-12 similarity with three point mutations, while the other 10 isolates displayed amino acid substitutions at previously non-reported sites. Amino acid sequence analyses of these 10 isolates displayed 96-100% identity to blaSHV-10 (2 isolates with 3-6 point mutations), blaSHV-18 (one isolate with 4 point mutations), blaSHV-58 (4 isolates with 4-5 point mutations), and blaSHV-91 (3 isolates with 3-7 point mutations). These mutations altered SHV-enzyme pocket dimensions and its binding sites chargeability. The blaSHV phylogeny analysis revealed occurrence of variants in closely related lineages with blaSHV-5 and blaSHV-12 with possibility of blaSHV gene transfer between human and birds. The occurrence of these variants in Egypt could help in epidemiological studies and could explain the emergent resistance to ß-lactams.

Nigella sativa seed extract: 1. Enhancement of sheep macrophage immune functions in vitro.

Nigella sativa (N. sativa) seed, Black cumin, immunomodulatory activity has been investigated in human and mice. Little is known about the immunomodulatory effect of Nigella sativa (N. sativa) seed extract on animals' immune cells, specifically, antigen presenting cells such as macrophages. This study focused on the immunomodulatory effect of N. sativa seed extract on sheep macrophage functions in vitro. Sheep peripheral blood monocytes were isolated and derived to macrophages (MDM). The MDM were cultured with N. sativa seed extract and their morphological changes, phagocytic activity, nitric oxide production, and microbicidal activity were investigated. Marked morphological changes were observed in MDM cultured with N. sativa seed extract including cell size enlargement; increase in both cytoplasmic space and cytoplasmic granules. Significant increases in phagocytic activity to Candida albicans yeast and in number of yeast engulfed per individual MDM were observed in cells cultured with seed extract. MDM capacity to produce nitric oxide was higher in the culture media of the seed extract-cultured cells compared to the control. Interestingly, prominent enhancement in MDM microbicidal activity to yeast or bacteria was observed in MDM cultured with N. sativa seed extract confirming the potent immunostimulatory effect of the extract. From this study, it could be concluded that N. sativa seed extract can enhance macrophages' important innate immune functions that could control infectious diseases and regulate adaptive immunity.

Pressure generated on a simulated mandibular oral analog by impression materials in custom trays of different design.

PURPOSE: The purpose was to measure the pressure exerted under a simulated mandibular edentulous impression at different locations using commonly used impression materials and four impression tray configurations. MATERIALS AND METHODS: This study was performed using an oral analog that simulated an edentulous mandibular arch. Three pressure transducers were embedded in the oral analog-one pressure transducer in the anterior ridge area, and the other two in the right and left buccal shelves. Four configurations of custom trays were fabricated: trays with no relief, with and without holes; and trays with relief, with and without holes. The impression materials tested were light body polysulfide, light body vinyl polysiloxane, medium body vinyl polysiloxane, and irreversible hydrocolloid. The custom tray and the oral analog were mounted using a reline jig, and a Satec universal testing machine was used to apply a constant pressure of 1 kg/cm(2) over a period of 5 minutes on the loaded custom tray. Eighty impressions for the 16 groups (n = 5) were made, and pressures were recorded every 10 seconds. Factorial ANOVA and Tukey Multiple Comparison Test were used to analyze the results (p < 0.05). RESULTS: A significant difference was found in the pressure produced using different impression materials. Irreversible hydrocolloid and medium body vinyl polysiloxane produced significantly higher pressure than light body polysulfide and light body vinyl polysiloxane impression materials. The presence of holes and/or relief significantly altered the magnitude of pressure produced by irreversible hydrocolloid and medium body vinyl polysiloxane but not light body polysulfide and light body vinyl polysiloxane. CONCLUSION: All impression materials produced pressure during simulated mandibular edentulous impression making. For making mandibular edentulous impressions, low-viscosity impression materials-light body polysulfide and light body vinyl polysiloxane-are recommended. Tray modification was not important in changing the amount of pressure produced for the low-viscosity impression materials.

Transjugular liver biopsy in patients with end-stage renal disease.

PURPOSE: To assess the efficacy and safety of transjugular liver biopsy (TJLB) in patients with end-stage renal disease (ESRD) who are undergoing hemodialysis treatment. MATERIALS AND METHODS: Forty-six consecutive patients with liver disease who were undergoing hemodialysis were included in this study. An 18-gauge Tru-cut transjugular needle with a 20-mm throw was used to obtain liver tissue. All procedures were performed under fluoroscopic guidance. A single pathologist reviewed the biopsy specimens and assessed the size of fragments, number of portal tracts, and adequacy of the specimens for histologic diagnosis. All complications were recorded. The results were compared with the outcomes of percutaneous liver biopsy carried out at our institution in 32 patients with ESRD. RESULTS: TJLB and percutaneous biopsy techniques yielded adequate specimens for histologic diagnosis in all patients. The mean length of the largest fragments of tissue obtained via the transjugular and percutaneous routes were 16 mm +/- 4 and 14 mm +/- 3, respectively (P = NS). There were no major complications among patients who underwent TJLB. Percutaneous liver biopsy was complicated by hemorrhage in four of 32 patients (12%), three of whom required blood transfusion. CONCLUSION: TJLB is an effective and safe technique to obtain liver tissue in patients with ESRD and is associated with a lower complication rate than percutaneous liver biopsy.

Uterine artery embolization treatment of uterine fibroids: effect on ovarian function in younger women.

PURPOSE: To evaluate how uterine artery embolization (UAE) treatment for uterine fibroids (UF) affects ovarian function in young Middle Eastern women. MATERIALS AND METHODS: In this prospective study, 32 patients (mean age, 34 y; range, 26-45 y) underwent UAE treatment of symptomatic fibroids. Serum follicle-stimulating hormone (FSH) levels were measured before and after the embolization treatment. Preprocedural levels were determined on the second day of the menstrual cycle. Postprocedural levels were measured 3 months and 6 months after embolization. A detailed history of menstrual cycles was obtained before and after UAE. RESULTS: Thirty premenopausal patients had normal menses before UAE. Mean FSH levels before and 3 months after UAE were 6.83 IU/L +/- 1.8 and 6.99 IU/L +/- 1.67, respectively (P =.66). Normal menstruation resumed 2-3 months after the procedure. In two perimenopausal women, who had irregular menses and decreased ovarian reserve, mean FSH levels increased transiently from 22 and 30 IU/L to 40 and 48 IU/L, respectively, 3 months after UAE; they developed transient amenorrhea. CONCLUSION: In this study, UAE had no clinically relevant adverse effects on normally functioning ovaries and could be used safely in the treatment of symptomatic fibroids in premenopausal women. Larger studies are required for further support of this observation.