SARS-CoV-2 outbreak: role of viral proteins and genomic diversity in virus infection and COVID-19 progression.

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection is the cause of coronavirus disease 2019 (COVID-19); a severe respiratory distress that has emerged from the city of Wuhan, Hubei province, China during December 2019. COVID-19 is currently the major global health problem and the disease has now spread to most countries in the world. COVID-19 has profoundly impacted human health and activities worldwide. Genetic mutation is one of the essential characteristics of viruses. They do so to adapt to their host or to move to another one. Viral genetic mutations have a high potentiality to impact human health as these mutations grant viruses unique unpredicted characteristics. The difficulty in predicting viral genetic mutations is a significant obstacle in the field. Evidence indicates that SARS-CoV-2 has a variety of genetic mutations and genomic diversity with obvious clinical consequences and implications. In this review, we comprehensively summarized and discussed the currently available knowledge regarding SARS-CoV-2 outbreaks with a fundamental focus on the role of the viral proteins and their mutations in viral infection and COVID-19 progression. We also summarized the clinical implications of SARS-CoV-2 variants and how they affect the disease severity and hinder vaccine development. Finally, we provided a massive phylogenetic analysis of the spike gene of 214 SARS-CoV-2 isolates from different geographical regions all over the world and their associated clinical implications.

Amoebic Dysentery Complicated by Hypovolemic Shock and Sepsis in an Infant with Severe Acute Malnutrition: A Case Report.

Diarrheal disease continues to be a leading cause of death in children under five years old in developing countries, where it is responsible for the death of approximately half a million children each year. Establishing the cause of diarrheal disease can be difficult in developing areas due to the lack of diagnostic tests, and thus empirical therapies are often required. In these settings, the choice of antibiotic (or the choice to not give it) depends on suspected agents, host conditions and local epidemiology. Herein, we report a representative case of a ten-month-old male patient with severe acute malnutrition (SAM) admitted to the Emergency Paediatric Clinic in Port Sudan for amoebic dysentery complicated by hypovolemic shock and sepsis, treated by target therapy for Entamoeba histolytica infection associated with empiric antibiotic therapy. Due to the absence of clinical improvement, Ciprofloxacin was added to the first-line treatment. This case highlights that in low-income countries amoebiasis, especially in children with SAM, may result in life-threatening complications. Although stool microscopy remains the most used diagnostic test in these settings, a novel inexpensive, easy to use and rapid diagnostic test would be warranted to reach a microbiological diagnosis and guide clinical decision. Further studies will be necessary to identify the patterns of antimicrobial resistance in order to appropriately manage these complicated cases.

New Models for Predicting Pore Pressure and Fracture Pressure while Drilling in Mixed Lithologies Using Artificial Neural Networks.

Precise prediction of pore pressure and fracture pressure is a crucial aspect of petroleum engineering. The awareness of both fracture pressure and pore pressure is essential to control the well. It helps in the elimination of the problems related to drilling, waterflooding project, and hydraulic fracturing job such as fluid loss, kick, differential sticking, and blowout. Avoiding these problems enhances the performance and reduces the cost of operation. Several researchers proposed many models for predicting pore and fracture pressures using well log information, rock strength properties, or drilling data. However, some of these models are limited to one type of lithology such as clean and compacted shale formation, applicable only for the pressure generated by under compaction, and some of them cannot be used in unloading formations. Recently, artificial intelligence techniques showed a great performance in petroleum engineering applications. Hence, in this paper, two artificial neural network models are developed to estimate both pore pressure and fracture pressure through the use of 2820 data sets obtained from drilling data in mixed lithologies of sandstone, carbonate, and shale. The proposed artificial neural network (ANN) models achieved accurate estimation of pore and fracture pressures, where the coefficients of determination (R 2) for pore and fracture pressures are 0.974 and 0.998, respectively. Another data set from the Middle East was used to validate the developed models. The models estimated the pore and fracture pressures with high R 2 values of 0.90 and 0.99, respectively. This work demonstrates the validity and reliability of the developed models to calculate pore and fracture pressures from real-time surface drilling parameters by considering the formation type to overcome the limitation of previous models.

New Correlation for Calculating Water Saturation Based on Permeability, Porosity, and Resistivity Index in Carbonate Reservoirs.

Water saturation assessment is recognized as one of the most critical aspects of formation evaluation, reserve estimation, and prediction of the production performance of any hydrocarbon reservoir. Water saturation measurement in a core laboratory is a time-consuming and expensive task. Many scientists have attempted to estimate water saturation accurately using well-logging data, which provides a continuous record without information loss. As a result, numerous models have been developed to relate reservoir characteristics with water saturation. By expanding the use and advancement of soft computing approaches in engineering challenges, petroleum engineers applied them to estimate the petrophysical parameters of the reservoir. In this paper, two techniques are developed to estimate the water saturation in terms of porosity, permeability, and formation resistivity index through the use of 383 data sets obtained from carbonate core samples. These techniques are the nonlinear multiple regression (NLMR) technique and the artificial neural network (ANN) technique. The proposed ANN model achieved outstanding performance and better accuracy for calculating the water saturation than the empirical correlation using NLMR and Archie equation with a high coefficient of determination (R 2) of 0.99, a low average relative error of 1.92, a low average absolute relative error of 13.62, and a low root mean square error of 0.066. To the best of our knowledge, the current research establishes a novel foundation using the ANN model in the estimation of water saturation.

Restarting elective orthopaedic surgery as COVID-19 lockdown restrictions are reduced : have patient perceptions towards surgery changed?

AIMS: The COVID-19 pandemic drastically affected elective orthopaedic services globally as routine orthopaedic activity was largely halted to combat this global threat. Our institution (University College London Hospital, UK) previously showed that during the first peak, a large proportion of patients were hesitant to be listed for their elective lower limb procedure. The aim of this study is to assess if there is a patient perception change towards having elective surgery now that we have passed the peak of the second wave of the pandemic. METHODS: This is a prospective study of 100 patients who were on the waiting list of a single surgeon for an elective hip or knee procedure. Baseline characteristics including age, American Society of Anesthesiologists (ASA) grade, COVID-19 risk, procedure type, and admission type were recorded. The primary outcome was patient consent to continue with their scheduled surgical procedure. Subgroup analysis was also conducted to define if any specific patient factors influenced decision to continue with surgery. RESULTS: Overall, 88 patients (88%) were happy to continue with their scheduled procedure at the earliest opportunity. Patients with an ASA grade I were most likely to agree to surgery, followed by patients with ASA grades II, then those with grade III (93.3%, 88.7%, and 78.6% willingness, respectively). Patients waitlisted for an injection were least likely to consent to surgery, with just 73.7% agreeing. In all, there was a large increase in the proportion of patient willingness to continue with surgery compared to our initial study during the first wave of the pandemic. CONCLUSION: As COVID-19 lockdown restrictions are lifted after the second peak of the pandemic, we are seeing greater willingness to continue with scheduled orthopaedic surgery, reinforcing a change in patient perception towards having elective surgery. However, we must continue with strict COVID-19 precautions in order to minimize viral transmission as we increase our elective orthopaedic services going forward. Cite this article: Bone Jt Open 2021;2(10):865-870.

Evaluating the biomethane potential from the anaerobic co-digestion of palm oil mill effluent, food waste, and sewage sludge in Malaysia.

The ever-increasing organic waste generation in Malaysia is a significant contributor to greenhouse gas (GHG) emissions. However, organic wastes can be utilized to produce biogas by anaerobic digestion, which is a promising option for both energy and material recovery from organic wastes with high moisture content. Therefore, this study was formulated to investigate the feasibility of anaerobic co-digestion of three types of organic wastes generated in significantly huge quantities in Malaysia, namely palm oil mill effluent (POME), food waste (FW), and sewage sludge (SWS). The biomethane potential (BMP) test was used to evaluate the biomethane potential from these organic wastes under mesophilic conditions to establish a stable and balanced microbial community, which may lack in mono-digestion, to improve biogas production. Comparative performance was made at different food to microorganism (F/M) ratios to investigate methane production in three groups of assays, namely A, B, and C. In groups A and B, the effect of F/M ratio variation on methane production was investigated, while in group C, the effect of varying the co-substrate mixture on methane yield was examined. The findings showed that the highest methane yields achieved for mono-digestion of POME and SWS in group A were 164.44 mL-CH4/g-CODadded and 65.34 mL-CH4/g-CODadded, respectively, at an F/M ratio of 0.8 and 197.90 mL-CH4/g-CODadded for FW in group B at an F/M ratio of 0.5. In addition, the highest methane yield achieved from the anaerobic co-digestion was at 151.47 mL-CH4/g-CODadded from the co-digestion of the POME and SWS (50:50) at an F/M ratio of 1.7 in group A. Both AD and AcoD were tested to fit into two kinetic models: the modified Gompertz and the transfer function models. The results showed that the modified Gompertz model had a better fit and was more adjusted to the experimental results for both AD and AcoD. The importance of this research lies in the economics of anaerobically co-digesting these abundance feedstocks and the variations in their characteristics which were found to increase their methane yield and process efficiency in anaerobic co-digestion.

Head and neck injury in major trauma in Ireland: a multicentre retrospective analysis of patterns and surgical workload.

PURPOSE: Head and neck injuries are common in major trauma patients, but the prevalence is poorly documented in the literature. This study aims to investigate this further, particularly in the context of increasing development of Irish and European trauma systems. AIMS: To determine the prevalence of, and patterns behind head and neck injury in major trauma in an Irish population. MATERIALS AND METHODS: The Trauma Audit Research Network database was analysed for major trauma patients (injury severity score > 15) with head and neck injuries admitted to any of the 26 participating hospitals in the Republic of Ireland between 2014 and 2017. The data was studied for patterns in the epidemiology of injuries and outcomes. RESULTS: A total of 5364 patients were identified. Males were affected more than females (M:F 2.1:1). The most common mechanism of injury was falls. There were 1272 counts of soft tissue injury, and 5814 counts of bony injury recorded within the cohort. Twenty-six percent of patients underwent some form of surgical procedure. Median length of hospital stay was 8 days, and the 30-day survival rate was 90%. CONCLUSIONS: A substantial number of Irish major trauma patients of all ages and genders sustain some form of head and neck injury. It produces significant injury and surgical workload involving input from multiple disciplines.

Oral Contraceptive Types in Relation to ABO Blood Groups Among Saudi Women of Different Reproductive Age Groups and Impact on Venous Thromboembolism.

Saudi women have recently started using oral contraceptives (OCs), which has led to risk of venous thromboembolism (VTE). The risk varies with the type of OC generations used, and with OC use the risk for VTE increases by 2- to 6-fold. This study evaluated the effect of OC types in relation to ABO blood group on the risk of VTE among Saudi women. Thrombin generation (TG) was measured in the plasma of the women in the presence and absence of platelet rich plasma, platelet poor plasma and thrombomodulin or activated protein C. OC usage increased TG parameters ETP and Peak height by 9.81% and 16.04%, respectively. An increased risk of VTE was seen among women on third generation OCs as compared to those on second generation products. Within OC generations, we found that for women using fourth generation OCs, their ETP increased by 36.18% as compared to those using second generation and by 6.07% in those using third generation compared to those using second generation. There was significant difference with respect to ABO blood groups and OC generation types, but larger sample size is required. Women who are 40 years and older and using third generation OC had a higher risk of having thrombosis (11.84%), as compared to those using second generation OC (8.79%) and to those using fourth generation OC (5.03%). An association between different OC groups and non-O blood group in thrombosis generation was noted. TG parameters were significantly increased in relation to BMI when comparing to OC users versus non-users. In addition, inhibition of TG parameters in the presence of recombinant human thrombomodulin (TM) and activated protein C (APC) were significantly increased.

The effects of oral contraceptive usage on thrombin generation and activated protein C resistance in Saudi women, with a possible impact of the body mass index.

BACKGROUND AND OBJECTIVES: The effect of oral contraceptive (OC) usage on coagulation has been studied worldwide. However, no such studies have been conducted in Saudi Arabia on Saudi women using OCs. The aim of this study was to investigate the effects of OC-induced changes of thrombin generation (TG) in the absence and presence of activated protein C (APC) or thrombomodulin (TM) in Saudi women. METHODS: A total of 115 adult women, 47 on oral contraception (OC users) and 68 controls (not using OCs) were recruited from the obstetrics-gynecology outpatient clinic in Saudi Arabia. OCs that were used in this study include the following: Marvelon, Gynera, Cerrazetem, Yasmine, Microlut, Gracial and Diane. The plasma calibrated automated thrombinography (CAT) was used to determine TG which was expressed as endogenous thrombin potential (ETP; nM/min), lag time (min), peak (nM) and time-to-peak (ttpeak; min). In the presence of TM or APC, TG parameters were expressed relative to the parameters in the absence of TM or APC. RESULTS AND CONCLUSION: As in other populations, our study demonstrated that OC usage induced prothrombotic changes in plasma of Saudi women, including resistance to the inhibitory actions of TM and APC. More specifically, OC usage in our population predominantly influenced TG and APC/TM sensitivity in overweight and obese individuals, a finding that needs confirmation in large cohort studies. The effects of APC and TM on TG parameters showed a positive association, and the correlation coefficients were higher in OC users for both ETP and peak values.

Thrombin Generating Capacity and Phenotypic Association in ABO Blood Groups.

Individuals with blood group O have a higher bleeding risk than non-O blood groups. This could be explained by the lower levels of FVIII and von Willebrand Factor (VWF) levels in O individuals. We investigated the relationship between blood groups, thrombin generation (TG), prothrombin activation and thrombin inactivation. Plasma levels of VWF, FVIII, antithrombin, fibrinogen, prothrombin and α2Macroglobulin (α2M) levels were determined. TG was measured in platelet rich (PRP) and platelet poor plasma (PPP) of 217 healthy donors and prothrombin conversion and thrombin inactivation were calculated. VWF and FVIII levels were lower (75% and 78%) and α2M levels were higher (125%) in the O group. TG is 10% lower in the O group in PPP and PRP. Less prothrombin was converted in the O group (86%) and the thrombin decay capacity was lower as well. In the O group, α2M plays a significantly larger role in the inhibition of thrombin (126%). In conclusion, TG is lower in the O group due to lower prothrombin conversion, and a larger contribution of α2M to thrombin inactivation. The former is unrelated to platelet function because it is similar in PRP and PPP, but can be explained by the lower levels of FVIII.

Colonoscopic findings and management of patients with outbreak typhoid fever presenting with lower gastrointestinal bleeding.

Lower gastrointestinal bleeding (LGIB) along with intestinal perforation is a well-known complication of typhoid fever. Reports of colonoscopic appearance and intervention of typhoid perforation involve only few cases. This series reports the colonoscopic findings and the role of colonoscopic hemostatic interventions in controlling the bleeding ileocolonic lesions. During the typhoid fever outbreak in Sulaymaniyah City in Iraqi Kurdistan Region, we received 52 patients with LGIB manifesting as fresh bleeding per rectum or melena. We performed total colonoscopy with ileal intubation for all cases. The findings were recorded and endoscopic hemostatic intervention with adrenaline-saline injection and argon plasma coagulation was applied to actively bleeding lesion. These patients were young, 11-30 years of age, with female preponderance. Blood culture was positive in 50 %. Colonoscopic findings were mostly located in the ileocecal region, although other areas of the colon were involved in many cases. Twenty-four percent of the cases required endoscopic hemostatic intervention by adrenaline injection with argon plasma coagulation which was effective in all patients except one who died in spite of surgical intervention in addition of endoscopic hemostasis. Dual endoscopic hemostatic intervention can be a safe and effective management option for patients with LGIB due to typhoid fever.

Lipid changes occuring in the course of hematological cancers.

The relationship between plasma lipid levels and mortality from cardiovascular diseases has been shown in many studies, but there has been far less investigation into their relationship to non-cardiovascular diseases. The aim of this study was to investigate the lipid profile of individuals with hematological malignancies and its relationship to disease activity. 238 patients were included in the study: 84 with acute leukemia, 62 with non-Hodgkin lymphoma, 35 with Hodgkin's lymphoma, 32 with multiple myeloma, and 25 with myeloproliferative syndrome. The HDL cholesterol level of the patients differed to that of the individuals in the control group in the active disease period for all the analyzed disorders, but only remained statistically significant in the acute leukemia and non-Hodgkin lymphoma groups during the remission period. Smaller differences were observed for the remaining lipid fractions, except for the triglyceride level, which increased in the active disease period in all the analyzed disorders except non-Hodgkin lymphoma. The most pronounced changes in the lipid fractions occurred in the HDL cholesterol level, and were the most remarkable for acute leukemia.

[The biology of HDL lipoprotein and its antisclerotic activity]. / Biologia lipoproteiny HDL i jej przeciwmiazdzycowe dzialanie.

Clinical and epidemiological studies showed an inverse relationship between the level of high-density lipoprotein (HDL) cholesterol and the development of atherosclerosis. This fact aroused more interest in HDLs and it was found that these lipoproteins have significance in malignant diseases. In this review the biochemical classification of plasma lipoproteins, the structure of HDL, and the structural characterization of HDL-apolipoproteins are presented. The synthesis of HDL cholesterol and factors that regulate their structure and function are also considered. We discuss the antiatherogenic activity of HDL through its reverse cholesterol transport and antioxidant, anti-inflammatory, antithrombotic, and profibrinolytic effects.

Morbidity and mortality in ESRD patients on regular hemodialysis: a single center experience.

This is a prospective study of the outcome of patients with end-stage renal disease (ESRD) on regular hemodialysis admitted to a referral hospital in Madinah Al Munawarah, Saudi Arabia during a six-month period from January-June 2003. Ninety four patients out of 395 (23.7%) patients on regular hemodialysis were admitted 125 times of whom 27 (28.7%) patients were admitted twice; males accounted for 58.5% of the patients. The mean hospital stay period was 9.1 days per patient. The major cause of ESRD was diabetes mellitus (40%) followed by hypertension (13.6%). The main cause for admission was the vascular access related problems (33.6%) followed by infection (31.2%) and cardiovascular causes (18.4%). Most of the admissions were in the general ward but 17 % of the total stay in hospital was in the intensive care unit. Twelve out of the 94 (12.7%) study patients died during the study period; five patients died of cardiac failure, three of septicemia, one of severe gastrointestinal bleeding and one of Wegner's syndrome complicated by severe intra-pulmonary bleeding. Two patients had sudden death (most likely due to cardiac disease). In conclusion, our experience with morbidity and mortality of the hemodialysis patients admitted to hospital is comparable to other places in the world.

Gastrointestinal parasite infestation.

Twenty-five percent of the world's population could be suffering parasitic infestation. Highest prevalence is in underdeveloped agricultural and rural areas in the tropical and subtropical regions. In some areas incidence may reach 90% of the population. In contrast, some major economic projects intended to promote local development have, paradoxically, caused parasitic proliferation, e.g. bilharziasis in Egypt and Sudan and Chagas disease in Brazil. The commonest cosmopolitan gastrointestinal parasite is Entamoeba histolytica. Some intestinal parasite are endemic in temperate climates, e.g. Entrobius vermicularis. The AIDS epidemic has increased the prevalence and severity of parasitic disease, particularly Strongyloides stercolaris. Tropical parasites are seen in Western people who travel to tropical countries. Radiology has acquired a major role in diagnosis and management of gastrointestinal parasite infestations and their complications.