Quasispecies dynamics and treatment outcome during early hepatitis C infection in a cohort of HIV-infected men

Hepatitis C virus (HCV) is emerging as one of the leading causes of morbidity and mortality in individuals infected with HIV and has overtaken AIDS-defining illnesses as a cause of death in HIV patient populations who have access to highly active antiretroviral therapy. For many years, the clonal analysis was the reference method for investigating viral diversity. In this thesis, a next generation sequencing (NGS) approach was developed using 454 pyrosequencing and Illumina-based technology. A sequencing pipeline was developed using two different NGS approaches, nested PCR, and metagenomics. The pipeline was used to study the viral populations in the sera of HCV-infected patients from a unique cohort of 160 HIV-positive patients with early HCV infection. These pipelines resulted in an improved understanding of HCV quasispecies dynamics, especially regarding studying response to treatment. Low viral diversity at baseline correlated with sustained virological response (SVR) while high viral diversity at baseline was associated with treatment failure. The emergence of new viral strains following treatment failure was most commonly associated with emerging dominance of pre-existing minority variants rather than re-infection. In the new era of direct-acting antivirals, next generation sequencing technologies are the most promising tool for identifying minority variants present in the HCV quasispecies populations at baseline. In this cohort, several mutations conferring resistance were detected in genotype 1a treatment-naïve patients. Further research into the impact of baseline HCV variants on SVR rates should be carried out in this population. A clearer understanding of the properties of viral quasispecies would enable clinicians to make improved treatment choices for their patients

Prevalence of HCV NS3 pre-treatment resistance associated amino acid variants within a Scottish cohort

Background: Protease inhibitors (PI) including boceprevir, telaprevir and simeprevir have revolutionised HCV genotype 1 treatment since their introduction. A number of pre-treatment resistance associated amino acid variants (RAVs) and polymorphisms have been associated with reduced response to treatment. Objectives: We measured the prevalence of RAVs/polymorphisms in a PI treatment-naïve HCV genotype 1 Scottish cohort using Sanger sequencing. Study design: Chronically infected, treatment-naïve, HCV genotype 1 patients (n = 146) attending NHS Greater Glasgow and Clyde clinics were investigated for RAVs/polymorphisms to the PIs boceprevir, telaprevir and simeprevir. The NS3/4A region was amplified by nested polymerase chain reaction. The 1.4 kb amplified product was sequenced using an ABI 3710XL DNA sequencer. Sequence analysis was performed using web-based ReCall (beta 2.10). Amino acid positions 36, 41, 43, 54, 55, 80, 109, 122, 155, 156, 168 and 170 were analysed for RAVs/polymorphisms. Results: Overall, 23.29% (34/146) of patients had an RAV or polymorphism detected. Overall, 13.69% (20/146) of patients had HCV virus that contained the Q8 K polymorphism. Other RAVs detected were: V36 M 0.70% (1/146), V36L 0.70% (1/146), T54S 6.85% (10/146), V55A 3.42% (5/146) and V/I170A 0.68% (1/146). Four patients had dual combinations of mutations (T54S + V36L; T54S + V55A and 2 patients with T54S + Q80K). Conclusions: Q80K was the most prevalent baseline polymorphism detected in the Scottish cohort. Simeprevir treatment is not recommended in patients infected with the Q80K genotype 1a variant. This highlights the need for baseline sequencing prior to administration of this drug in this population

Lupine as a potential agent against diet-induced obesity through adenosine monophosphateactivated protein kinase pathway: crude oil versus nanoemulsion formulations

Obesity represents a major challenge to the pharmaceutical community due to the minimal availability of anti-obesity drugs and the drawbacks of current weight-loss agents. The study described herein presents lupine oil, in two pharmaceutical formulations, as a potential anti-obesity agent via its effect on different physiological, biochemical, and hormonal parameters. Rats were divided into two groups; one group was continued on a standard commercial rodent diet and served as the non-obese control. The other group was fed a high-fat diet for 7 weeks to prepare an obese rat model. Then, the obese rats were divided into groups to receive 100 mg/kg of the crude lupine oil or nanoemulsion for 10 or 20 days. Lupine oil showed a potent body weight-reducing effect and improved insulin resistance. The oil altered obesity-induced hyperlipidemia and it enhanced the leptin/adiponectin/AMPK hormonal system in epididymal fat, serum, and liver, to which all the above physiological activities could be attributed. The nanoemulsion formulation of lupine oil significantly amplified the activity for all the above physiological and hormonal parameters when compared to the crude oil formulation. Lupine oil nanoemulsion could be used as a potential drug against diet-induced obesity

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Upper lip myomucosal flap for the repair of anterior oronasal fistula

Anterior oronasal fistula after cleft palatal repair is difficult to correct and it is consider challenging to many surgeons. Many techniques were used to repair this type of fistula without guarantee for success. Upper lip myomucosal flap is an alternative technique for the repair of this type of fistula. This is a retrospective descriptive case series study which included 10 patients diagnosed with anterior oronasal fistula after cleft palatal repair. They presented to Pediatric Surgery Department at the Faculty of Medicine, Mansoura University Children Hospital from the period between November 2013 and August 2014. In this technique, we do harvesting of the flap with measurement of its length and width, then baring the edge of the fistula with trying of its closure with local flaps. After that we suture the flap to the edge of the fistula and then evaluate the success rate. This study included 10 patients with age ranging from 15 to 72 months. The size of the fistula was less than 1 cm in six patients and more than 1 cm in four patients. The flap was used as an additional layer repair in seven patients and as the only layer for the repair in three patients. This technique was found to be successful in 70% of the patients with good healing without any recurrent fistula. We concluded that the use of this technique is feasible; however, its efficacy should be tested in larger number of patients to be considered as an option for the treatment of anterior oronasal fistula.Keywords: oronasal fistula, upper lip myomucosal flap, lip fla

A new ELISA kit which uses a combination of Plasmodium falciparum extract and recombinant Plasmodium vivax antigens as an alternative to IFAT for detection of malaria antibodies

BACKGROUND: The methods most commonly used to measure malarial antibody titres are the Indirect Fluorescence Antibody Test (IFAT), regarded as the gold standard, and the Enzyme-Linked ImmunoSorbent Assay (ELISA). The objective here was to assess the diagnostic performance, i.e. the sensitivity and specificity, of a new malaria antibody ELISA kit in comparison to IFAT. This new ELISA kit, the ELISA malaria antibody test (DiaMed), uses a combination of crude soluble Plasmodium falciparum extract and recombinant Plasmodium vivax antigens. METHODS: Two groups were used: 95 samples from malaria patients to assess the clinical sensitivity and 2,152 samples from blood donors, who had not been exposed to malaria, to assess the clinical specificity. RESULTS: The DiaMed ELISA test kit had a clinical sensitivity of 84.2% and a clinical specificity of 99.6% as compared with 70.5% and 99.6% respectively, using the IFAT method. The ELISA method was more sensitive than the IFAT method for P. vivax infections (75% vs. 25%). However, in 923 malaria risk donors the analytical sensitivity of the ELISA test was 40% and its specificity 98.3%, performances impaired by large numbers of equivocal results non-concordant between ELISA and IFAT. When the overall analytical performances of ELISA was compared to IFAT, the ELISA efficiency J index was 0.84 versus 0.71 for IFAT. Overall analytical sensitivity was 93.1% and the analytical specificity 96.7%. Overall agreement between the two methods reached 0.97 with a reliability k index of 0.64. CONCLUSION: The DiaMed ELISA test kit shows a good correlation with IFAT for analytical and clinical parameters. It may be an interesting method to replace the IFAT especially in blood banks, but further extensive investigations are needed to examine the analytical performance of the assay, especially in a blood bank setting

Real-time wearable device for predicting a long covid patient's condition

This paper aims to develop a wearable device that can be able to Predict the long covid-19 patients’ conditions, to notify the doctors on a real-time basis. Long covid-19 patients suffer a lot during their daily activities especially if the lasting symptom is related to the respiratory system. By developing a system, that is easy and comfortable to wear during normal daily life, we believe that we will be able to predict the long covid-19 patients’ condition. The system should first detect and analyze the patient’s breathing pattern using artificial intelligence then store the patient’s breathing pattern along with his status in an online database, then notify the doctors in case of a critical situation. To train the model the breathing pattern of current long covid patients and normal people was captured during doing daily activities such as walking, sitting, and climbing stairs. We hope that the developed system will help in easing the suffering of long covid patients by providing better monitoring of their health

Contribution of Gravity Data for Structural Characterization of the Ifni Inlier, Western Anti-Atlas, Morocco: Hydrogeological Implications

The Sidi Ifni region in southwest Morocco is mainly composed of crystalline rocks with limited groundwater storage capacity. These water resources drain in particular fault zones with high fracture permeability. The main objective of this study is to describe the geological structure of the region to optimize future drilling locations. The gravity data were processed using various techniques, such as total horizontal gradient, tilt derivative, and Euler deconvolution, in conjunction with the interpretation of the geological data, to create a new structural map. This map confirms the presence of many previously identified or inferred faults and identifies significant new faults with their respective trends and depths. Analysis of this map shows that major faults are oriented NNESSW and NE-SW, while minor faults are oriented E-W, NW-SE, and NNW-SSE. The superposition of the hydrogeological data and the structural map reveals that the high groundwater flow values in the boreholes are located in the vicinity of the major faults and talwegs. The structures deduced from the filtering and interpretation of the gravity data suggest that the hydrogeological system of the Ifni Inlier is controlled by its structures. To confirm this impact, a high-resolution electrical resistivity map (7200 Hz) was used, with penetration depths ranging from 84 to 187 m. Negative boreholes, located in high resistivity ranges corresponding to sound basement formations without fault crossings, showed high resistivity values. The positive holes, located in anomalies with low linear resistivity, revealed the impact of fault crossings, which drain water and tend to decrease the resistivity values of the formations. Therefore, these new structural maps will assist in planning future hydrogeological studies in this area