Recommendations for Uniform Variant Calling of SARS-CoV-2 Genome Sequence across Bioinformatic Workflows

Genomic sequencing of clinical samples to identify emerging variants of SARS-CoV-2 has been a key public health tool for curbing the spread of the virus. As a result, an unprecedented number of SARS-CoV-2 genomes were sequenced during the COVID-19 pandemic, which allowed for rapid identification of genetic variants, enabling the timely design and testing of therapies and deployment of new vaccine formulations to combat the new variants. However, despite the technological advances of deep sequencing, the analysis of the raw sequence data generated globally is neither standardized nor consistent, leading to vastly disparate sequences that may impact identification of variants. Here, we show that for both Illumina and Oxford Nanopore sequencing platforms, downstream bioinformatic protocols used by industry, government, and academic groups resulted in different virus sequences from same sample. These bioinformatic workflows produced consensus genomes with differences in single nucleotide polymorphisms, inclusion and exclusion of insertions, and/or deletions, despite using the same raw sequence as input datasets. Here, we compared and characterized such discrepancies and propose a specific suite of parameters and protocols that should be adopted across the field. Consistent results from bioinformatic workflows are fundamental to SARS-CoV-2 and future pathogen surveillance efforts, including pandemic preparation, to allow for a data-driven and timely public health response.

Foliar application of triacontanol ameliorates heat stress through regulation of the antioxidant defense system and improves yield of eggplant

Abstract Transplanting time and genotype contribute to improving crop yield and quality of eggplant (Solanum melongena L.). A field experiment was conducted to investigate the impact of foliar applied of triacontanol (TRIA) and eggplant genotypes 25919, Nirala, 28389 and Pak-10927,transplanted on 1 March,15 March, and 1 April on exposure to high air temperature conditions. The experiment was performed according to Randomized Complete Block Design and the data was analyzed by using Tuckey,s test . The TRIA was applied at 10µM at flowering stage; distilled water was used as the control. Rate of photosynthesis and transpiration, stomatal conductance, water use efficiency, and effects on antioxidative enzymes (superoxide dismutase, catalase and peroxidase) were evaluated. The 10µM TRIA increased photosynthesis rate and water use efficiency and yield was improved in all genotypes transplanted at the different dates. Foliar application of 10µM TRIA increased antioxidative enzyme activities (SOD, POD & CAT) and improved physiological as well as biochemical attributes of eggplant genotypes exposed to high heat conditions. Highest activity of dismutase enzyme 5.41mg/1g FW was recorded in Nirala genotype in second transplantation. Whereas, lowest was noted in PAK-10927 (2.30mg/g FW). Maximum fruit yield was found in accession 25919 (1.725kg per plant) at 1st transplantation with Triacontanol, whereas accession PAK-10927 gave the lowest yield (0.285 kg per plant) at control treatment on 3rd transplantation. Genotype, transplanting date and application of TRIA improved growth, yield and quality attributes under of heat stress in eggplant.

Groote Schuur Hospital neurosurgical intensive care unit: A 2-year review of admission characteristics

Background

At Groote Schuur Hospital (GSH), the neurosurgical intensive care unit (NsICU) is a 6-bed unit headed by a specialist neurosurgeon with extensive experience in neurocritical care, working in close collaboration with intensivists from the Division of Critical Care. There is currently no detailed analysis of the demographics, diagnosis and management of patients admitted to the NsICU at GSH.

Objectives

To provide a detailed descriptive analysis of the demographics, diagnosis and management of patients admitted to the NsICU at GSH from 1 January 2020 to 31 December 2021.

Methods

A retrospective descriptive analysis was done of patients who received treatment in the NsICU from 1 January 2020 to 31 December 2021.

Results

A total of 685 patients were admitted to the unit over a 2-year period, with a male preponderance (68.2%). The average age was 42.5 (standard deviation (SD) 17.2) years. The most common neurosurgical diagnoses were traumatic brain injuries (39.6%), brain tumours (22.6%) and aneurysmal subarachnoid haemorrhages (9.9%). Emergency admissions comprised 76.6% of the total and 86.7% of patients were admitted postoperatively. Three hundred and seventy-two patients (54.3%) required mechanical ventilation, 132 (19.3%) required both an intracranial pressure (ICP) monitor and brain tissue oxygenation monitor, 86 (12.5%) needed placement of an external ventricular drain, 50 (7.3%) needed placement of a tracheostomy tube and 16 (2.3%) needed placement of an ICP monitor only. The average duration of stay was 5.5 (1.3) days and NsICU mortality over 2 years was 11.1%.

Conclusion

The NsICU at GSH manages predominantly male trauma patients and a significant number of admitted patients require specialised invasive intracranial monitoring.

Contribution of the study

This is the first in-depth analysis of patients managed in a dedicated neurosurgical intensive care unit in South Africa. The work defines the patient population, neurosurgical pathologies and service level requirements that would likely be encountered by teams building a similar service.

Dynamics of parasite growth in genetically diverse Plasmodium falciparum isolates

Multiple parasite lineages with different proliferation rates or fitness may coexist within a clinical malaria isolate, resulting in complex growth interactions and variations in phenotype. To elucidate the dynamics of parasite growth in multiclonal isolates, we measured growth rates (GRs) of three Plasmodium falciparum Cambodian isolates, including IPC_3445 (MRA-1236), IPC_5202 (MRA-1240), IPC_6403 (MRA-1285), and parasite lineages previously cloned from each of these isolates by limiting dilution. Following synchronization, in vitro cultures of each parasite line were maintained over four consecutive asexual cycles (192 h), with thin smears prepared at each 48-h cycle to estimate GR and fold change in parasitemia (FCP). Cell cycle time (CCT), the duration it takes for ring-stage parasites to develop into mature schizonts, was measured by monitoring the development of 0-3-h post-invasion rings for up to 52 h post-incubation. Laboratory lines 3D7 (MRA-102) and Dd2 (MRA-150) were used as controls. Significant differences in GR, FCP, and CCT were observed between parasite isolates and clonal lineages from each isolate. The parasite lines studied here have well-defined growth phenotypes and will facilitate basic malaria research and development of novel malaria interventions. These lines are available to malaria researchers through the MR4 collection of NIAID's BEI Resources Program.

Development and validation of a rapid and easy-to-perform point-of-care lateral flow immunoassay (LFIA) for the detection of SARS-CoV-2 spike protein

Development and validation of rapid and easy-to-perform diagnostics continue to be a high priority during the current COVID-19 pandemic. Although vaccines are now widely available, early detection and consistent transmission control provide ideal means to mitigate the spread of SARS-CoV-2. Nucleic acid-based real-time PCR tests are widely acknowledged as the gold standard for reliable diagnosis of COVID-19 infection. These tests are based on detecting viable or nonviable viral nucleic acids. SARS-CoV-2 spike protein is an alternative and ideal target for SARS-CoV-2 diagnosis in the early phase of infection, but point-of-care kits to detect the SARS-CoV-2 spike protein are limited. Here we describe a rapid and convenient method based on Lateral Flow Immunoassay (LFIA) to detect SARS-CoV-2 spike proteins, including SARS-CoV-2 variants (A.23.1, B.1.1.1, 1.617.2, B.1.1.7, B.1.351, P.1, N501Y, R.1, P681H, P3, UK, and South African) within 5 to 10 minutes. We generated highly specific monoclonal antibodies (mAbs) against rationally designed SARS-CoV-2 spike protein. Matched pair mAbs were selected by epitope mapping and employed as antigen capture reagents by spotting onto a nitrocellulose membrane and as detector reagents by conjugation with colloidal gold nanoparticles. We evaluated the performance of the LFIA using recombinant spike proteins of SARS-CoV-2 and several SARS-CoV-2 variants. The specificity of the LFIA was assessed using heat-inactivated SARS-CoV-2 and related human coronaviruses (HCoV-OC43, HCoV-229E, HCoV-HKU1, and HCoV-NL63) and an FDA-approved respiratory pathogens (RP) panel. The assay exhibited 98% specificity and acceptable performance with respect to the minimum limit of detection (25 ng/test) in validation tests. This new LFIA provides improved performance for the early diagnosis of SARS-CoV-2, particularly for home monitoring and in situations with limited access to molecular methods.

Towards increased accuracy and reproducibility in SARS-CoV-2 next generation sequence analysis for public health surveillance

During the COVID-19 pandemic, SARS-CoV-2 surveillance efforts integrated genome sequencing of clinical samples to identify emergent viral variants and to support rapid experimental examination of genome-informed vaccine and therapeutic designs. Given the broad range of methods applied to generate new viral genomes, it is critical that consensus and variant calling tools yield consistent results across disparate pipelines. Here we examine the impact of sequencing technologies (Illumina and Oxford Nanopore) and 7 different downstream bioinformatic protocols on SARS-CoV-2 variant calling as part of the NIH Accelerating COVID-19 Therapeutic Interventions and Vaccines (ACTIV) Tracking Resistance and Coronavirus Evolution (TRACE) initiative, a public-private partnership established to address the COVID-19 outbreak. Our results indicate that bioinformatic workflows can yield consensus genomes with different single nucleotide polymorphisms, insertions, and/or deletions even when using the same raw sequence input datasets. We introduce the use of a specific suite of parameters and protocols that greatly improves the agreement among pipelines developed by diverse organizations. Such consistency among bioinformatic pipelines is fundamental to SARS-CoV-2 and future pathogen surveillance efforts. The application of analysis standards is necessary to more accurately document phylogenomic trends and support data-driven public health responses.

Propagation of SARS-CoV-2 in Calu-3 Cells to Eliminate Mutations in the Furin Cleavage Site of Spike

SARS-CoV-2 pathogenesis, vaccine, and therapeutic studies rely on the use of animals challenged with highly pathogenic virus stocks produced in cell cultures. Ideally, these virus stocks should be genetically and functionally similar to the original clinical isolate, retaining wild-type properties to be reliably used in animal model studies. It is well-established that SARS-CoV-2 isolates serially passaged on Vero cell lines accumulate mutations and deletions in the furin cleavage site; however, these can be eliminated when passaged on Calu-3 lung epithelial cell lines, as presented in this study. As numerous stocks of SARS-CoV-2 variants of concern are being grown in cell cultures with the intent for use in animal models, it is essential that propagation methods generate virus stocks that are pathogenic in vivo. Here, we found that the propagation of a B.1.351 SARS-CoV-2 stock on Calu-3 cells eliminated viruses that previously accumulated mutations in the furin cleavage site. Notably, there were alternative variants that accumulated at the same nucleotide positions in virus populations grown on Calu-3 cells at multiple independent facilities. When a Calu-3-derived B.1.351 virus stock was used to infect hamsters, the virus remained pathogenic and the Calu-3-specific variants persisted in the population. These results suggest that Calu-3-derived virus stocks are pathogenic but care should still be taken to evaluate virus stocks for newly arising mutations during propagation.

Correlation Study of the Most Important Environmental Influencing Factors on the Razi MMR Vaccine

Measles, mumps, and rubella (MMR) are among the most important viral infectious diseases in Iran and neighboring countries. After using a trivalent vaccine for these three diseases for a long time, in recent years, these diseases have been significantly controlled in Iran. One of the important points of storing the vaccine is that the vaccine strains are highly temperature-sensitive viruses. Due to tropical climatic conditions in Iran, the cold chain may not be achievable during the storage and transmission of the MMR vaccine. Therefore, the efficacy of the vaccine may be affected. This study aimed to evaluate the MMR vaccine potency at different temperatures (stress tests) and frequent light exposures. All quality control tests in the form of stability studies were performed on the samples from three consecutive batches produced during a full-scale Razi production. The samples were stored at 2-8, 22-25, 35-37, and 42-45°C in specific time intervals, exposed to frequent light, and underwent freezing/thawing conditions. According to the results, the storage of the vaccine at high temperatures caused a decrease in potency and increased moisture content in the vaccine vials. The best temperature for maintenance and transportation of MMR is 2-8°C. The time and frequency of light exposure may affect the vaccine potency. Based on the sensitivity of the vaccine strains to environmental conditions, the development of plans for storage and transportation of vaccines in different situations and training the vaccine injection staff seem necessary.

Characteristics of warfarin underprescription in older adults with atrial fibrillation

Objectives

The prevalence of atrial fibrillation (AF) and atrial flutter (AFl) increases with age. Prior research suggests that underprescription of anticoagulants, such as warfarin, in older adults can lead to increased morbidity and mortality. We analyzed rates and patterns of warfarin prescription in older adults.

Methods

In this prospective observational study, we enrolled 2179 consecutive patients with admission diagnosis of AF or AFl. Those placed on a non-warfarin anticoagulation (189 patients) were excluded. Patients were then divided into “older cohort” (≥75 years of age) and “younger cohort” (<75 years of age). Within the older cohort, prescription patterns of warfarin were analyzed. Serial prospective follow-up was 3.1±2.06 years.

Results

Of the 1990 patients, 46.9% were ≥75 years older, of which 51.1% were prescribed warfarin. There was no difference between mean CHA2DS2-VASc score and warfarin prescription (OR=1.06 (95% CI 0.93–1.21), p=0.388) in the older cohort. After adjusting for hypertension, glomerular filtration rate, and Black race, appropriate warfarin prescription in older adults was independently associated with lower aspirin prescription rates (OR=0.57 (95% CI 0.43–0.75), p<0.001), lower body mass index (OR=1.03 (95% CI 1.01–10.6), p=0.018), and lower hemoglobin levels (OR=1.11 (95% CI 1.04–1.19), p=0.002).

Conclusions

In our study, adults 75 years and older with AF and AFl tended to have lower rates of warfarin prescription despite higher CHA2DS2-VASc score and higher risk of thromboembolic events. Anemia, lower weight, and aspirin use were characteristics associated with warfarin underprescription. These patterns can shed light on clinicians' perceived hesitancy to anticoagulate certain older adults.

Funding Acknowledgement

Type of funding sources: None.

Improving adherence to cholesterol lowering guidelines through an interactive digital tool

Background

Statins are the cornerstone of primary and secondary prevention of atheroscleoric cardiovascular disease (ASCVD). Our previous retrospective analysis of 1042 consecutive patient encounters at a large urban academic institution found that one in five patients were not prescribed an appropriate statin therapy. These patients tended to be younger, of Black race, and met statin-eligibility solely via a 10-year ASCVD risk score ≥7.5%. Only one-third of patients had follow-up cholesterol levels ordered to monitor treatment efficacy.

Purpose

To improve adherence to cholesterol guidelines at our academic institution.

Methods

We implemented multiple interventions over a four-month period to support clinical decision making of guideline directed statin therapy: a) development of an online interactive tool, b) physician education on updated cholesterol guidelines and utilization of the tool, c) display of guideline summary in the workspace, and d) a documentation reminder in the electronic health record. We randomly selected encounter dates, from which 622 consecutive patient visits were analyzed. The primary outcome measures were: prescription rates of statins, documentation of a 10-year ASCVD risk score, and follow-up cholesterol levels ordered to monitor treatment efficacy.

Results

Out of the 622 patients, 232 met statin indication. In this post-intervention group, statin prescriptions rates improved when compared to the pre-intervention group (90.5% vs 82.3%, p=0.006). Among the patients who met statin indication solely via a 10-year ASCVD risk score ≥7.5%, there was an increase in documentation of the calculated 10-year ASCVD risk score (72.3% vs 57.8%; p=0.039) and in statin prescription rate (90.8% vs 67.6%; p<0.001). In addition, there was an increase in follow-up cholesterol levels ordered in all patients included in our study who met statin indication (64.1% vs 33.3%; p<0.001).

Conclusion

Our study showed higher rates of statin prescription, 10-year ASCVD risk score documentation, and treatment monitoring after multiple interventions, including an easily accessible online interactive tool, at a large urban academic institution.

Funding Acknowledgement

Type of funding sources: None. Statin Prescription Rates

Current development of Zika virus vaccines with special emphasis on virus-like particle technology

Introduction: Zika virus disease received little attention until its recent explosive emergence around the globe. The devastating consequences of this pandemic include congenital Zika syndrome (CZS) and the neurological autoimmune disorder Guillain-Barré syndrome. These potential outcomes prompted massive efforts to understand the course of Zika infection and to develop therapeutic and prophylactic strategies for treatment and prevention of disease.Area covered: Preclinical and clinical data demonstrate that a safe and efficacious vaccine for protection against Zika virus infection is possible in the near future. Nevertheless, significant knowledge gaps regarding the outcome of a mass vaccination strategy exist and must be addressed. Zika virus circulates in flavivirus-endemic regions, an ideal Zika vaccine should avoid the potential of antibody-dependent enhancement from exposure to dengue virus. Prevention of CZS is the primary goal for immunization, and the vaccine must provide protection against intrauterine transmission for use during pregnancy and in women of childbearing age. Ideally, a vaccine should also prevent sexual transmission of the virus through mucosal protection.Expert opinion: This review describes current vaccine approaches against Zika virus with particular attention to the application of virus-like particle (VLP) technology as a strategy for solving the challenges of Zika virus immunization.

Generation of structured coherent extreme ultraviolet beams from an MgO crystal

Short wavelength high-harmonic sources are undergoing intense development for applications in spectroscopy and microscopy. Despite recent progress in peak and average power, spatial control over coherent extreme ultraviolet (XUV) beams remains a formidable challenge due to the lack of suitable optical elements for beam shaping and control. Here we demonstrate a robust and precise approach that structures XUV high-order harmonics in space as they are emitted from a nanostructured MgO crystal. Our demonstration paves the way for bridging the numerous applications of shaped light beams from the visible to the short wavelengths, with potential uses for applications in microscopy and nanoscale machining.

A cautionary perspective regarding the isolation and serial propagation of SARS-CoV-2 in Vero cells

An array of SARS-CoV-2 virus variants have been isolated, propagated and used in in vitro assays, in vivo animal studies and human clinical trials. Observations of working stocks of SARS-CoV-2 suggest that sequential propagation in Vero cells leads to critical changes in the region of the furin cleavage site, which significantly reduce the value of the working stock for critical research studies. Serially propagating SARS-CoV-2 in Vero E6 cells leads to rapid increases in genetic variants while propagation in other cell lines (e.g. Vero/hSLAM) appears to mitigate this risk thereby improving the overall genetic stability of working stocks. From these observations, investigators are urged to monitor genetic variants carefully when propagating SARS-CoV-2 in Vero cells.

A Virus-Like Particle-Based Vaccine Candidate against the Tick-Borne Powassan Virus Induces Neutralizing Antibodies in a Mouse Model

Powassan virus (POWV) is a tick-borne flavivirus circulating in North America and the Russian Far East that can cause severe neuroinvasive diseases, including encephalitis, meningitis, and meningoencephalitis. The reported neuroinvasive case fatality is about 10%, and approximately 50% of the survivors from the neuroinfection exhibit long-lasting or permanent neurological sequelae. Currently, treatment of POWV infection is supportive, and no FDA-approved vaccines or specific therapeutics are available. A novel Powassan vaccine candidate was created using virus-like particle technology (POW-VLP) and assembled with the viral structural proteins pre-Membrane (prM) and Envelope (E). Western blot immunoassay demonstrated high antigenicity of POW-VLP structural proteins. Transmission electron microscopy indicated that the POW-VLP exhibited icosahedral morphology typical of flaviviruses. A dose-escalation study in a murine model was performed to test immunogenicity and safety. Serum antibody was tested by ELISA, demonstrating that POW-VLP afforded 100% seroconversion to the E protein. Reporter viral-particle neutralization assay demonstrated high levels of neutralizing antibodies in the serum of immunized mice. Hybridomas expressing monoclonal antibodies were produced following POW-VLP immunization. The POW-VLP vaccine candidate created in this study provides a strategy for inducing protective antibodies against Powassan neuroinvasive infection.

Amelioration of N,N'-dimethylhydrazine induced colon toxicity by epigallocatechin gallate in Wistar rats

Colon cancer is a life-threatening disease all over the world and is linked to constant oxidative stress and inflammation. Epigallocatechin gallate (EGCG), is a naturally occurring flavone possessing health benefiting pharmacological properties including antioxidant, anti-inflammatory and free radical scavenging properties. Our study investigates the role of EGCG on N,N'-dimethylhydrazine (DMH), a toxic environmental pollutant, induced colon toxicity. To investigate the effect of EGCG, Wistar rats were given EGCG for 7 days at the two doses of 10 and 20 mg/kg body weight and DMH was injected on the seventh day in all the group rats except the control. Our results indicate that DMH administration increased the oxidative stress (MDA) and depleted the glutathione and antioxidant enzyme activities (SOD, CAT, GR, GST and GPx) which was significantly ameliorated by EGCG treatment. Additionally DMH treatment upregulated inflammatory markers expression (NF-κB, COX-2 and IL-6) and enhanced mucosal damage in the colon. EGCG treatment significantly reduced inflammation and restored the normal histoarchitecture of the colon. We can conclude from the present study findings that EGCG protects the colon from DMH toxicity through its antioxidant and anti-inflammatory potential.

Vitamin D and UV exposure in construction workers-a randomized control trial using text messaging to promote positive behaviours

BACKGROUND

The aim of this study was to determine whether a text messaging intervention (supported by a smartphone application) would be effective in the promotion of sun-safe behaviours. Both excessive and insufficient exposure to ultra-violet (UV) radiation were considered.

METHODS

A randomized control crossover trial was conducted. 112 participants from nine sites in the United Kingdom contributed to the study. There were three intervention waves, two in winter (Vitamin D-focussed) and one in summer (UV exposure-focussed). Stages of Change, Standard Erythemal (UV) Dose and assayed blood samples (Vitamin D) were employed to evaluate the effectiveness throughout the 21-day data collection periods.

RESULTS

The intervention was effective in promoting positive progression in Stages of Change for Vitamin D; and this in turn was predictive of increased Vitamin D levels in participants. More limited positive findings were found with respect to UV exposure. Overall, for those in the Intervention, Vitamin D levels were significantly predicted to increase during both of the winter data collection waves.

CONCLUSIONS

Interventions of this type are recommended to promote healthy Vitamin-D levels in construction workers.

Zika Virus-Like Particle (VLP) vaccine displaying Envelope (E) protein CD loop antigen elicits protective and specific immune response in a murine model

Zika virus (ZIKV) is a mosquito-borne flavivirus associated with Congenital Zika Syndrome (CZS), reflecting a wide range of congenital abnormalities in fetuses and infants infected with ZIKV before birth. ZIKV infections have also been associated with the neurological autoimmune disorder known as Guillian-Barré syndrome (GBS). To date, no vaccines or antiviral strategies are licensed for ZIKV. We used rational design to develop a novel ZIKV vaccine candidate using a Woodchuck Hepatitis core Antigen (WHcAg) Virus-Like Particle (VLP) scaffold for displaying selected antigens from the ZIKV Envelope (E) protein. A Zika-VLP vaccine candidate containing the CD Loop sub-structural domain from ZIKV E protein Domain III (WHcAg CD Loop) elicited a strong immune response in a murine model. Analysis of serum immunoglobulins demonstrated induction of both Th1- and Th2- mediated immune response. No cross-reacting antibodies were detected between Zika, dengue and yellow fever virus, demonstrating a high level of specificity for the ZIKV CD Loop antigen. Immunization with the WHcAg CD Loop vaccine candidate demonstrated immunoprotection in a murine model of ZIKV infection, stimulating protective antibodies associated with antibody-dependent cellular cytotoxicity (ADCC) and complement-dependent cytotoxicity (CDC) activities. The WHcAg CD Loop candidate may represent a safer vaccine for preventing antibody dependent enhancement (ADE).

Protective role of diosmin against testosterone propionate-induced prostatic hyperplasia in Wistar rats: Plausible role of oxidative stress and inflammation

Benign prostatic hyperplasia (BPH) is an important key health concern for aging men. Polyphenolic compounds have been found to possess important roles in the inhibition of numerous ailments that involve reactive oxygen species and inflammation. Diosmin is a citrus flavone that possesses antioxidant, anti-inflammatory, antiproliferative, and anticancer activities, so based on these properties of diosmin, we decided to evaluate its effect on testosterone propionate (TP)-induced BPH. A total of 30 Wistar rats were randomly assigned to five groups having six animals in each. This study was of 28 days in which TP (5 mg kg−1) was administered to induce BPH in the last 10 days of the study. It was found that diosmin at the doses of 20 and 40 mg kg−1significantly reduced malondialdehyde and xanthine oxidase formation in a dose-dependent manner; however, it replenished catalase, glutathione (GSH), and GSH-dependent enzymes, that is, glutathione peroxidase, glutathione reductase, and glutathione- S-transferase significantly against TP-induced BPH. Further, immunohistochemical study showed that diosmin alleviated inflammatory markers (nuclear factor kappa-light-chain-enhancer of activated B cells, cyclooxygenase-2, and interleukin-6). It was also found that diosmin downregulated the expression of androgen receptor and decreased the prostate-specific antigen concentration dose-dependently, significantly against TP-induced BPH. Diosmin also restored histoarchitecture of the prostate in a dose-dependent manner. Findings from the present study revealed the protective role of diosmin against TP-induced BPH in Wistar rats.

Effect of maturation conditions on light and temperature requirements during seed germination of Citrullus colocynthis from the Arabian Desert

Seed germination of Citrullus colocynthis, as in many other species of Cucurbitaceae, is inhibited by light, particularly at low temperatures. Germination response to light and temperature has been attributed to day length and temperature during seed maturation. This study assessed the effects of these factors on the germination response of C. colocynthis to temperature and light quality. Ripe fruits were collected from natural habitats during December and February and germinated at three temperatures (15/25, 20/30 and 25/35 °C) in five light treatments (dark, white light and Red:Far Red (R:FR) ratios of 0.30, 0.87 and 1.19). Additionally, unripe fruits were also collected from natural habitats and completed their maturation in growth chambers under different day lengths (6, 16 and 24 h of darkness) at 10/20 °C, and in darkness at both 10/20 °C and 25/35 °C. Mature seeds of the different treatments were germinated in the same five light treatments at 15/25 °C. Germination was significantly higher in the dark than that in any light treatment. Seeds matured at higher temperatures (i.e. seeds from the December collection and those matured at 25/35 °C) had significantly higher germination than those matured at lower temperatures (i.e. seeds from the February collection and those matured at 10/20 °C). Dark germination was significantly higher for the December collection than for the February collection. Seeds of the two collections germinated in the dark only at 15/25 °C. However, seeds matured in a growth chamber at 10/20 °C in darkness germinated at 15/25 °C in all light treatments, except for the R:FR ratio 0.30. Seeds of the different treatments failed to germinate in FR-rich light. This study demonstrates that both temperature and day length during seed maturation play significant roles in the germination response of C. colocynthis. Additionally, the dark requirement for germination is likely beneficial for species with the larger seeds, such as C. colocynthis, which produce bigger seedlings that are able to emerge from deep soils and are competitively superior under dense vegetation and resource-limited conditions.

Attracting medical students and doctors into surgical training in the UK and Ireland

AIMS

Core surgical training (CST) programmes in the UK have seen a significant reduction in competition ratios over the past five years. This study aimed to determine motivating factors and perceived barriers to pursuing a career in surgery amongst junior doctors in training and medical students attending an annual conference.

METHODS

A self-reported, electronic questionnaire was distributed to medical students, foundation year doctors, and doctors in postgraduate surgical training programmes (DIPST) who attended the Association of Surgeons in Training (ASiT) Conference in 2016. Respondents ranked factors attracting them to a career in surgery and factors that could improve perceptions of surgical careers. Chi-square test was used to test for differences between groups (a = 0.05, R Studio, V3.3.1).

RESULTS

Of 394 respondents (response rate = 50.9%), 44.9% were medical students or foundation doctors ('Pre-CST') and 55.1% were DIPST ('Peri/post-CST'). Practical application of skills (97.4%), enjoyment of the theatre environment (95.4%) and positive experiences in surgical firms (84.7%) were primary driving factors towards a surgical career. Availability of private practice (32.2%), and sustainability of consultant jobs (49.0%) had less influence. For 'Pre-CST' respondents, role models (82.8% pre-CST v 74.9% peri-post CST, p < 0.05) and defined career progression (67.2% pre-CST v 47.0% peri-post CST, p < 0.001) were particularly important. 91% of all respondents agreed that a better balance of training and service within worked hours would improve perceptions of surgery.

CONCLUSION

Addressing the motivating factors and perceived barriers to surgical careers will help bolster recruitment of the future surgical workforce.

Critical care usage after major gastrointestinal and liver surgery: a prospective, multicentre observational study

BACKGROUND

Patient selection for critical care admission must balance patient safety with optimal resource allocation. This study aimed to determine the relationship between critical care admission, and postoperative mortality after abdominal surgery.

METHODS

This prespecified secondary analysis of a multicentre, prospective, observational study included consecutive patients enrolled in the DISCOVER study from UK and Republic of Ireland undergoing major gastrointestinal and liver surgery between October and December 2014. The primary outcome was 30-day mortality. Multivariate logistic regression was used to explore associations between critical care admission (planned and unplanned) and mortality, and inter-centre variation in critical care admission after emergency laparotomy.

RESULTS

Of 4529 patients included, 37.8% (n=1713) underwent planned critical care admissions from theatre. Some 3.1% (n=86/2816) admitted to ward-level care subsequently underwent unplanned critical care admission. Overall 30-day mortality was 2.9% (n=133/4519), and the risk-adjusted association between 30-day mortality and critical care admission was higher in unplanned [odds ratio (OR): 8.65, 95% confidence interval (CI): 3.51-19.97) than planned admissions (OR: 2.32, 95% CI: 1.43-3.85). Some 26.7% of patients (n=1210/4529) underwent emergency laparotomies. After adjustment, 49.3% (95% CI: 46.8-51.9%, P<0.001) were predicted to have planned critical care admissions, with 7% (n=10/145) of centres outside the 95% CI.

CONCLUSIONS

After risk adjustment, no 30-day survival benefit was identified for either planned or unplanned postoperative admissions to critical care within this cohort. This likely represents appropriate admission of the highest-risk patients. Planned admissions in selected, intermediate-risk patients may present a strategy to mitigate the risk of unplanned admission. Substantial inter-centre variation exists in planned critical care admissions after emergency laparotomies.

Whole genome sequencing, variant analysis, phylogenetics, and deep sequencing of Zika virus strains

The recent emergence of Zika virus (ZIKV) has been concentrated in the Caribbean, Southeastern United States, and South- and Central America; resulting in travel-based cases being reported around the globe. As multi-disciplinary collaborations are combatting the ZIKV outbreak, the need to validate the sequence of existing strains has become apparent. Here, we report high-quality sequence data for multiple ZIKV strains made publicly available through the National Institutes of Health- (NIH) funded biorepository, BEI Resources (www.beiresources.org). Next-generation sequencing, 3' rapid amplification of cDNA ends (RACE), and viral genome annotation pipelines generated GenBank sequence records for 16 BEI Resources strains. Minor variants, consensus mutations, and consensus insertions/deletions were identified within the viral stocks using next-generation sequencing (NGS) and consensus changes were confirmed with Sanger sequencing. Bioinformatics analyses of the sequencing results confirm that the virus stocks available to the scientific research community through BEI Resources adequately represent the viral population diversity of ZIKV.

Phenolics, tocopherols and fatty acid profiling of wild and commercial mushrooms from Pakistan

Mushrooms can be used as nutraceutical or functional foods to maintain and promote good health. In the present study, wild Ganoderma lucidum and four commercial mushrooms, Pleurotus ostreatus, Volvariella volvacea, Hericium erinaceus and Lentinus edodes, collected from Pakistan were screened for phenolics, tocopherols and fatty acid contents. High performance liquid chromatography analysis of phenolic acids showed that chlorogenic acid, ferulic acid, gallic acid, p-Coumaric and caffeic acids were observed in selected mushrooms. H. erinaceus contained high amounts of chlorogenic acid (11.49±0.1 µ/g of dry weight) and ferulic acid (7.84±0.7 µg/g of dry weight). γ-tocopherol and lutein were present in all studied mushrooms. Lutein contents were higher in H. erinaceus (2.42±0.087 µg/g of DW) followed by V. volvacea> P. ostreatus> L. edodes. γ-tocopherol was observed in the range of 74.25±3.01 to 29.65±1.2 µg/g of dry weight. GC/MS analysis of fatty acids showed that linoleic acid (18’:2n6c), oleic acid (18’:1n9c), palmitic acid (C16:0), stearic acid (C18:0), linolenic acid (18’:3n3) and nonadecanoic acid (C19-0), were the main fatty acids found in selected mushrooms. The unsaturated fatty acids were predominated over saturated fatty acids. It is concluded that selected mushrooms are good sources of antioxidant compounds and unsaturated fatty acids.

An Echocardiographic Study of the Right Ventricular Diastolic Function in Systemic Hypertension and Its Relation with the Left Ventricular Homologous Changes

Diastolic dysfunction is a major predictor of mortality and morbidity in hypertensive patients. Not only LV, the RV is also expected to be affected in this overall procedure. To observe the Echocardiographic changes of diastolic function of the RV in systemic HTN and their relation with similar parameters of the LV was the objective. TDI was used in association with standard Doppler modality. In this cross-sectional study, 50 hypertensive subjects were studied who were devoid of any other conditions that may influence the diastolic function of the RV from 01 May 2012 to 31 October 2012 at Bangabandhu Sheikh Mujib Medical University (BSMMU), Dhaka, Bangladesh. In addition to 2D and M-mode evaluation, standard Doppler and pulsed tissue Doppler assessment of both ventricles were performed. Measurements were obtained for diastolic as well as systolic function of both ventricles. The RV diastolic parameters were impaired in both standard Doppler and tissue Doppler analysis in association with LV parameters. Systolic functions (LV FS and RV TAPSE) were preserved. Doppler-derived tricuspid peak E and E/A were related negatively to septal thickness, but tissue Doppler-derived RV Em/Am showed negative association with both RVAWT and septal thickness. RV RTm was related positively to RVAWT. The RV diastolic parameters showed positive relation with the LV similar parameters both in standard Doppler (E peak velocity, E/A ratio and EDT) and tissue Doppler (Em peak velocity, Em/Am and PCTm) assessment. So, in systemic HTN, LV diastolic dysfunction is also associated with diastolic disturbances of the RV. Pulsed tissue Doppler is a useful tool to detect the changes. RV diastolic parameters correlate well with those of the LV. Prolongation of the active relaxation (RTm) phase of RV is due to its increased wall thickness.

Internal Fixation of Transverse Patella Fractures Using Cannulated Cancellous Screws with Anterior Tension Band Wiring

Aims: To evaluate the effectiveness and safety of anterior tension band wiring technique using two cannulated cancellous screws in patients with transverse (AO34-C1) or transverse with mildly comminuted (AO34-C2) patellar fractures.

Materials and Methods: This is a prospective study of 25 patients with transverse fracture or transverse fracture with mildly comminuted patella fractures. All the patients were treated with open reduction and internal fixation using two parallel cannulated screws and 18G stainless steel wire as per the tension band principle.

Results: There were eighteen males (72%) and seven females (28%). The age group ranged from 24 to 58 years, with mean age of 38 years. The most common mode of injury was fall (72%) followed by road traffic accident (20%) and violent quadriceps contraction (8%). Transverse fracture was present in 60% and transverse fracture with mild comminution in 40% of patients. Mean time to achieve union was 10.7 weeks (range 8-12 weeks). Mean ROM at three months was 113.8 degree (90-130) and at final follow up this improved to 125.4 degrees (range 100-140). There was one case of knee stiffness and no case of implant failure was observed. Patients were evaluated using Bostman scoring, the mean score at three months being 26.04 which improved to 27.36 at the end of final follow up at one year.

Conclusion: Cannulated cancellous screws with anterior tension band wiring is a safe, reliable and reproducible method in management of transverse patellar fractures, with less chances of implant failure and soft tissue irritation.

Exogenous progesterone exacerbates running response of adolescent female mice to repeated food restriction stress by changing α4-GABAA receptor activity of hippocampal pyramidal cells

Adolescent females are particularly vulnerable to mental illnesses with co-morbidity of anxiety, such as anorexia nervosa (AN). We used an animal model of AN, called activity-based anorexia (ABA), to investigate the neurobiological basis of vulnerability to repeated, food restriction (FR) stress-evoked anxiety. Twenty-one of 23 adolescent female mice responded to the 1st FR with increased wheel-running activity (WRA), even during the limited period of food access, thereby capturing AN's symptoms of voluntary FR and over-exercise. Baseline WRA was an excellent predictor of FR-elicited WRA (severity of ABA, SOA), with high baseline runners responding to FR with minimal SOA (i.e., negative correlation). Nine gained resistance to ABA following the 1st FR. Even though allopregnanolone (3α-OH-5α-pregnan-20-one, THP), the metabolite of progesterone (P4), is a well-recognized anxiolytic agent, subcutaneous P4 to these ABA-resistant animals during the 2nd FR was exacerbative, evoking greater WRA than the counterpart resistant group that received oil vehicle, only. Moreover, P4 had no WRA-reducing effect on animals that remained ABA-vulnerable. To explain the sensitizing effect of P4 upon the resistant mice, we examined the relationship between P4 treatment and levels of the α4 subunit of GABAARs at spines of pyramidal cells of the hippocampal CA1, a parameter previously shown to correlate with resistance to ABA. α4 levels at spine membrane correlated strongly and negatively with SOA during the 1st ABA (prior to P4 injection), confirming previous findings. α4 levels were greater among P4-treated animals that had gained resistance than of vehicle-treated resistant animals or of the vulnerable animals with or without P4. We propose that α4-GABAARs play a protective role by counterbalancing the ABA-induced increase in excitability of CA1 pyramidal neurons, and although exogenous P4's metabolite, THP, enhances α4 expression, especially among those that can gain resistance, it also interferes with α4-GABAARs' protective role by desensitizing α4-GABAARs.

Results of treatment of distal extra: articular femur fractures with locking plates using minimally invasive approach--experience with 25 consecutive geriatric patients

PURPOSE

Fractures involving the femur in older adults are reasonably common. The aim of this study was to evaluate the results of MIPO technique using locking plates in geriatric patients for distal extra-articular femur fractures.

METHODS

About 25 consecutive patients with distal extra-articular femur fractures aged 60 years and above were treated using locking plates and minimally invasive technique. Patients were studied prospectively over a period of 3 years. Parameters studied included patient demographics, fracture type, time taken for the surgery, time to union and any complications.

RESULTS

Mean age of patients was 66.5 years. Nineteen (76%) patients were females. Most of fractures in our study were type 33A2 fractures (64%). Average time to full weight bearing was 14.32 weeks, and fractures united at an average of 16.88 weeks. There were two (8%) patients with superficial infection, two (8%) with implant tenderness. One (4%) patient developed knee stiffness. Five (20%) patients had extension lag of average 5°. One (4%) patient sustained a peri-implant fracture at 2 months. None of the patients developed non-union or delayed union. According to criteria laid by Schatzker's and Lambert, excellent results were achieved in 22 (88%) patients.

CONCLUSIONS

Outcome of minimally invasive fixation of distal extra-articular femur fractures with locking plates in patients of age 60 years and above seems to be good with high union rate despite high prevalence of osteoporosis and comminution.

Hydrogen sulphide-induced relaxation of porcine peripheral bronchioles

BACKGROUND AND PURPOSE

Hydrogen sulphide (H2S) is an endogenous gasotransmitter. Although it has been shown to elicit responses in vascular and other smooth muscle preparations, a role for endogenously produced H2S in mediating airway tone has yet to be demonstrated. Therefore, the aim of this study was to determine whether H2S is produced within the airways and to determine the functional effect on airway tone.

EXPERIMENTAL APPROACH

Small peripheral airways (<5 mm in diameter) from porcine lungs were set up in isolated tissue baths, pre-contracted with the muscarinic agonist carbachol, and then exposed to either the H2S donor sodium hydrosulphide (NaHS), or the precursor L-cysteine. H2S production from L-cysteine or 3-mercaptopyruvate in tissue homogenates was measured by the methylene blue assay. Expression of the H2S-synthesizing enzymes cystathionine β-synthase (CBS), cystathionine γ lyase (CSE) and 3-mercaptopyruvate sulphurtransferase (3-MST) were measured by Western blotting.

KEY RESULTS

NaHS caused a large relaxation of the airways, which was inhibited partially by pre-contraction with KCl or exposure to tetraethylammonium, but not glibenclamide, paxilline or 4-aminopyridine. L-cysteine also caused a relaxation of the airways which was inhibited by the CBS inhibitor aminooxyacetic acid. Tissue homogenates from airways exposed to L-cysteine or 3-mercaptopyruvate in vitro showed a significant production of H2S. Western blotting demonstrated immunoreactivity to CBS, CSE and 3-MST enzymes in the airways.

CONCLUSIONS AND IMPLICATIONS

These data demonstrate that H2S can be produced endogenously within porcine airways causing relaxation. The mechanism of relaxation depends, in part, on K(+) channel activity.

18-β Glycyrrhetinic acid alleviates 2-acetylaminofluorene-induced hepatotoxicity in Wistar rats

2-Acetylaminofluorene (2-AAF) is a known hepatic carcinogen which leads to tumour formation in rodents. 18-β Glycyrrhetinic acid (18 β-GA) derived from liquorice plant has various pharmacological properties such as anti-ulcer, anti-inflammatory, antiviral, hepatoprotective and antioxidant. This study is designed to elucidate the chemopreventive properties of 18 β-GA against 2-AAF-induced liver toxicity in Wistar rats and evaluated its effect on inflammatory and tumour promotion marker and activities of different oxidative stress enzymes. Administration of 2-AAF at the dose of (50 mg/kg body weight (b.w.) intraperitoneally (i.p.)) for five consecutive days induces hepatic toxicity, inflammation, oxidative stress and hyperproliferation. Pretreatment with 18 β-GA at two different doses (45 and 75 mg kg−1 b.w.) significantly ameliorates 2-AAF-induced increased lipid peroxidation, alanine transaminase and aspartate transaminase, xanthine oxidase activities and activities of phase-II detoxifying enzymes along with the levels of glutathione content. Administration of 18 β-GA also significantly restored the expressions of proliferating cell nuclear antigen, cyclooxygenase 2, inducible nitric oxide synthase and nuclear factor κB. Furthermore, histological observations also support the preventive effects of 18 β-GA. Our findings suggest that pretreatment with 18 β-GA showed potential hepatoprotective effects via attenuation of oxidative stress, inflammation and hyperproliferation.

Associations between functional polymorphisms in the NFκB signaling pathway and response to anti-TNF treatment in Danish patients with inflammatory bowel disease

Antitumor necrosis factor-α (TNF-α) is used for treatment of severe cases of inflammatory bowel diseases (IBD), including Crohn's disease (CD) and ulcerative colitis (UC). However, one-third of the patients do not respond to the treatment. Genetic markers may predict individual response to anti-TNF therapy. Using a candidate gene approach, 39 mainly functional single nucleotide polymorphisms (SNPs) in 26 genes regulating inflammation were assessed in 738 prior anti-TNF-naive Danish patients with IBD. The results were analyzed using logistic regression (crude and adjusted for age, gender and smoking status). Nineteen functional polymorphisms that alter the NFκB-mediated inflammatory response (TLR2 (rs3804099, rs11938228, rs1816702, rs4696480), TLR4 (rs5030728, rs1554973), TLR9 (rs187084, rs352139), LY96 (MD-2) (rs11465996), CD14 (rs2569190), MAP3K14 (NIK) (rs7222094)), TNF-α signaling (TNFA (TNF-α) (rs361525), TNFRSF1A (TNFR1) (rs4149570), TNFAIP3(A20) (rs6927172)) and other cytokines regulated by NFκB (IL1B (rs4848306), IL1RN (rs4251961), IL6 (rs10499563), IL17A (rs2275913), IFNG (rs2430561)) were associated with response to anti-TNF therapy among patients with CD, UC or both CD and UC (P ⩽ 0.05). In conclusion, the results suggest that polymorphisms in genes involved in activating NFκB through the Toll-like receptor (TLR) pathways, genes regulating TNF-α signaling and cytokines regulated by NFκB are important predictors for the response to anti-TNF therapy among patients with IBD. Genetically strong TNF-mediated inflammatory response was associated with beneficial response. In addition, the cytokines IL-1β, IL-6 and IFN-γ may be potential targets for treating patients with IBD who do not respond to anti-TNF therapy. These findings should be examined in independent cohorts before these results are applied in a clinical setting.

Carvacrol ameliorates thioacetamide-induced hepatotoxicity by abrogation of oxidative stress, inflammation, and apoptosis in liver of Wistar rats

The present study was designed to investigate the protective effects of carvacrol against thioacetamide (TAA)-induced oxidative stress, inflammation and apoptosis in liver of Wistar rats. In this study, rats were subjected to concomitant prophylactic oral pretreatment of carvacrol (25 and 50 mg kg(-1) body weight (b.w.)) against the hepatotoxicity induced by intraperitoneal administration of TAA (300 mg kg(-1) b.w.). Efficacy of carvacrol against the hepatotoxicity was evaluated in terms of biochemical estimation of antioxidant enzyme activities, histopathological changes, and expressions of inflammation and apoptosis. Carvacrol pretreatment prevented deteriorative effects induced by TAA through a protective mechanism in a dose-dependent manner that involved reduction of oxidative stress, inflammation and apoptosis. We found that the protective effect of carvacrol pretreatment is mediated by its inhibitory effect on nuclear factor kappa B activation, Bax and Bcl-2 expression, as well as by restoration of histopathological changes against TAA administration. We may suggest that carvacrol efficiently ameliorates liver injury caused by TAA.