Insights into the evolution of mutations in SARS-CoV-2 non-spike proteins

The COVID-19 pandemic has been driven by the emergence of SARS-CoV-2 variants with mutations across all the viral proteins. Although mutations in the spike protein have received significant attention, understanding the prevalence and potential impact of mutations in other viral proteins is essential for comprehending the evolution of SARS-CoV-2. Here, we conducted a comprehensive analysis of approximately 14 million sequences of SARS-CoV-2 deposited in the GISAID database until December 2022 to identify prevalent mutations in the non-spike proteins at the global and country levels. Additionally, we evaluated the energetics of each mutation to better understand their impact on protein stability. While the consequences of many mutations remain unclear, we discuss potential structural and functional significance of some mutations. Our study highlights the ongoing evolutionary process of SARS-CoV-2 and underscores the importance of understanding changes in non-spike proteins.

Justifying the implementation of intraoperative computed tomography for midface fracture treatment in improving outcomes

Intraoperative CT scanning is the international standard for treating midface fractures as it allows intraoperative assessment of reduction and fixation. To our knowledge, no NHS hospital in the UK has this facility yet due to the financial and logistical burden of its implementation. The aim of this study was to determine if complications including the requirement for a return to theatre (RTT) could have been predicted from the post-fixation CT scan. All treated midface fractures that had presented to a regionalised major trauma centre within two years (01 January 2020 - 31 December 2021) were identified. Those developing complications including RTT were determined. All postoperative CT scans (including those without complication or RTT) were re-analysed with the clinicians blinded to the outcomes to determine the positive predictive value (PPV) and negative predictive value (NPV) of requiring RTT to alter plate position intraoperatively based on CT scan alone. In all, there were eight episodes of unplanned return to theatre, resulting in an overall RTT rate of 8/119 (6.7%). When only analysing patients treated for orbital fractures this RTT rises to 8/40 (20%). Of those eight patients who had a postoperative CT and required RTT, this could have been predicted in 7/8 (87.5%). A total of 16/44 (36.4%) patients that did not have RTT would have additionally been recommended to have the plate position altered based on CT alone. Based upon those that had a CT, the PPV of CT alone being able to predict those requiring RTT was 40.6% and the NPV 96.2%. Our results would suggest intraoperative CT would likely have prevented eight patients requiring RTT in two years and could have improved outcomes in 16 cases. In preventing RTT as well as potentially improving the outcomes of a further 16 cases in maxillofacial surgery, the purchase of an intraoperative CT scanner could yield net savings of £75534-£114990 over two years.

Identification and characterization of aurintricarboxylic acid as a potential inhibitor of SARS-CoV-2 PLpro

As the global health crisis due to evolution of mutations in SARS-CoV-2 continues, it is important to develop several effective antivirals to control the disease. Targeting papain-like protease (PLpro) of SARS-CoV-2 for drug development is a promising strategy due to its dual role in promoting viral replication and dysregulating host immune responses. Here, we screened a library of compounds to find potential inhibitors of PLpro. We find aurintricarboxylic acid (ATA) inhibits PLpro with K_i and IC₅₀ values of 16 μM and 30 μM, respectively. The binding of ATA to PLpro was further characterized using isothermal titration calorimetry, differential scanning fluorimetry, dynamic light scattering and circular dichroism spectrometry. In vitro assays showed the antiviral potential of ATA with IC₅₀ of 50 μM. In vivo efficacy was studied in Syrian hamsters and the results are being discussed.

Local neighborhood gradient pattern: A feature descriptor for content based image retrieval

Local feature descriptors are efficient encoders for capturing repeated local patterns in many of the computer vision applications. Majority of such descriptors consider only limited local neighborhood pixels to encode a pattern. One of the major issues while considering more number of neighborhood pixels is that it increases the dimensionality of the feature descriptor. The proposed descriptor addresses these issues by describing an effective encoding pattern with optimal feature vector length. In this paper, we have proposed Local Neighborhood Gradient Pattern (LNGP) for Content-Based Image Retrieval (CBIR) in which the relationship between a set of neighbours and the centre pixel is considered to obtain a compact 8-bit pattern in the respective pixel position. The relationship of the gradient information of immediate, next-immediate, and diagonal neighbours with the centre pixel is considered for pattern formation, and thus the local information based on pixels in three directions are captured. The experiments are conducted on benchmarked image retrieval datasets such as Wang’s 1K, Corel 5K, Corel 10K, Salzburg (Stex), MIT-Vistex, AT & T, and FEI datasets and it is observed that the proposed descriptor yields average precision of 71.88%, 54.57%, 40.66%, 71.85%, 86.12%, 82.54%, and 68.54% respectively in the mentioned datasets. The comparative analysis of the recent descriptors indicates that the proposed descriptor performs efficiently in CBIR applications.

Evaluating Stability and Activity of SARS-CoV-2 PLpro for High-throughput Screening of Inhibitors

Because of the essential roles of SARS-CoV-2 papain-like protease (PLpro) in the viral polyprotein processing and suppression of host immune responses, it is a crucial target for drug discovery against COVID-19. To develop robust biochemical methodologies for inhibitor screening against PLpro, extensive characterization of recombinant protein is important. Here we report cloning, expression, and purification of the recombinant SARS-CoV-2 PLpro, and explore various parameters affecting its stability and the catalytic activity. We also report the optimum conditions which should be used for high-throughput inhibitor screening using a fluorogenic tetrapeptide substrate.

Structural insights into SARS-CoV-2 proteins

The unprecedented scale of the ongoing COVID-19 pandemic has catalyzed an intense effort of the global scientific community to unravel different aspects of the disease in a short time. One of the crucial aspects of these developments is the determination of more than three hundred experimental structures of SARS-CoV-2 proteins in the last few months. These include structures of viral non-structural, structural, and accessory proteins and their complexes determined by either X-ray diffraction or cryo-electron microscopy. These structures elucidate the intricate working of different components of the viral machinery at the atomic level during different steps of the viral life cycle, including attachment to the host cell, viral genome replication and transcription, and genome packaging and assembly of the virion. Some of these proteins are also potential targets for drug development against the disease. In this review, we discuss important structural features of different SARS-CoV-2 proteins with their function, and their potential as a target for therapeutic interventions.

Renal salt-wasting syndrome induced by neoadjuvant chemotherapy containing cisplatin – A case report

Hyponatremia is one of the most common electrolyte abnormality seen in oncology practice. The underlying pathogenetic mechanism for chemotherapy-induced hyponatremia is renal salt-wasting syndrome (RSWS) and syndrome of inappropriate antidiuretic hormone secretion (SIADH). Fluid restriction is the treatment of choice in SIADH, whereas salt supplements is the mode of treatment in RSWS. Hence, differentiation between RSWS and SIADH is very important though difficult. Case reports of cisplatin (cis-dichloro-diammine-platinum-2)-induced RSWS and SIADH are rare in the literature. We report about a patient who developed hyponatremia, hypokalemia with excessive urinary excretion of sodium and potassium, renal glycosuria, and aminoaciduria on the third day of the first cycle of cisplatin-containing chemotherapy.

Craniospinal Irradiation in Medulloblastoma using High Energy Medical Linear Accelerator: an Innovative Approach to Planning Technique

BACKGROUND

Craniospinal irradiation (CSI) of medulloblastoma poses technological challenges due to the involvement of large treatment volume. Commonly, the whole treatment length is covered with two different isocentric plans in which the junction is shifted after every five fractions to overcome the possibility of hot and cold spot.

OBJECTIVE

This study aims to evaluate dosimetrically and clinically the innovative planning technique for the CSI which doesn't need re-planning and re-setup of patients after every five fractions.

MATERIAL AND METHODS

Computed tomography was done for fifteen (ten children and five adults) patients diagnosed with medulloblastoma. Treatment planning for 36 Gray (Gy) in 20 fractions (#) at the rate of 1.8Gy/# was done on the treatment planning system. A single plan for children was created with two bilateral fields of 6 Mega Voltage (MV) energy for cranium and one posterior field of 6 MV for spinal cord (C1-S2). Two plans for adult patients were created, first plan was with two bilateral fields of 6 MV for cranium and two posterior oblique fields of 6 MV for cervical and the part of thoracic spinal cord (up to T8-T9). The second plan was with a single posterior field of 15 MV covering remaining thoracic (T8-T9 to T12), lumbar and sacrum (up to lower border of S2) spine. After careful evaluation of all the plans, treatment was delivered; acute toxicities were recorded.

RESULTS

95% of prescribed dose was received by more than 95% of planning target volume in all the plans with the acceptable hot spot and good homogeneity index. All the patients reported common radiation induced acute toxicities (headache, vomiting, weakness) during radiotherapy.

CONCLUSION

The new planning technique for CSI has acceptable dosimetric and acute clinical possibilities; therefore it can be used for CSI for improved homogeneous dose delivery.

The perils of inhibiting deficient factors

Essentials Anticoagulation in patients with factor X deficiency is an evidence-poor area. A patient with factor X deficiency was anticoagulated with warfarin followed by rivaroxaban. Warfarin may be a safer anticoagulant option than rivaroxaban in hereditary factor X deficiency. A baseline coagulation screen should be performed prior to commencement of anticoagulation.

SUMMARY

We report a case of a previously undiagnosed factor X deficiency in an 83-year-old man who had no previous bleeding history despite multiple hemostatic challenges. He was anticoagulated with warfarin for atrial fibrillation without bleeding complications; however, major hemorrhage occurred soon after a switch to rivaroxaban.

Factors associated with treatment delays in pediatric refractory convulsive status epilepticus

OBJECTIVE

To identify factors associated with treatment delays in pediatric patients with convulsive refractory status epilepticus (rSE).

METHODS

This prospective, observational study was performed from June 2011 to March 2017 on pediatric patients (1 month to 21 years of age) with rSE. We evaluated potential factors associated with increased treatment delays in a Cox proportional hazards model.

RESULTS

We studied 219 patients (53% males) with a median (25th-75th percentiles [p₂₅-p₇₅]) age of 3.9 (1.2-9.5) years in whom rSE started out of hospital (141 [64.4%]) or in hospital (78 [35.6%]). The median (p₂₅-p₇₅) time from seizure onset to treatment was 16 (5-45) minutes to first benzodiazepine (BZD), 63 (33-146) minutes to first non-BZD antiepileptic drug (AED), and 170 (107-539) minutes to first continuous infusion. Factors associated with more delays to administration of the first BZD were intermittent rSE (hazard ratio [HR] 1.54, 95% confidence interval [CI] 1.14-2.09; p = 0.0467) and out-of-hospital rSE onset (HR 1.5, 95% CI 1.11-2.04; p = 0.0467). Factors associated with more delays to administration of the first non-BZD AED were intermittent rSE (HR 1.78, 95% CI 1.32-2.4; p = 0.001) and out-of-hospital rSE onset (HR 2.25, 95% CI 1.67-3.02; p < 0.0001). None of the studied factors were associated with a delayed administration of continuous infusion.

CONCLUSION

Intermittent rSE and out-of-hospital rSE onset are independently associated with longer delays to administration of the first BZD and the first non-BZD AED in pediatric rSE. These factors identify potential targets for intervention to reduce time to treatment.

Visceral Adiposity Is an Independent Determinant of Hypercoagulability as Measured by Thrombin Generation in Morbid Obesity

Introduction  Increased visceral adipose tissue (VAT) has been shown to be associated with the development of insulin resistance, type 2 diabetes, stroke, and ischemic heart disease. It remains unknown whether fat distribution impacts on coagulation markers and/or the risk of venous thrombosis. This study evaluates markers of hypercoagulability in class III obesity (body mass index [BMI] >40 kg/m 2 ) compared with nonobese controls. We further investigated whether hypercoagulability was influenced by VAT, metabolic syndrome, and metabolic markers, including adiponectin. Patients and Methods  Ninety patients were recruited from the obesity clinic at King's College Hospital from November 2009 to December 2011. The inclusion criteria were class III obesity (BMI ≥40 kg/m 2 ) and age 18 to 65 years. A control group (healthy ambulatory participants, with a BMI < 30 kg/m 2 ) was recruited from volunteers responding to advertisement. Abdominal VAT and subcutaneous adipose tissue surface areas were determined by evaluation of a single-slice CT at spinal vertebra L4. Results  Thrombin generation revealed a significantly increased peak and endogenous thrombin potential in patients compared with controls. Lag time and time to peak (ttP) were also significantly prolonged in patients. VAT was found to have the strongest association with thrombin generation parameters: lag time (β = 0.378; p  < 0.001), peak thrombin (0.378; p  = 0.04), and ttP (β = 0.373; p  = 0.001). BMI was found to be a predictor for lag time only (β = 0.313; p  = 0.003). SAT was not associated with any of the thrombin generation parameters (data not shown). VAT was found to be an independent determinant of peak thrombin, lag time, and ttP. The study suggests not only fat mass but also fat distribution, particularly visceral adiposity, mediates hypercoagulability in obesity.

Neural stem cell progeny regulate stem cell death in a Notch and Hox dependent manner

Cell death is a prevalent, well-controlled and fundamental aspect of development, particularly in the nervous system. In Drosophila, specific neural stem cells are eliminated by apoptosis during embryogenesis. In the absence of apoptosis, these stem cells continue to divide, resulting in a dramatically hyperplastic central nervous system and adult lethality. Although core cell death pathways have been well described, the spatial, temporal and cell identity cues that activate the cell death machinery in specific cells are largely unknown. We identified a cis-regulatory region that controls the transcription of the cell death activators reaper, grim and sickle exclusively in neural stem cells. Using a reporter generated from this regulatory region, we found that Notch activity is required for neural stem cell death. Notch regulates the expression of the abdominalA homeobox protein, which provides important spatial cues for death. Importantly, we show that pro-apoptotic Notch signaling is activated by the Delta ligand expressed on the neighboring progeny of the stem cell. Thus we identify a previously undescribed role for progeny in regulating the proper developmental death of their parental stem cells.

Caspase-2 impacts lung tumorigenesis and chemotherapy response in vivo

Caspase-2 is an atypical caspase that regulates apoptosis, cell cycle arrest and genome maintenance, although the mechanisms are not well understood. Caspase-2 has also been implicated in chemotherapy response in lung cancer, but this function has not been addressed in vivo. Here we show that Caspase-2 functions as a tumor suppressor in Kras-driven lung cancer in vivo. Loss of Caspase-2 leads to enhanced tumor proliferation and progression. Despite being more histologically advanced, Caspase-2-deficient tumors are sensitive to chemotherapy and exhibit a significant reduction in tumor volume following repeated treatment. However, Caspase-2-deficient tumors rapidly rebound from chemotherapy with enhanced proliferation, ultimately hindering long-term therapeutic benefit. In response to DNA damage, Caspase-2 cleaves and inhibits Mdm2 and thereby promotes the stability of the tumor-suppressor p53. Caspase-2 expression levels are significantly reduced in human lung tumors with wild-type p53, in agreement with the model whereby Caspase-2 functions through Mdm2/p53 regulation. Consistently, p53 target genes including p21, cyclin G1 and Msh2 are reduced in Caspase-2-deficient tumors. Finally, we show that phosphorylation of p53-induced protein with a death domain 1 leads to Caspase-2-mediated cleavage of Mdm2, directly impacting p53 levels, activity and chemotherapy response. Together, these studies elucidate a Caspase-2-p53 signaling network that impacts lung tumorigenesis and chemotherapy response in vivo.

A highly efficient and compact long pulse Nd:YAG rod laser with 540 J of pulse energy for welding application

We have developed an efficient and high average power flash lamp pumped long pulse Nd:YAG laser capable of generating 1 kW of average output power with maximum 540 J of single pulse energy and 20 kW of peak power. The laser pulse duration can be varied from 1 to 40 ms and repetition rate from 1 to 100 Hz. A compact and robust laser pump chamber and resonator was designed to achieve this high average and peak power. It was found that this laser system provides highest single pulse energy as compared to other long pulsed Nd:YAG laser systems of similar rating. A slope efficiency of 5.4% has been achieved, which is on higher side for typical lamp pumped solid-state lasers. This system will be highly useful in laser welding of materials such as aluminium and titanium. We have achieved 4 mm deep penetration welding of these metals under optimized conditions of output power, pulse energy, and pulse duration. The laser resonator was optimized to provide stable operation from single shot to 100 Hz of repetition rate. The beam quality factor was measured to be M(2) ~ 91 and pulse-to-pulse stability of ±3% for the multimode operation. The laser beam was efficiently coupled through an optical fiber of 600 μm core diameter and 0.22 numerical aperture with power transmission of 90%.

Localization of a major susceptibility locus influencing preterm birth

Preterm birth (PTB) is a complex trait, but little is known regarding its major genetic determinants. The objective of this study is to localize genes that influence susceptibility to PTB in Mexican Americans (MAs), a minority population in the USA, using predominantly microfilmed birth certificate-based data obtained from the San Antonio Family Birth Weight Study. Only 1302 singleton births from 288 families with information on PTB and significant covariates were considered for genetic analysis. PTB is defined as a childbirth that occurs at <37 completed weeks of gestation, and the prevalence of PTB in this sample was 6.4%. An ∼10 cM genetic map was used to conduct a genome-wide linkage analysis using the program SOLAR. The heritability of PTB was high (h(2) ± SE: 0.75 ± 0.20) and significant (P = 4.5 × 10(-5)), after adjusting for the significant effects of birthweight and birth order. We found significant evidence for linkage of PTB (LOD = 3.6; nominal P = 2.3 × 10(-5); empirical P = 1.0 × 10(-5)) on chromosome 18q between markers D18S1364 and D18S541. Several other chromosomal regions (2q, 9p, 16q and 20q) were also potentially linked with PTB. A strong positional candidate gene in the 18q linked region is SERPINB2 or PAI-2, a member of the plasminogen activator system that is associated with various reproductive processes. In conclusion, to our knowledge, perhaps for the first time in MAs or US populations, we have localized a major susceptibility locus for PTB on chromosome 18q21.33-q23.

Women's views on and adherence to low-molecular-weight heparin therapy during pregnancy and the puerperium

BACKGROUND

Non-adherence to prescribed medication represents a significant factor associated with treatment failure. Pregnant women identified at risk of venous thromboembolism are increasingly being prescribed low-molecular-weight heparin (LMWH) during pregnancy and the puerperium. It is important to understand women's views on and adherence to LMWH during pregnancy and the puerperium, so that women gain maximum benefit from the treatment.

OBJECTIVES

To monitor women's adherence to enoxaparin, when prescribed during pregnancy and the puerperium, and explore their beliefs about the enoxaparin therapy prescribed.

PATIENTS/METHODS

A prospective cohort study involving 95 nullparous and multiparous women prescribed enoxaparin for recognized antenatal indications. Adherence to enoxaparin was assessed through self-completion of a diary, additionally verified through laboratory tests. An adapted beliefs about medication questionnaire was administered to women during their pregnancy.

RESULTS

Women were highly adherent to enoxaparin: antenatally, mean percentage adherence 97.92%; postnatally, mean percentage adherence 93.37% (paired t-test, P = 0.000). In the cohort of women we followed, their perceived necessity for enoxaparin therapy outweighed any concerns they had regarding enoxaparin antenatally, necessity-concerns differential 2.20. In some women, however, this perceived necessity does decrease postnatally.

CONCLUSIONS

Our results suggest that most women prescribed enoxaparin are highly adherent to their therapy during the antenatal period and that women's antenatal beliefs about enoxaparin are able to predict a decrease in postnatal adherence. Our results have important clinical implications, particularly when women are initiated on LMWH just during the postnatal period.

Purification and Structural Characterization of Sulfated Polysaccharide from Sargassum myriocystum and its Efficacy in Scavenging Free Radicals

Sulfated polysaccharides from marine algae are one of the commercially beneficial compounds with a range of pharmaceutical and biomedical applications. They are testified to be effective against free radicals and related health complications. This study aims to determine the antioxidant potential of the sulfated polysaccharide from Sargassum myriocystum, followed by its purification and structural characterization. Amount of extract obtained was 5% from 10 g of plant material. The carbohydrate and sulfate content were found to be 31 and 0.34 mg/10 g of plant material, respectively. Total sulfated polysaccharide extract showed a good radical scavenging activity at lower concentrations. The active principle from the total sulfated polysaccharide was fractionated in anion exchange and gel filtration columns followed by structural characterization using Fourier transform infrared and nuclear magnetic resonance spectroscopy. Fraction 12 closely matched with the Fourier transform infrared and nuclear magnetic resonance spectra of fucoidan. Based on the results obtained, we conclude that sulfated polysaccharide from Sargassum myriocystum is identified as Fucoidan with potential radical scavenging activity compared to butylated hydroxyl toluene.

Phenytoin-induced gingival overgrowth

Gingival overgrowth is a common adverse effect of therapy with Phenytoin, having important medical and cosmetic implications. Poor periodontal hygiene is an important risk factor for severity of Phenytoin-induced gingival overgrowth (PIGO), which is a time-dependent process. There is complex interplay of altered fibroblast biology, connective tissue turnover, inflammatory processes, and growth factors on a background of genetic susceptibility to produce increase in various components of interstitial matrix in PIGO tissue. Treatment options have included change of PHT to another anti-seizure drug, measures to improve periodontal hygiene and gingivectomy. There is conclusive evidence that folic acid supplementation significantly decreases the incidence of PIGO.