Whole exome sequencing identifies a novel variant causing cockayne syndrome type I in a consanguineous Pakistani family

BACKGROUND

Cockayne syndrome (CS) is a rare neurodegenerative disorder characterized by impaired neurological functions, cachectic dwarfism, microcephaly and photosensitivity. Complementation assays identify two groups of this disorder, CS type I (CSA) and CS type II (CSB), caused by mutations in ERCC8 and ERCC6, respectively.

OBJECTIVES

This study aimed to investigate the genetic basis of a consanguineous Pakistani family with three affected individuals presenting with typical clinical symptoms of CS.

METHODS

We employed whole exome sequencing of the proband and then Sanger sequenced all the family members to confirm its segregation in the family. Different bioinformatics tools were used to predict pathogenicity of this variant.

RESULTS

Variants were filtered according to the pedigree structure. We identified a novel homozygous variant (c.202A>T; p.Ile68Phe) in ERCC8 gene in the proband. The variant was found to segregate in the family.

CONCLUSIONS

These findings add to the genetic heterogeneity of ERCC8 and expands the mutation spectrum. Also, identification of this variant can facilitate prenatal diagnosis/genetic counselling set ups in Pakistan where this disease largely remains undiagnosed.

A Journey of Innovation: 40 years of Pioneering Medical Education at the Aga Khan University Medical College in Karachi, Pakistan

This article presents an overview of Aga Khan University's (AKU) pioneering medical education initiatives over the past 40 years, exploring its impact on healthcare in the region and its commitment to advancing medical education and research in the developing world. Established in 1983 as the first private university in Pakistan, AKU has evolved into a global institution with a focus on improving healthcare standards and addressing healthcare needs in the developing world. The article also discusses the undergraduate and postgraduate medical education programs at AKU Medical College, Pakistan, highlighting their unique features and pioneering approaches to medical education. The institution's journey highlights its ability to adapt to the evolving healthcare landscape while maintaining a focus on quality and excellence, offering a model for other institutions striving to meet healthcare needs in low- and middle-income countries.

Shining insights: Deciphering the biogenic synthesis of Ajuga bracteosa-mediated gold nanoparticles with advanced microscopy techniques

In this study, gold nanoparticles (AuNPs) were bioreduced from Ajuga bracteosa, a medicinal herb known for its therapeutic properties against various diseases. Different fractions of the plant extract were used, including the methanolic fraction (ABMF), the n-hexane fraction (ABHF), the chloroform fraction (ABCF), and the aqueous extract for AuNPs synthesis. The characterization of AuNPs was performed using UV-Vis spectrophotometry, FT-IR, XRD, EDX, and TEM. UV-Vis spectroscopy confirmed the formation of AuNPs, with peaks observed at 555 nm. FT-IR analysis indicated strong capping of phytochemicals on the surface of AuNPs, which was supported by higher total phenolic contents (TPC) and total flavonoid contents (TFC) in AuNPs. XRD results showed high crystallinity and a smaller size distribution of AuNPs. TEM analysis revealed the spherical shape of AuNPs, with an average size of 29 ± 10 nm. The biologically synthesized AuNPs exhibited superior antibacterial, antioxidant, and cytotoxic activities compared to the plant extract fractions. The presence of active biomolecules in A. bracteosa, such as neoclerodan flavonol glycosides, diterpenoids, phytoecdysone, and iridoid glycosides, contributed to the enhanced biological activities of AuNPs. Overall, this research highlights the potential of A. bracteosa-derived AuNPs for various biomedical applications due to their remarkable therapeutic properties and effective capping by phytochemicals. RESEARCH HIGHLIGHTS: This research underscores the growing significance of herbal medicine in contemporary healthcare by exploring the therapeutic potential of Ajuga bracteosa and gold nanoparticles (AuNPs). The study highlights the notable efficacy of A. bracteosa leaf extracts and AuNPs in treating bacterial infections, demonstrating their bactericidal effects on a range of strains. The anti-inflammatory properties of plant extracts and nanoparticles are evidenced through paw edema method suggesting their applicability in managing inflammatory conditions. These findings position A. bracteosa and AuNPs as potential candidates for alternative and effective approaches to modern medication.

The antihyperglycemic potential of pyrazolobenzothiazine 1, 1-dioxide novel derivative in mice using integrated molecular pharmacological approach

Diabetes Mellitus is a metabolic disease characterized by elevated blood sugar levels caused by inadequate insulin production, which subsequently leads to hyperglycemia. This study was aimed to investigate the antidiabetic potential of pyrazolobenzothiazine derivatives in silico, in vitro, and in vivo. Molecular docking of pyrazolobenzothiazine derivatives was performed against α-glucosidase and α-amylase and compounds were selected based on docking score, bonding interactions and low root mean square deviation (RMSD). Enzyme inhibition assay against α-glucosidase and α-amylase was performed in vitro using p-nitrophenyl-α-D-glucopyranoside (PNPG) and starch substrate. Synthetic compound pyrazolobenzothiazine (S1) exhibited minimal conformational changes during the 100 ns MD simulation run. S1 also revealed effective IC50 values for α-glucosidase (3.91 µM) and α-amylase (8.89 µM) and an enzyme kinetic study showed low ki (- 0.186 µM, - 1.267 µM) and ki' (- 0.691 µM, - 1.78 µM) values with the competitive type of inhibition for both enzymes α-glucosidase and α-amylase, respectively. Moreover, studies were conducted to check the effect of the synthetic compound in a mouse model. A low necrosis rate was observed in the liver, kidney, and pancreas through histology analysis performed on mice. Compound S1 also exhibited a good biochemical profile with lower sugar level (110-115 mg/dL), increased insulin level (25-30 μM/L), and low level of cholesterol (85 mg/dL) and creatinine (0.6 mg/dL) in blood. The treated mice group also exhibited a low % of glycated haemoglobin (3%). This study concludes that S1 is a new antidiabetic-agent that helps lower blood glucose levels and minimizes the complications associated with type-II diabetes.

Impact of MLL::AF9 Gene Rearrangement on Survival of Acute Myeloid Leukaemia Patients: An Insight into Pakistani Population

OBJECTIVE

To ascertain the frequency of the MLL::AF9 gene rearrangement and its association with survival in Pakistani patients suffering from acute myeloid leukaemia (AML).

STUDY DESIGN

Analytical study. Place and Duration of the Study: Department of Haematology, National Institute of Blood Diseases and Bone Marrow Transplantation, Karachi, Pakistan, from 2015 to 2020.

METHODOLOGY

Patients without a history of past AML chemotherapy, aged from 10 to 75 years, were included. Individuals with metastatic cancer, chronic myeloid leukaemia, or other haematological conditions were excluded. Identifying the MLL::AF9 gene involved RNA extraction, cDNA synthesis, and Real-time PCR amplification. The Chi-square test was used to examine the relationship between survival and the MLL::AF9 mutation. A Welch two-sample t-test was used to evaluate survival days depending on the MLL::AF9 gene rearrangement, while ANOVA was used to analyse survival days across various death statuses.

RESULTS

The mean age of 130 patients was 36.65 ± 13.01 years, with 64.62% being males. The most common leukaemia type was AML-M2 (n = 32, 24.62%). During the study follow-up, 22.31% were still alive, 40.77% died, and the status of 36.92% were unknown. MLL::AF9 gene rearrangement was present in 11.54%. The group with MLL::AF9 gene rearrangement had significantly longer mean 'survival days' (1,542.33 ± 926.07) compared to the group without the gene rearrangement (206.42 ± 359.57, p <0.001).

CONCLUSION

MLL-AF9 mutation was present in 11.54%. Age and MLL::AF9 gene rearrangement were significant predictors of survival in leukaemia patients.

KEY WORDS

Acute myeloid leukaemia, MLL::AF9, Gene rearrangement, Survival.

Dynamic Imaging of Blood Coagulation Within the Hematoma of Patients With Acute Hemorrhagic Stroke

BACKGROUND

The dynamics of blood clot (combination of Hb [hemoglobin], fibrin, and a higher concentration of aggregated red blood cells) formation within the hematoma of an intracerebral hemorrhage is not well understood. A quantitative neuroimaging method of localized coagulated blood volume/distribution within the hematoma might improve clinical decision-making.

METHODS

The deoxyhemoglobin of aggregated red blood cells within extravasated blood exhibits a higher magnetic susceptibility due to unpaired heme iron electrons. We propose that coagulated blood, with higher aggregated red blood cell content, will exhibit (1) a higher positive susceptibility than noncoagulated blood and (2) increase in fibrin polymerization-restricted localized diffusion, which can be measured noninvasively using quantitative susceptibility mapping and diffusion tensor imaging. In this serial magnetic resonance imaging study, we enrolled 24 patients with acute intracerebral hemorrhage between October 2021 to May 2022 at a stroke center. Patients were 30 to 70 years of age and had a hematoma volume >15 cm3 and National Institutes of Health Stroke Scale score >1. The patients underwent imaging 3×: within 12 to 24 (T1), 36 to 48 (T2), and 60 to 72 (T3) hours of last seen well on a 3T magnetic resonance imaging system. Three-dimensional anatomic, multigradient echo and 2-dimensional diffusion tensor images were obtained. Hematoma and edema volumes were calculated, and the distribution of coagulation was measured by dynamic changes in the susceptibilities and fractional anisotropy within the hematoma.

RESULTS

Using a coagulated blood phantom, we demonstrated a linear relationship between the percentage coagulation and susceptibility (R2=0.91) with a positive red blood cell stain of the clot. The quantitative susceptibility maps showed a significant increase in hematoma susceptibility (T1, 0.29±0.04 parts per millions; T2, 0.36±0.04 parts per millions; T3, 0.45±0.04 parts per millions; P<0.0001). A concomitant increase in fractional anisotropy was also observed with time (T1, 0.40±0.02; T2, 0.45±0.02; T3, 0.47±0.02; P<0.05).

CONCLUSIONS

This quantitative neuroimaging study of coagulation within the hematoma has the potential to improve patient management, such as safe resumption of anticoagulants, the need for reversal agents, the administration of alteplase to resolve the clot, and the need for surgery.

Undergraduate Medical Education Curriculum Reforms in Pakistan: A Mixed Methods Study of Academic Leadership Perspectives

PURPOSE

Periodic revision of undergraduate medical education (UGME) curricula is an essential part of evidence-based educational practices. Pakistan's national UGME curriculum, last updated in 2005, was reviewed, and recommended updates were made in 2022. The authors explore academic medical school leaders' perspectives about the proposed reforms, gaps within the existing curriculum, and how to ensure the reform implementation is effective, collaborative, and feedback-driven.

METHOD

Using a mixed methods approach, data were collected from April-July 2022. Academic leadership (principals, who could designate vice principals or medical educators) at all medical schools across Pakistan (n = 117) were invited. Agreement with each of 20 proposed reforms was measured via a survey employing a Likert scale. A semi-structured interview guide expanded on the survey questions with probes.

RESULTS

Eighty-eight survey responses, from private (59; 67.0%) and public (29; 33.0%) institutions, were obtained (75.2% response rate). Participants recommended most of the proposed reforms. The 3 reforms that received the highest agreement were teaching professionalism as an integral part of the curriculum (83; 94.3%), mandating bedside procedural skills training (80; 90.9%), and including patient safety in the UGME curriculum (79; 89.8%). Including multidisciplinary tumor boards and surgical oncology had the lowest agreement (26; 29.5%). Fifteen interviews were conducted, which revealed 3 major themes: perceptions about changes to the curricular content; limitation of human and financial resources as barriers to reform implementation; and recommendations for effective implementation of an updated curriculum.

CONCLUSIONS

The findings reflect an overall positive attitude of academic medical school leadership toward the 20 proposed UGME curriculum reforms, which could aid with on-the-ground implementation. However, major limitations, such as a lack of trained faculty and financial resources, must be addressed. The authors propose future research on the resources required for implementing UGME reforms and the reforms' impact after national implementation.

Assessment of Babesia spp. prevalence in various domestic animals across Southern Punjab, Pakistan

Parasitic diseases, notably babesiosis, exert a substantial impact on the global cattle industry, posing challenges to commerce, economies, and human health. This study, conducted in Southern Punjab, Pakistan, aimed to assess the prevalence of Babesia spp. across various livestock species using microscopic and PCR methods. A total of 180 blood samples (60 from each district) were systematically collected from apparently healthy animals, with 36 samples obtained from each domestic animal species, including camel, cattle, buffalo, goat, and sheep, noting that 12 samples were collected from each district for each animal species. Overall prevalence was determined to be 32.8% (59/180), with varying rates among species: 25.0% in cattle, 41.66% in buffalo, 30.55% in goats, 33.3% in sheep, and 33.3% in camels. Microscopic examination revealed slightly varied infection rates among large and small domestic animals (22.2%), while PCR results indicated a 32.8% overall infection rate in both large and small domestic animals, with no statistical significance. District-wise analysis showed regional variations, with Muzaffargarh recording a prevalence rate of 23.33% through microscopic examination, while Lodhran and Bahawalpur recorded 21.67%. PCR results revealed higher rates (38.33%, 26.67%, and 33.33%, respectively), underlining the importance of employing PCR for accurate detection. Examining ruminant types, large ruminants exhibited a 32.4% infection rate, while small domestic animals showed 33.3%, with no significant difference (p=0.897). District-wise prevalence showcased significant variation, with Muzaffargarh demonstrating a 25% prevalence, Lodhran 22%, and Bahawalpur 22%, through microscopic examination. PCR results displayed 38.33%, 27%, and 33.3%, respectively, with no statistical significance. Detailed analysis of individual districts highlighted variations in infection rates among camels, cattle, buffalo, goats, and sheep. The binomial test indicated significant differences through microscopic analysis (P=0.011) but non-significant variations through PCR (P=0.065), emphasizing the precision of PCR. Regional variations in prevalence, notably with Punjab exhibiting the highest frequency (33.87%) and KPK the lowest (13.24%), suggest potential influences from varying veterinary practices and environmental factors. This study underscores the pivotal role of PCR alongside microscopy for accurate babesiosis diagnosis. These findings contribute to the broader understanding of babesiosis prevalence, emphasizing the necessity of advanced molecular techniques for informed control measures.

Microplastic contamination in the agricultural soil-mitigation strategies, heavy metals contamination, and impact on human health: a review

Microplastic pollution has emerged as a critical global environmental issue due to its widespread distribution, persistence, and potential adverse effects on ecosystems and human health. Although research on microplastic pollution in aquatic environments has gained significant attention. However, a limited literature has summarized the impacts of microplastic pollution the agricultural land and human health. Therefore, In the current review, we have discussed how microplastic(s) affect the microorganisms by ingesting the microplastic present in the soil, alternatively affecting the belowground biotic and abiotic components, which further elucidates the negative effects on the above-ground properties of the crops. In addition, the consumption of these crops in the food chain revealed a potential risk to human health throughout the food chain. Moreover, microplastic pollution has the potential to induce a negative impact on agricultural production and food security by altering the physiochemical properties of the soil, microbial population, nutrient cycling, and plant growth and development. Therefore, we discussed in detail the potential hazards caused by microplastic contamination in the soil and through the consumption of food and water by humans in daily intake. Furthermore, further study is urgently required to comprehend how microplastic pollution negatively affects terrestrial ecosystems, particularly agroecosystems which drastically reduces the productivity of the crops. Our review highlights the urgent need for greater awareness, policy interventions, and technological solutions to address the emerging threat of microplastic pollution in soil and plant systems and mitigation strategies to overcome its potential impacts on human health. Based on existing studies, we have pointed out the research gaps and proposed different directions for future research.

Biochar and saline soil: mitigation strategy by incapacitating the ecological threats to agricultural land

Soil salinity caused a widespread detrimental issue that hinders productivity in agriculture and ecological sustainability, while waste-derived soil amendments like biochar have drawn attention for their capacity to act as a mitigating agent, by enhancing the physical and chemical features of soil, and contributing to the recovery of agricultural waste resources. However, the information concerning biochar and salinity which affect the physicochemical characteristics of soils, crop physiology, and growth is limited. To investigate whether biochar mitigates the salinity stress on wheat crop seedlings, we grow them with salinity stress (120 mM), and biochar (20 tons ha-1), and its interactive effects. The soil properties of soil organic carbon (SOC), soil organic matter (SOM), dissolved organic carbon (DOC), and soil available phosphorus (SAP) decreased in the saline soil by 36.71%, 46.97%, 26.31%, and 15.00%, while biochar treatment increased SOC, DOC, and SAP contents by 7.42%, 31.57%, and 15.00%, respectively. On the other hand, dissolved organic nitrogen (DON) contents decreased in all the treatments compared to the control. The root growth traits, SPAD values, leaf nitrogen, photosynthetic parameters, antioxidant enzymes, and reactive oxygen species decreased in the saline treatment while increasing in the biochar and interactive treatment. Thus, these activities resulted in higher leaves and root biomass in the biochar treatment alone and interactive treatment of salinity and biochar. According to principal component analysis, redundancy analysis, and the mantel test, using biochar in conjunction with salinity treatment was found to be more effective than salinity treatment alone. The results of this study suggest that biochar can be used as a sustainable agricultural technique and a means of mitigation agent by lowering soil salinity while increasing the biomass of crops.

Enhancing nitrogen use efficiency and yield of maize (Zea mays L.) through Ammonia volatilization mitigation and nitrogen management approaches

Management of nitrogen (N) fertilizer is a critical factor that can improve maize (Zea mays L.) production. On the other hand, high volatilization losses of N also pollute the air. A field experiment was established using a silt clay soil to examine the effect of sulfur-coated urea and sulfur from gypsum on ammonia (NH3) emission, N use efficiency (NUE), and the productivity of maize crop under alkaline calcareous soil. The experimental design was a randomized complete block (RCBD) with seven treatments in three replicates: control with no N, urea150 alone (150 kg N ha-1), urea200 alone (200 kg N ha-1), urea150 + S (60 kg ha-1 S from gypsum), urea200 + S, SCU150 (sulfur-coated urea) and SCU200. The results showed that the urea150 + S and urea200 + S significantly reduced the total NH3 by (58 and 42%) as compared with the sole application urea200. The NH3 emission reduced further in the treatment with SCU150 and SCU200 by 74 and 65%, respectively, compared to the treatment with urea200. The maize plant biomass, grain yield, and total N uptake enhanced by 5-14%, 4-17%, and 7-13, respectively, in the treatments with urea150 + s and urea200 + S, relative to the treatment with urea200 alone. Biomass, grain yield, and total N uptake further increased significantly by 22-30%, 25-28%, and 26-31%, respectively, in the treatments with SCU150 and SCU200, relative to the treatment with urea200 alone. The applications of SCU150 enhanced the nitrogen use efficiency (NUE) by (72%) and SCU200 by (62%) respectively, compared with the sole application of urea200 alone. In conclusion, applying S-coated urea at a lower rate of 150 kg N ha-1 compared with a higher rate of 200 kg N ha-1 may be an effective way to reduce N fertilizer application rate and mitigate NH3 emission, improve NUE, and increase maize yield. More investigations are suggested under different soil textures and climatic conditions to declare S-coated urea at 150 kg N ha-1 as the best application rate for maize to enhance maize growth and yield.

Factors Influencing Maintenance of Alignment and Functional Improvement Following Adult Spinal Deformity Surgery: A 3-Year Outcome Analysis

STUDY DESIGN

This was a retrospective review.

OBJECTIVE

To assess the factors contributing to durability of surgical results following adult spinal deformity (ASD) surgery.

SUMMARY OF BACKGROUND

Factors contributing to the long-term sustainability of ASD correction are currently undefined.

MATERIALS AND METHODS

Operative ASD patients with preoperatively (baseline) and 3-year postoperatively radiographic/health-related quality of life data were included. At 1 and 3 years postoperatively, a favorable outcome was defined as meeting at least three of four criteria: (1) no proximal junctional failure or mechanical failure with reoperation, (2) best clinical outcome (BCO) for Scoliosis Research Society (SRS) (≥4.5) or Oswestry Disability Index (ODI) (<15), (3) improving in at least one SRS-Schwab modifier, and (4) not worsening in any SRS-Schwab modifier. A robust surgical result was defined as having a favorable outcome at both 1 and 3 years. Predictors of robust outcomes were identified using multivariable regression analysis with conditional inference tree for continuous variables.

RESULTS

We included 157 ASD patients in this analysis. At 1 year postoperatively, 62 patients (39.5%) met the BCO definition for ODI and 33 (21.0%) met the BCO for SRS. At 3 years, 58 patients (36.9%) had BCO for ODI and 29 (18.5%) for SRS. Ninety-five patients (60.5%) were identified as having a favorable outcome at 1 year postoperatively. At 3 years, 85 patients (54.1%) had a favorable outcome. Seventy-eight patients (49.7%) met criteria for a durable surgical result. Multivariable adjusted analysis identified the following independent predictors of surgical durability: surgical invasiveness >65, being fused to S1/pelvis, baseline to 6-week pelvic incidence and lumbar lordosis difference >13.9°, and having a proportional Global Alignment and Proportion score at 6 weeks.

CONCLUSIONS

Nearly 50% of the ASD cohort demonstrated good surgical durability, with favorable radiographic alignment and functional status maintained up to 3 years. Surgical durability was more likely in patients whose reconstruction was fused to the pelvis and addressed lumbopelvic mismatch with adequate surgical invasiveness to achieve full alignment correction.

Mask exhibits trxG-like behavior and associates with H3K27ac marked chromatin

The Trithorax group (trxG) proteins counteract the repressive effect of Polycomb group (PcG) complexes and maintain transcriptional memory of active states of key developmental genes. Although chromatin structure and modifications appear to play a fundamental role in this process, it is not clear how trxG prevents PcG-silencing and heritably maintains an active gene expression state. Here, we report a hitherto unknown role of Drosophila Multiple ankyrin repeats single KH domain (Mask), which emerged as one of the candidate trxG genes in our reverse genetic screen. The genome-wide binding profile of Mask correlates with known trxG binding sites across the Drosophila genome. In particular, the association of Mask at chromatin overlaps with CBP and H3K27ac, which are known hallmarks of actively transcribed genes by trxG. Importantly, Mask predominantly associates with actively transcribed genes in Drosophila. Depletion of Mask not only results in the downregulation of trxG targets but also correlates with diminished levels of H3K27ac. The fact that Mask positively regulates H3K27ac levels in flies was also found to be conserved in human cells. Strong suppression of Pc mutant phenotype by mutation in mask provides physiological relevance that Mask contributes to the anti-silencing effect of trxG, maintaining expression of key developmental genes. Since Mask is a downstream effector of multiple cell signaling pathways, we propose that Mask may connect cell signaling with chromatin mediated epigenetic cell memory governed by trxG.

Sarcococca saligna fabricated gold nanoparticles alleviated in vitro oxidative stress and inflammation in human adipose-derived stem cells

Oxidative stress is a destructive phenomenon that affects various cell structures including membranes, proteins, lipoproteins, lipids, and DNA. Oxidative stress and inflammation owing to lifestyle changes may lead to serious diseases such as Cancers, Gout, and Arthritis etc. These disorders can be prevented using different therapeutic strategies including nanomedicine. Biosynthesized gold nanoparticles (GNPs) because of their anti-inflammatory and antioxidant bioactivities can be key player in reversal of these ailments. This study was carried out to evaluate the anti-inflammatory and antioxidant potential of bio fabricated GNPs with Sarcococca saligna (S. saligna) extract on injured human adipose-derived Mesenchymal stem cells (hADMSCs). GNPs were characterized by ultraviolet-visible (UV-Vis) spectroscopy, Scanning Electron Microscopy (SEM), x-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), and energy dispersive x-ray (EDS). Phytochemical screening of biosynthesized GNPs exhibited a significant release of polyphenols, that is, total phenolic content (TPC) and total flavonoid content (TFC). GNPs priming amended the in vitro injury caused by Monosodium Iodoacetate (MIA) as exhibited by improved cell viability, wound closure response and superoxide dismutase activity (SOD). The anti-inflammatory conduct assessed through NF-κB pathway and other associated inflammatory markers reported down-regulation of TNF-α (0.644 ± 0.045), IL-1β (0.694 ± 0.147) and IL-6 (0.622 ± 0.112), apoptosis causing genes like Caspase-3 (0.734 ± 0.13) and BAX (0.830 ± 0.12), NF-κB pathway, p65 (0.672 ± 0.084) and p105 (0.539 ± 0.083) associated genes. High SOD activity (95 ± 5.25%) revealed by treated hADMSCs with GNPs also supported the antioxidant role of GNPs in vitro model. This study concludes that S. saligna bio fabricated GNPs priming may improve the therapeutic potential of hADMSCs against chronic inflammatory problems by regulating NF-κB pathway.

Molecular distribution of biocide resistance genes and susceptibility to biocides among vancomycin resistant Staphylococcus aureus (VRSA) isolates from intensive care unit (ICU) of cardiac hospital- A first report from Pakistan

Background

The study was conducted with the aim to investigate the VRSA isolates in terms of their susceptibility to routinely used biocides influenced by the co-occurrence of biocide resistant gene (BRGs) and efflux pumps genes.

Methodology

Frequently touched surfaces within intensive care unit (ICU) of cardiac hospital were classified into three primary sites i.e., structure, machines and miscellaneous. Over a period of six months (January 2021 to July 2021) twenty three swabs samples were collected from these sites. Subsequently, these samples underwent both phenotypic and molecular methods for VRSA isolation and identification. Susceptibility and efficacy testing of biocides (benzalkonium chloride (BAC), cetrimide (CET) and chlorhexidine gluconate (CHG)) were evaluated using microdilution broth and suspension method. Furthermore, specific primers were used for singleplex PCR targeting BRGs (cepA, qacA, and qacE) and efflux pump (norA, norB, norC, sepA, mepA and mdeA) associated genes.

Results

We found that 72.2 % S. aureus demonstrate the presence of vanA or vanB genes with no significant difference among three sites (p > 0.05). cepA is the most dominant BRGs followed by qacA and qacE from structure site as compared to other sites (p < 0.05). BAC showed reduced biocide susceptibility and MIC50. There was no significant difference between presence or absence of BRGs and high MIC values of VRSA isolates from all three sites. However, efflux pump genes (EFPGs) particularly norA and norA + sepA had a significant association with BRGs and reduced biocide.

Conclusion

BAC is the most effective disinfectant against VRSA. Proper and controlled use of BAC is required to overcome the VRSA contamination. We recommend continuous monitoring of the BRGs prevalence for better prevention of microorganism dissemination and infection control in hospitals.

Investigation of vibration's effect on driver in optimal motion cueing algorithm

The increased sensation error between the surroundings and the driver is a major problem in driving simulators, resulting in unrealistic motion cues. Intelligent control schemes have to be developed to provide realistic motion cues to the driver. The driver's body model incorporates the effects of vibrations on the driver's health, comfort, perception, and motion sickness, and most of the current research on motion cueing has not considered these factors. This article proposes a novel optimal motion cueing algorithm that utilizes the driver's body model in conjunction with the driver's perception model to minimize the sensation error. Moreover, this article employs H∞ control in place of the linear quadratic regulator to optimize the quadratic cost function of sensation error. As compared to state of the art, we achieve decreased sensation error in terms of small root-mean-square difference (70%, 61%, and 84% decrease in case of longitudinal acceleration, lateral acceleration, and yaw velocity, respectively) and improved coefficient of cross-correlation (3% and 1% increase in case of longitudinal and lateral acceleration, respectively).

Review of current literature on gestational trophoblastic neoplasia

BACKGROUND

Gestational Trophoblastic Neoplasia (GTN) is a disease of the reproductive age group with an incidence rate of <1% among all tumors involving the female reproductive tract. It occurs because of aberrant fertilization. Patients are diagnosed early because of aggravated symptoms during pregnancy. Moreover, patients also bleed from the tumor sites, which leads to early presentation. A cure rate of 100% can be achieved with adequate treatment.

MAIN BODY

In this literature review, the authors have brought to attention the risk factors, classification, and various treatment options in GTN patients according to their stratification as per the WHO scoring system. Patients are categorized into low and high risk based on the FIGO scoring system. Patients with low risk are treated with single-agent methotrexate or actinomycin-D. Despite the superiority of actinomycin-D in terms of efficacy, methotrexate remains the first choice of therapy in low-risk patients due to its better toxicity profile. Multi-agent chemotherapy with etoposide, methotrexate, actinomycin-D, cyclophosphamide and vincristine (EMA-CO) leads to complete remission in 93% of high-risk GTN patients. Around 40% of patients with incomplete responses are salvaged with platinum-based multi-agent chemotherapy. Isolated chemo-resistant clones can be salvaged with surgical interventions.

CONCLUSION

The mortality in patients with GTN has significantly reduced over time. With adequate multi-disciplinary support, patients with GTN can ultimately be cured and can spend every day healthy reproductive life.

Soil nutrient levels regulate the effect of soil microplastic contamination on microbial element metabolism and carbon use efficiency

Microplastics (MPs) are emerging environmental contaminants in soil ecosystems that disrupt the soil carbon (C) pool. Therefore, the response of microbial metabolism to MP-contaminated soil is crucial for soil-C stabilization. We undertook factorial experiments in a greenhouse with three types of soil microplastics with three levels of soil nutrients and undertook soil physiochemical analyses after 60 days. The present study revealed how the presence of degradable polylactic acid (PLA) and non-degradable polyethylene (PE) MPs affects soil microbial nutrient limitation and C use efficiency (CUE) at varying nutrient concentrations. The presence of PLA in soil with low nutrient levels led to a significant increase (29%) in the activities of nitrogen (N)-acquiring enzymes. In contrast, the presence of MPs had no effect on C- and N-acquiring enzymes. The occurrence of PE caused a 41% reduction in microbial C limitation in high-nutrient soils, and microbial nutrient metabolism was limited by the occurrence of MPs in soils amended with nutrients. A strong positive correlation between microbial C and nutrient limitation in the soil indicates that addressing C limitation followed by amendment of soil with MPs could potentially intensify microbial N limitation in soils with varying nutrients. In comparison, the microbial CUE increased by 10% with the application of degradable MPs (PLA) to soils with a low nutrient status. These findings highlight the significant influence of both degradable PLA and non-degradable PE MPs on soil microbial processes and C dynamics. In conclusion, PLA enhances metabolic efficiency in nutrient-rich soils, potentially aiding C utilization, whereas PE reduces microbial C limitation, offering promise for soil C sequestration strategies. Our findings underscore the importance of considering MPs in soil ecosystem studies and in broader sustainability efforts.

MicroRNAs as Molecular Biomarkers for the Characterization of Basal-like Breast Tumor Subtype

Breast cancer is a heterogeneous disease highlighted by the presence of multiple tumor variants and the basal-like breast cancer (BLBC) is considered to be the most aggressive variant with limited therapeutics and a poor prognosis. Though the absence of detectable protein and hormonal receptors as biomarkers hinders early detection, the integration of genomic and transcriptomic profiling led to the identification of additional variants in BLBC. The high-throughput analysis of tissue-specific micro-ribonucleic acids (microRNAs/miRNAs) that are deemed to have a significant role in the development of breast cancer also displayed distinct expression profiles in each subtype of breast cancer and thus emerged to be a robust approach for the precise characterization of the BLBC subtypes. The classification schematic of breast cancer is still a fluid entity that continues to evolve alongside technological advancement, and the transcriptomic profiling of tissue-specific microRNAs is projected to aid in the substratification and diagnosis of the BLBC tumor subtype. In this review, we summarize the current knowledge on breast tumor classification, aim to collect comprehensive evidence based on the microRNA expression profiles, and explore their potential as prospective biomarkers of BLBC.

Disparities in patient-resident physician communication and counseling: A multi-perspective exploratory qualitative study

Effective communication between physicians and patients plays an integral role in clinical care. Gaps in a physician's ability to ensure effective communication, especially with patients from diverse backgrounds, are known causes of medical errors. This study explores the potential biases and disparities in patient-resident communication, which may influence a patient's quality of care. This exploratory qualitative study was conducted at the largest academic medical center in Pakistan. Purposive sampling was used to approach participants from surgery, medicine, obstetrics and gynecology, pediatrics and family medicine. Faculty, fellows and residents working in these departments and medical students in their fourth and fifth years of undergraduate education with prior experience of at least one month in these specialties during their clinical rotations were included. Focus group discussions (FGDs) lasting 45-60 minutes were conducted with each cohort of healthcare professionals separately, using a semi-structured interview guide. Sixty participants (19 males and 41 females, mean age: 32.9, SD: 10.9) took part in the study. Thematic analysis revealed five major themes. Four themes focused on residents' biases and patient disparities hindering patient-resident communication: (1) patient-resident gender discordance (2) ethnicity and language barriers, (3) differing social class of the patient, and (4) challenging patient-resident interactions (patients resistant to treatment, exceedingly inquisitive and those with multiple attendants, etc.). The fifth theme identified the need for a communication skills curriculum in postgraduate medical education. Opposite gender and discordant socioeconomic/cultural backgrounds of patients pose a challenge to effective patient-physician communication. Self-identification and awareness of residents' biases when interacting with patients can ensure their active elimination and improve their communication skills. Integrating these components in a standardized curriculum within postgraduate programs can enable resident-physicians to provide the same level of care and communicate more efficiently with patients of all backgrounds.

Barriers to research productivity amongst postgraduate trainees: results from a survey of 333 medical and surgical residents

PURPOSE

We aimed to determine the perceptions of, barriers to, and predictors of research engagement amongst residents at a national level in Pakistan.

METHODS

This cross-sectional study used REDCap for online survey dissemination to residents from 12 institutes accredited by the national accreditation body (College of Physicians and Surgeons Pakistan) for core medical and surgical specialties. Logistic regression was used to estimate associations between likelihood of publications and participant characteristics.

RESULTS

The response rate was 79% (333/423), with 171 (51%) medical and 162 (49%) surgical residents. The mean ± standard deviation age was 28.8 ± 2.7 years; 137 (41%) were males and 195 (59%) females. More than half the residents, 202 (61%), had received research training, but 189 (57%) scored <33% on basic research knowledge. While most residents agreed on the positive impact of research on their careers (P = .012) and realized that they should be involved in it (P = .33), they also strongly believed that it was difficult to engage in research during training (P < .01). Only 60 (18%) trainees had published a paper in local and 37 (11%) in international journals, respectively. The most significant barriers to conducting research included time limitation due to clinical work, lack of financial support, and unavailability of data (P < .01).

CONCLUSION

Residents have a positive attitude towards research. However, research engagement among residents is low. Improving research mentorship and creating systems that enable protected time and institutional access to data are needed to increase research output of postgraduate trainees. Key messages What is already known on this topic Postgraduate trainees benefit academically from research conducted during residency training. However, in low- and middle-income countries like Pakistan, research output among residents has remained low over the years. The nation has consistently produced very little research. What this study adds The current study helped shed light on the reasons for low research productivity amongst medical and surgical residents in Pakistan. How this study might affect research, practice, or policy The potential predictors for low research involvement highlighted in this study necessitate modification of the existing national residency curriculum to increase research engagement and productivity among residents. Not only can the potential factors be improved, but the study also helps in bringing stakeholders' attention to increasing research opportunities in Pakistan.

The Green Synthesis of Silver Nanoparticles from Avena fatua Extract: Antifungal Activity against Fusarium oxysporum f.sp. lycopersici

Using plant extracts as eco-friendly reducing and stabilizing agents for the synthesis of nanoparticles has gained significant attention in recent years. The current study explores the green synthesis of silver nanoparticles (AgNPs) using the Avena fatua extract and evaluates their antifungal activity against Fusarium oxysporum f.sp. lycopersici (Fol), a fungal plant pathogen. A green and sustainable approach was adopted to synthesize silver nanoparticles before these nanoparticles were employed for anti-fungal activity. The primary indication that AgNPs had formed was performed using UV-vis spectroscopy, where a strong peak at 425 nm indicated the effective formation of these nanoparticles. The indication of important functional groups acting as reducing and stabilizing agents was conducted using the FTIR study. Additionally, morphological studies were executed via SEM and AFM, which assisted with more effectively analyzing AgNPs. Crystalline behavior and size were estimated using powder XRD, and it was found that AgNPs were highly crystalline, and their size ranged from 5 to 25 nm. Synthesized AgNPs exhibited significant antifungal activity against Fol at a concentration of 40 ppm. Furthermore, the inhibitory index confirmed a positive correlation between increasing AgNPs concentration and exposure duration. This study suggests that the combined phytochemical mycotoxic effect of the plant extract and the smaller size of synthesized AgNPs were responsible for the highest penetrating power to inhibit Fol growth. Moreover, this study highlights the potential of using plant extracts as reducing and capping agents for the green synthesis of AgNPs with antifungal properties. The study concludes that A. fatua extract can synthesize antifungal AgNPs as a sustainable approach with robust antifungal efficacy against Fol, underscoring their promising potential for integration into plant protection strategies.

Photophysical and biological aspects of α, β-unsaturated ketones: Experimental and in silico approach

In this work, four fluorinated α, β-unsaturated ketones named as 3-(3-bromophenyl)-1-(3-(trifluoromethyl)phenyl)prop-2-en-1-one (1), 3-(4-methoxyphenyl)-1-(3-(trifluoromethyl)phenyl) prop-2-en-1-one (2), 3-(3-bromo-5-chloro-2-hydroxyphenyl)-1-(3-(trifluoromethyl)phenyl) prop-2-en-1-one (3) and 3-(2-hydroxy-5-methylphenyl)-1-(3-(trifluoromethyl)phenyl)prop-2-en-1-one (4) were synthesized by Claisen-Schmidt reaction. The synthesized molecules were then characterized through ultraviolet-visible spectroscopy (UV-Vis), Fourier transform infrared (FTIR), 1 H-NMR, 13 C-NMR, and mass spectrometry. The antioxidant potential, Urease inhibition, and interaction of compounds 1-4 with Salmon sperm DNA were experimentally explored and supported by molecular docking studies. The synthesized compounds strongly interact with SS-DNA through intercalative mode. It was noticed that compound 1 served as potent Urease inhibitor while compound 4 as better antioxidant among synthesized compounds. Moreover, frontier molecular orbitals, nonlinear optical (NLO) properties, natural bond orbitals, molecular electrostatic potential, natural population analysis, and photophysical properties of synthesized compounds were accomplished through density functional theory and time-dependent density functional theory. The band gap of all the compounds have been worked out using Taucs method. In addition to that, a precise comparative account of UV and IR data obtained from theoretical and experimental findings showed good agreement between theoretical and experimental data. The findings of our studies reflected that compounds 1-4 possess better NLO properties than Urea standard and the band gap data also reflected their prospective use towards optoelectronic materials. The better NLO behavior of compounds was attributed to the noncentrosymmetric structure of synthesized compounds.

Lead identification against Mycobacterium tuberculosis using highly enriched active molecules against pantothenate synthetase

The Pantothenate synthetase (PS) from the Mycobacterium tuberculosis (Mtb) holds a crucial role in the survival and robust proliferation of bacteria through its catalysis of coenzyme A and acyl carrier protein synthesis. The present study undertook the PS drug target in complex with a co-crystallized ligand and subjected it to docking and virtual screening approaches. The experimental design encompassed three discrete datasets: an active dataset featuring 136 compounds, an inactive dataset comprising 56 compounds, and a decoys dataset curated from the zinc library, comprising an extensive compilation of approximately 53,000 compounds. The compounds' binding energies were observed to be in the range of -5 to ∼-14 kcal/mol. Additionally, binding energy results were further refined through Enrichment Factor analysis (EF). EF is a new statistical approach which uses the scores obtained from docking-based virtual screening and predicts the precision of the scoring function. Remarkably, the Enrichment Factor (EF) analysis produced exceptionally favorable outcomes, attaining an EF of approximately 49% within the uppermost 1% fraction of the compound distribution. Finally, a total of eight compounds, evenly distributed between the active dataset and the decoys dataset, emerged as potent inhibitors of the Pantothenate synthetase (PS) enzyme. The analysis of inhibition constants and binding energy revealed a notable correlation, with an r-squared value (r2) of 0.912 between the two parameters. Furthermore, the shortlisted compounds were subjected to 100 ns MD simulation to determine their stability and dynamics behavior. The decoy compounds that have been identified, exhibiting properties comparable to the active compounds, are postulated as potential candidates for targeting the Pantothenate synthetase (PS) enzyme to treat Mtb infection. Nevertheless, in the pursuit of a comprehensive investigation, it is advisable to undertake additional experimental validation as a component of the subsequent study.Communicated by Ramaswamy H. Sarma.

Purification and characterization of novel isoforms of the polyphenol oxidase from Malus domestica fruit pulp

Polyphenol oxidases (PPOs), belong to the group of oxidoreductases that are copper containing enzymes and are responsible for plant browning. PPOs are extensively distributed in plant kingdom and can oxidize wide range of aromatic compounds of industrial importance. The aim of this study was purification and characterization of PPO isoforms from the fruit pulp of Golden delicious apple. High performance liquid chromatography was used to purify the two novel isoforms of PPO and further their molecular weights (45 and 28 kDa) were determined using sodium dodecyl sulfate polyacrylamide gel electrophoresis. The purified isoforms have optimum pH (6.5), optimum temperature (40°C), the Vmax (4.45 μM/min) and Km (74.21 mM) with catechol substrate. The N-terminal microsequences of both PPO isoforms were determined using a pulse liquid protein sequencer and found to be AKITFHG (28 kDa) and APGGG (45 kDa). Polyphenol oxidases are efficiently used in the pharmaceutical, paper and pulp, textiles and food industries. Recently, the PPOs have been used for bioremediation and in the development of biosensors.

The interleukin-11 receptor variant p.W307R results in craniosynostosis in humans

Craniosynostosis is characterized by the premature fusion and ossification of one or more of the sutures of the calvaria, often resulting in abnormal features of the face and the skull. In cases in which growth of the brain supersedes available space within the skull, developmental delay or cognitive impairment can occur. A complex interplay of different cell types and multiple signaling pathways are required for correct craniofacial development. In this study, we report on two siblings with craniosynostosis and a homozygous missense pathogenic variant within the IL11RA gene (c.919 T > C; p.W307R). The patients present with craniosynostosis, exophthalmos, delayed tooth eruption, mild platybasia, and a basilar invagination. The p.W307R variant is located within the arginine-tryptophan-zipper within the D3 domain of the IL-11R, a structural element known to be important for the stability of the cytokine receptor. Expression of IL-11R-W307R in cells shows impaired maturation of the IL-11R, no transport to the cell surface and intracellular retention. Accordingly, cells stably expressing IL-11R-W307R do not respond when stimulated with IL-11, arguing for a loss-of-function mutation. In summary, the IL-11R-W307R variant, reported here for the first time to our knowledge, is most likely the causative variant underlying craniosynostosis in these patients.

Multiple myeloma and its rare paraneoplastic manifestations simmering under the surface

Paraneoplastic syndromes are complex clinical manifestations that occur because of the underlying malignancy in which the malignant cells produce hormones, cytokines, peptides or antibodies that causes symptoms and may affect multiple organ systems. These paraneoplastic conditions may be associated with different solid and hematological malignancies. Multiple Myeloma (MM) accounts for 10-15 % of hematological malignancies and 1-2 % of all malignancies. It is associated with some atypical clinical and laboratory paraneoplastic manifestations. Although there is a low incidence of these paraneoplastic, significant knowledge of these manifestations may assist in making a differential diagnosis in cases of doubt. The clinical presentation may vary and be evident even before or after the diagnosis of malignancy. These include vascular, neurological, dermatological, physiological, and other atypical conditions. Furthermore, these rare paraneoplastic manifestations need more valid, relevant scientific information, as most information about these conditions is derived from case reports. After the literature search, we have reported the paraneoplastic manifestations associated with multiple myeloma, published in the English literature, and the cognate management in this review article. To our knowledge, this is the first review article discussing various paraneoplastic manifestations of multiple myeloma.

Optimization of Filler Compositions of Electrically Conductive Polypropylene Composites for the Manufacturing of Bipolar Plates

In this research, polypropylene (PP)-graphite composites were prepared using the melt mixing technique in a twin-screw extruder. Graphite, multi-walled carbon nanotubes (MWCNT), carbon black (CB), and expanded graphite (EG) were added to the PP in binary, ternary, and quaternary formations. The graphite was used as a primary filler, and MWCNT, CB, and EG were added to the PP-graphite composites as secondary fillers at different compositions. The secondary filler compositions were considered the control input factors of the optimization study. A full factorial design of the L-27 Orthogonal Array (OA) was used as a Design of Experiment (DOE). The through-plane electrical conductivity and flexural strength were considered the output responses. The experimental data were interpreted via Analysis of Variance (ANOVA) to evaluate the significance of each secondary filler. Furthermore, statistical modeling was performed using response surface methodology (RSM) to predict the properties of the composites as a function of filler composition. The empirical model for the filler formulation demonstrated an average accuracy of 83.9% and 93.4% for predicting the values of electrical conductivity and flexural strength, respectively. This comprehensive experimental study offers potential guidelines for producing electrically conductive thermoplastic composites for the manufacturing of bipolar fuel cell plates.

Impact of the China-Pakistan Economic Corridor on the China-Europe and China-Middle East trading route selection

This research examines the potential impact of the China-Pakistan Economic Corridor (CPEC) on the selection of trading routes between China, the Middle East, and Europe, with a specific focus on the transportation of a 40-foot standard container carrying general commodities. The study compares traditional routes with the new CPEC routes in terms of time, distance, and cost. The findings indicate that the new CPEC routes offer reduced travel time and distance when compared to the traditional routes across all provinces involved. The research reveals that the cost of road transportation along the new CPEC route is lower for Xinjiang province, but higher for the other provinces. By utilizing the new CPEC routes, the time required for goods to travel from China to the Middle East and Europe will be reduced by 10 to 20 days. Furthermore, the distance covered in this trade route will be shortened by 3,000 to 10,000 kilometres. Specifically, the province of Xinjiang in western China stands to benefit significantly from the new CPEC routes, saving approximately $2,000 on trade with the Middle East and Europe. These findings highlight the potential advantages and economic benefits that can be realized by leveraging the CPEC for trade between China, the Middle East, and Europe, particularly in terms of reduced transportation time and distance.

Phytochemical-Mediated Biosynthesis of Silver Nanoparticles from Strobilanthes glutinosus: Exploring Biological Applications

The application of green synthesis for silver nanoparticles in nanomedicine has experienced significant growth. Strobilanthes glutinosus, a plant primarily located in the Himalayas, remains largely unexplored. Considering the biomedical value of S. glutinosus, phytochemicals from this plant were used for the biosynthesis of silver nanoparticles. Silver nanoparticles were synthesized from aqueous extract of root and leaves of Strobilanthes glutinosus. The synthesized silver nanoparticles were characterized using UV-Vis spectrophotometry, Fourier-transform infrared spectroscopy, transmission electron microscopy, and X-ray diffraction. Total phenolic and flavonoid contents of plants were determined and compared with nanoparticles. The biomedical efficacy of plant extracts and silver nanoparticles was assessed using antioxidant and antibacterial assays. The UV-Vis spectra of leaf- and root-extract-mediated AgNPs showed characteristic peaks at 428 nm and 429 nm, respectively. TEM images revealed the polycrystalline and spherical shapes of leaf- and root-extract-mediated AgNPs with size ranges of 15-60 nm and 20-52 nm, respectively. FTIR findings shown the involvement of phytochemicals of root and leaf extracts in the reduction of silver ions into silver nanoparticles. The crystalline face-centered cubic structure of nanoparticles is depicted by the XRD spectra of leaf and root AgNPs. The plant has an ample amount of total phenolic content (TPC) and total flavonoid content (TFC), which enhance the scavenging activity of plant samples and their respective AgNPs. Leaf and root AgNPs have also shown good antibacterial activity, which may enhance the medicinal value of AgNPs.

A homozygous founder variant in PDE2A causes paroxysmal dyskinesia with intellectual disability

Intellectual developmental disorder with paroxysmal dyskinesia or seizures (IDDPADS, OMIM#619150) is an ultra-rare childhood-onset autosomal recessive movement disorder manifesting paroxysmal dyskinesia, global developmental delay, impaired cognition, progressive psychomotor deterioration and/or drug-refractory seizures. We investigated three consanguineous Pakistani families with six affected individuals presenting overlapping phenotypes partially consistent with the reported characteristics of IDDPADS. Whole exome sequencing identified a novel missense variant in Phosphodiesterase 2A (PDE2A): NM_002599.4: c.1514T > C p.(Phe505Ser) that segregated with the disease status of individuals in these families. Retrospectively, we performed haplotype analysis that revealed a 3.16 Mb shared haplotype at 11q13.4 among three families suggesting a founder effect in this region. Moreover, we also observed abnormal mitochondrial morphology in patient fibroblasts compared to controls. Belonging to diverse age groups (13 years-60 years), patients presented paroxysmal dyskinesia, developmental delay, cognitive abnormalities, speech impairment, and drug-refractory seizures with variable onset of disease (as early as 3 months of age to 7 years). Together with the previous reports, we observed that intellectual disability, progressive psychomotor deterioration, and drug-refractory seizures are consistent outcomes of the disease. However, permanent choreodystonia showed variability. We also noticed that the later onset of paroxysmal dyskinesia manifests severe attacks in terms of duration. Being the first report from Pakistan, we add to the clinical and mutation spectrum of PDE2A-related recessive disease raising the total number of patients from six to 12 and variants from five to six. Together, with our findings, the role of PDE2A is strengthened in critical physio-neurological processes.

A novel frameshift variant in UBA2 causing split-hand/foot malformations in a Pakistani family

Split-hand/foot malformation (SHFM) shows diverse heterogeneity and manifests with reduced penetrance and variable expressivity. This study investigated the underlying genetic cause of a family segregating SHFM. Exome sequencing followed by Sanger sequencing identified a novel single nucleotide heterozygous variant (NC_000019.9 (NM_005499.3):c.1118del) in UBA2 cosegregating in the family in an autosomal dominant manner. Our findings conclude that reduced penetrance and variable expressivity are the two remarkable and unusual features of SHFM.

Expression of Chitinase and shRNA Gene Exhibits Resistance to Fungi and Virus

With the increasing global population, saving crops from diseases caused by different kinds of bacteria, fungi, viruses, and nematodes is essential. Potato is affected by various diseases, destroying many crops in the field and storage. In this study, we developed potato lines resistant to fungi and viruses, Potato Virus X (PVX) and Potato Virus Y (PVY), by inoculating chitinase for fungi and shRNA designed against the mRNA of the coat protein of PVX and PVY, respectively. The construct was developed using the pCAMBIA2301 vector and transformed into AGB-R (red skin) potato cultivar using Agrobacterium tumefaciens. The crude protein extract of the transgenic potato plant inhibited the growth of Fusarium oxysporum from ~13 to 63%. The detached leaf assay of the transgenic line (SP-21) showed decreased necrotic spots compared to the non-transgenic control when challenged with Fusarium oxysporum. The transgenic line, SP-21, showed maximum knockdown when challenged with PVX and PVY, i.e., 89 and 86%, while transgenic line SP-148 showed 68 and 70% knockdown in the PVX- and PVY-challenged conditions, respectively. It is concluded from this study that the developed transgenic potato cultivar AGB-R showed resistance against fungi and viruses (PVX and PVY).

Green Synthesis of Zinc Oxide (ZnO) Nanoparticles from Green Algae and Their Assessment in Various Biological Applications

The biosynthesis of algal-based zinc oxide (ZnO) nanoparticles has shown several advantages over traditional physico-chemical methods, such as lower cost, less toxicity, and greater sustainability. In the current study, bioactive molecules present in Spirogyra hyalina extract were exploited for the biofabrication and capping of ZnO NPs, using zinc acetate dihydrate and zinc nitrate hexahydrate as precursors. The newly biosynthesized ZnO NPs were characterized for structural and optical changes through UV-Vis spectroscopy, Fourier transform infrared spectroscopy (FT-IR), X-ray diffraction (XRD), scanning electron microscopy (SEM), and energy dispersive X-ray spectroscopy (EDX). A color change in the reaction mixture from light yellow to white indicated the successful biofabrication of ZnO NPs. The UV-Vis absorption spectrum peaks at 358 nm (from zinc acetate) and 363 nm (from zinc nitrate) of ZnO NPs confirmed that optical changes were caused by a blue shift near the band edges. The extremely crystalline and hexagonal Wurtzite structure of ZnO NPs was confirmed by XRD. The involvement of bioactive metabolites from algae in the bioreduction and capping of NPs was demonstrated by FTIR investigation. The SEM results revealed spherical-shaped ZnO NPs. In addition to this, the antibacterial and antioxidant activity of the ZnO NPs was investigated. ZnO NPs showed remarkable antibacterial efficacy against both Gram-positive and Gram-negative bacteria. The DPPH test revealed the strong antioxidant activity of ZnO NPs.

Exome sequencing identifies a novel pathogenic variant in RAB3GAP1 causing Warburg Micro syndrome in a Pakistani family

BACKGROUND

Warburg Micro (WARBM) syndrome is a rare heterogeneous recessive genetic disorder characterized by ocular, neurological, and endocrine problems. To date, disease-causing variants in four genes have been identified to cause this syndrome; of these, RAB3GAP1 variants are the most frequent. Very little is known about WARBM syndrome in rural populations.

OBJECTIVES

This study aims to investigate the genetics underpinnings of WARBM syndrome in a Pashtun family with two patients from Pakistan. The patients presented with spastic diplegia, severe intellectual disability, microphthalmia, microcornea, congenital cataracts, optic atrophy, and hypogonadism.

METHODS

Magnetic resonance imaging (MRI) analysis revealed pronounced cerebral atrophy including corpus callosum hypoplasia and polymicrogyria. Exome sequencing and subsequent filtering identified a novel homozygous missense variant NM_001172435: c.2891A>G, p.Gln964Arg in the RAB3GAP1 gene. The variant was validated, and its segregation confirmed, by Sanger sequencing.

RESULTS

Multiple prediction tools assess this variant to be damaging, and structural analysis of the protein shows that the mutant amino acid residue affects polar contact with the neighboring atoms. It is extremely rare and is absent in all the public databases. Taken together, these observations suggest that this variant underlies Micro syndrome in our family and is extremely important for management and family planning.

CONCLUSIONS

Identification of this extremely rare variant extends the mutations spectrum of Micro syndrome. Screening more families, especially in underrepresented populations, will help unveil the mutation spectrum underlying this syndrome.

Experiences of Undergraduate Medical, Nursing Students and Faculty regarding Flipped Classroom: A Mixed Method Study at Private Medical University in Pakistan

The 'flipped classroom (FCR)' is a teaching pedagogy where students are actively involved in the learning process. It reduces passivity, enables students to become active learners through reasoning and concept application and facilitates student interaction with their peers and instructors. This instructional approach enhances retention and decreases distraction by engaging students.

OBJECTIVES

The purpose of this study was to train the faculty of the medical college and school of nursing in developing FCRs as an innovative teaching and learning strategy, to facilitate them in conducting flipped sessions for their students and to explore the experiences of medical, nursing students along with faculty members regarding the FCR they had attended and conducted.

SETTING

Private medical college.

PARTICIPANTS

A total of 442 students from medical college and school of nursing and midwifery participated in the evaluation survey with a female to male ratio of 339:103. Students who attended the flipped class sessions were included in the study sample. Students who did not complete the forms were excluded from the study. Nine faculty members who attended the workshop, agreed to facilitate the FCR session were invited to participate in the focus group discussion.

RESULTS

Both medical and nursing students found FCR format stimulating. A significantly higher proportion of medical students (73%) found the FCR more engaging and interesting than a traditional lecture as compared with nursing students (59%) (p=0.009). Similarly, 73% of medical students believed the learning objectives of both the non-face-to-face and face-to-face sessions were shared with them as compared with the 62% of nursing students who believed the same (p=0.002). A significantly higher proportion of medical (76%) versus nursing (61%) students found the FCR format more useful for application of their theoretical knowledge into clinical practice (p=0.030).

CONCLUSION

Students found the FCR more engaging and interesting in terms of applying theoretical knowledge into practice. Similarly, faculty found this strategy as effective but challenging in terms of involving and engaging students in the learning process. It is recommended to conduct more FCR sessions for an interactive and student-centred learning, but proper planning of the session and using variety of technological tools to engage learners is a key to success.

Biofabrication of Fe3O4 Nanoparticles from Spirogyra hyalina and Ajuga bracteosa and Their Antibacterial Applications

Iron oxide nanoparticles (NPs) have attracted substantial interest due to their superparamagnetic features, biocompatibility, and nontoxicity. The latest progress in the biological production of Fe₃O₄ NPs by green methods has improved their quality and biological applications significantly. In this study, the fabrication of iron oxide NPs from Spirogyra hyalina and Ajuga bracteosa was conducted via an easy, environmentally friendly, and cost-effective process. The fabricated Fe₃O₄ NPs were characterized using various analytical methods to study their unique properties. UV-Vis absorption peaks were observed in algal and plant-based Fe₃O₄ NPs at 289 nm and 306 nm, respectively. Fourier transform infrared (FTIR) spectroscopy analyzed diverse bioactive phytochemicals present in algal and plant extracts that functioned as stabilizing and capping agents in the fabrication of algal and plant-based Fe₃O₄ NPs. X-ray diffraction of NPs revealed the crystalline nature of both biofabricated Fe₃O₄ NPs and their small size. Scanning electron microscopy (SEM) revealed that algae and plant-based Fe₃O₄ NPs are spherical and rod-shaped, averaging 52 nm and 75 nm in size. Energy dispersive X-ray spectroscopy showed that the green-synthesized Fe₃O₄ NPs require a high mass percentage of iron and oxygen to ensure their synthesis. The fabricated plant-based Fe₃O₄ NPs exhibited stronger antioxidant properties than algal-based Fe₃O₄ NPs. The algal-based NPs showed efficient antibacterial potential against E. coli, while the plant-based Fe₃O₄ NPs displayed a higher zone of inhibition against S. aureus. Moreover, plant-based Fe₃O₄ NPs exhibited superior scavenging and antibacterial potential compared to the algal-based Fe₃O₄ NPs. This might be due to the greater number of phytochemicals in plants that surround the NPs during their green fabrication. Hence, the capping of bioactive agents over iron oxide NPs improves antibacterial applications.

Study protocol of DIVERGE, the first genetic epidemiological study of major depressive disorder in Pakistan

INTRODUCTION

Globally, 80% of the burdenof major depressive disorder (MDD) pertains to low- and middle-income countries. Research into genetic and environmental risk factors has the potential to uncover disease mechanisms that may contribute to better diagnosis and treatment of mental illness, yet has so far been largely limited to participants with European ancestry from high-income countries. The DIVERGE study was established to help overcome this gap and investigate genetic and environmental risk factors for MDD in Pakistan.

METHODS

DIVERGE aims to enrol 9000 cases and 4000 controls in hospitals across the country. Here, we provide the rationale for DIVERGE, describe the study protocol and characterise the sample using data from the first 500 cases. Exploratory data analysis is performed to describe demographics, socioeconomic status, environmental risk factors, family history of mental illness and psychopathology.

RESULTS AND DISCUSSION

Many participants had severe depression with 74% of patients who experienced multiple depressive episodes. It was a common practice to seek help for mental health struggles from faith healers and religious leaders. Socioeconomic variables reflected the local context with a large proportion of women not having access to any education and the majority of participants reporting no savings.

CONCLUSION

DIVERGE is a carefully designed case-control study of MDD in Pakistan that captures diverse risk factors. As the largest genetic study in Pakistan, DIVERGE helps address the severe underrepresentation of people from South Asian countries in genetic as well as psychiatric research.

Analysis of the ARTIC V4 and V4.1 SARS-CoV-2 primers and their impact on the detection of Omicron BA.1 and BA.2 lineage-defining mutations

The ARTIC protocol uses a multiplexed PCR approach with two primer pools tiling the entire SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) genome. Primer pool updates are necessary for accurate amplicon sequencing of evolving SARS-CoV-2 variants with novel mutations. The suitability of the ARTIC V4 and updated V4.1 primer scheme was assessed using whole genome sequencing of Omicron from clinical samples using Oxford Nanopore Technology. Analysis of Omicron BA.1 genomes revealed that 93.22 % of clinical samples generated improved genome coverage at 50× read depth with V4.1 primers when compared to V4 primers. Additionally, the V4.1 primers improved coverage of BA.1 across amplicons 76 and 88, which resulted in the detection of the variant-defining mutations G22898A, A26530G and C26577G. The Omicron BA.2 sub-variant (VUI-22JAN-01) replaced BA.1 as the dominant variant by March 2022, and analysis of 168 clinical samples showed reduced coverage across amplicons 15 and 75. Upon further interrogation of primer binding sites, a mutation at C4321T [present in 163/168 (97 %) of samples] was identified as a possible cause of complete dropout of amplicon 15. Furthermore, two mutations were identified within the primer binding regions for amplicon 75: A22786C (present in 90 % of samples) and C22792T (present in 12.5 % of samples). Together, these mutations may result in reduced coverage of amplicon 75, and further primer updates would allow the identification of the two BA.2-defining mutations present in amplicon 75: A22688G and T22679C. This work highlights the need for ongoing surveillance of primer matches as circulating variants evolve and change.

Hepatitis C prevalence and elimination planning in Pakistan, a bottom-up approach accounting for provincial variation

In Pakistan, substantial changes to hepatitis C virus (HCV) programming and treatment have occurred since the 2008 nationwide serosurvey estimated a 4.8% anti-HCV prevalence. In the absence of an updated national study, this analysis uses provincial data to estimate a national prevalence and the interventions needed to achieve elimination. Using a Delphi process, epidemiologic HCV data for the four provinces of Pakistan (accounting for 97% of the population) were reviewed with 21 subject-matter experts in Pakistan. Province-level estimates were inputted into a mathematical model to estimate the national HCV disease burden in the absence of intervention (Base), and if the World Health Organization (WHO) elimination targets are achieved by 2030 (80% reduction in new infections, 90% diagnosis coverage, 80% treatment coverage, and 65% reduction in mortality: WHO Elimination). An estimated 9,746,000 (7,573,000-10,006,000) Pakistanis were living with viraemic HCV as of January 1, 2021; a viraemic prevalence of 4.3% (3.3-4.4). WHO Elimination would require an annual average of 18.8 million screens, 1.1 million treatments, and 46,700 new infections prevented anually between 2022 and 2030. Elimination would reduce total infections by 7,045,000, save 152,000 lives and prevent 104,000 incident cases of hepatocellular carcinoma from 2015 to 2030. Blood surveys, programmatic data, and expert panel input uncovered more HCV infections and lower treatment numbers in the provinces than estimated using national extrapolations, demonstrating the benefits of a bottom-up approach. Screening and treatment must increase 20 times and 5 times, respectively, to curb the HCV epidemic in Pakistan and achieve elimination by 2030.

Macrophages M2 polarization is involved in lapatinib-mediated chemopreventive effects in the lung cancer

M2 polarized tumor-associated macrophages (TAMs) have a multifunctional role in cancer initiation, progression, metastasis, and contribute to chemotherapeutic resistance. Therefore, identifying M2 polarized TAMs is a potential target for cancer therapeutic intervention. The underlying mechanism that target the TAMs M2 polarized macrophages remains primarily uncharacterized; however, only a few compounds have been identified that inhibit TAMs M2 polarized macrophages. In this research, we investigated that lapatinib could effectively suppress the expression of IL^_13-induced M2 polarized macrophages surface markers i.e., CD163 and CD206, and downregulation of M2 genes such as Fizz1, Mrc1, Arg1, IL-10, Ym1, nd CCL2 in vitro. Moreover, lapatinib abrogated the M2 polarized macrophage-mediated cancer cells invasion and migration. Mechanistically, in our study, lapatinib inhibited IL-13 triggered STAT6 phosphorylation. Furthermore, in LLCs tumor model, lapatinib significantly reduced tumorigenesis, followed by the downregulation of percentages of M2 marker CD206⁺ and CD68⁺ in the tumor. This downregulation correlates with chemopreventive effect of lapatinib. All taken together, these results demonstrated that lapatinib effectively prevents the macrophage M2 polarization and indicates a potential mechanism for preventing the tumor growth via M2 polarized polarization intervention.

The symmetric and asymmetric impacts of green energy, eco-innovation, and urbanization in explaining low-carbon economy for Pakistan

Over the past three decades, global economic development patterns have considerably affected the natural environment, and economies have endured a plethora of environmental concerns as a result of the negative effects of climate change. Among them, Pakistan is the fifth most vulnerable country, and climate change has harmfully affected the ecological and socio-economic conditions of the country. In this regard, this study aimed to investigate the role of green energy consumption, eco-innovation, and urbanization while explaining the dream of low-carbon economy and environmental sustainability in the context of Pakistan using annual time series dataset spanning from 1990 to 2020. The short-run and long-run associations among explained and explanatory variables were investigated using the symmetric, asymmetric, and quantile autoregressive distributed lag models. The findings of the study demonstrated that low-carbon economy, green energy consumption, ecological innovation, urbanization, GDP per capita, and labor force are cointegrated for the long-term association in symmetric, asymmetric, and quantile autoregressive distributed lag models. Furthermore, green energy consumption and effective eco-innovation are the most important paths to ensure environmental sustainability, while urbanization, GDP per capita, and labor force contribute negatively to the low-carbon economy. The findings of the study provide a policy framework for the development of a comprehensive strategy to promote environmental sustainability in Pakistan by emphasizing green energy consumption, ecological innovation, and controlled urbanization, as well as the incorporation of environment friendly policies into economic development policies.

Frequency of Hyperuricemia in Type-2 Diabetes Mellites and its Relation with Diabetic Nephropathy

Objectives: To determine the frequency of Hyperuricemia in patients with type-2 Diabetes Mellitus and to compare frequency of Diabetic Nephropathy in Hypouricemic vs Normouricemic patients with type-2 Diabetes. Study Design: Cross-sectional analytical study. Duration and Place of Study: Medicine Department Combined Military Hospital Peshawar, from Dec 2018 to May 2019. Methodology: Patients from both genders with type 2 Diabetes having glycosylated hemoglobin (HbA1c) ≥6.5%, Fasting Blood glucose ≥ to 7.0 mmol/L or random blood glucose ≥11.1 mmol/L were recruited from out Patient department.Participants were tested for serum uric acid, fasting blood glucose, Glycosylated hemoglobin (HbA1c) and Spot Urine Albumin Creatinine Ratio after 8 hours fasting. Results: Out of 111 patients enrolled Hyperuricemia was present in 40 (36.04%) patients of which 21 (52.50%) were male and 19 (47.50%) were female. Diabetic Nephropathy was present in 43(38.74%). Out of 43 patients having diabetic nephropathy, 25 (58.14%) were having hyperuricemia. The study observed a linear relationship between serum uric acid and type-2 diabetes duration, fasting blood glucose levels, glycosylated hemoglobin (HbA1c) and urinary Albumin creatinine ratio. Conclusion: Hyperuricemia is positively linked with diabetic complications in majority of patients with type-2 diabetes. Serum uric acid levels can be used as an early diagnostic parameter and can prognosticate diabetic nephropathy.Keywords: Diabetes mellitus, Diabetic nephropathy, Hyperuricemia, Microalbuminuria

Homozygous frameshift variant in desmoglein 2 gene causes biventricular arrhythmogenic right ventricular cardiomyopathy

Arrhythmogenic right ventricular cardiomyopathy caused by a homozygous frameshift variant (c.2358delA) in DSG2.

Frequency of visual impairment in autistic children of autism school of Lahore, Pakistan

Autism is a condition in which abnormal development of the brain takes place, manifesting in the first 3 years of life. Visual impairment is one of the major factors of autism spectrum disorder (ASD), and measurement of visual impairment is necessary for proper management of the disorder. The purpose of this study is to determine the frequency of visual impairment associated with ASD in Lahore Pakistan. A descriptive cross-sectional study was conducted. A convenient and purposive sample of 127 students enrolled in various autism schools of Lahore was enrolled. Written informed consent of teacher’s autistic children was taken. Children having diseases like cerebral palsy, other developmental disorders, and/or serious cognitive disability were excluded from this study. Participant’s undergone ocular assessment including visual acuity, ocular motility examination, refraction, and fundoscopy. Data analysis was performed using SPSS-20 and Pearson’s chi-square analysis was conducted to determine the associations of refractive error and squint with ASD. A total of 127 participants were included in this study, of which 77 (60.6%) were male and 50 (39.4%) were female. More than 60% were emmetropes (having no refractive errors), 19 (15%) were having myopes, 15 (11.8%) were hypermetropic, and 9 (7.1%) were Astigmatic, while 20 were diagnosed with a squint. The major cause of visual impairment in autistic children was refractive errors 33.8% and squint 15.7%. A high frequency of visual impairment was present in autistic children in Lahore autistic schools. As vision is a basic right so we have to pay attention also toward autistic children, in that way every child should have screened for factors that are responsible for visual impairments, Identifying refractive errors in these children early and providing appropriate corrective lenses may help optimize their visual functioning and impact their activities of daily life positively.

Potentially probiotic Limosilactobacillus reuteri from human milk strengthens the gut barrier in T84 cells and a murine enteroid model

AIMS

At conception, the infant gut barrier is immature, gradually developing with regular intake of maternal milk. This study addressed whether the barrier-strengthening effect of breast feeding might be attributable, at least in part, to autochthonous beneficial human milk bacteria.

METHODS AND RESULTS

Twelve bacterial strains from the breast milk of Pakistani mothers who underwent cesarean delivery (NPL-88, NPL-157, NPL-179, NPL-181, NPL-388 (Limosilactobacillus reuteri), NPL-76, NPL-495, NPL-504 (Limosilactobacillus fermentum), NPL-415 (Lactobacillus pentosus), NPL-412, NPL-416 (Lactiplantibacilllus plantarum) and NPL-374 (Bifidobacterium longum) were shortlisted based on their tolerance to acidic pH (2.8-4.2) and bile (0.1-0.3%). The effect of these bacteria on gut barrier function in the presence and absence of pathogens was assessed as changes in transepithelial electrical resistance (TEER) in the human T84 colonic epithelial cell line and in murine enteroid-derived monolayers (EDMs). The TEER of T84 cells monolayers rose in the presence of most of the human milk strains, being most pronounced in case of L. reuteri NPL-88 (34% within five h), exceeding the effect of the well-known probiotic L. acidophilus (20%). qRT-PCR, western blot and immunofluorescent staining associated the increase in TEER with enhanced expression of tight junction proteins. Pretreatment of murine EDMs with NPL-88 also largely prevented the ability of the pathogen, Salmonella, to decrease TEER (87 ± 1.50%; P < 0.0001, n = 4).

CONCLUSIONS

Human milk lactic acid bacteria are potential probiotics that can strengthen gut barrier function and protect breastfed neonates against enteric infections.

A Novel Experience-Driven and Federated Intelligent Threat-Defense Framework in IoMT

The Artificial Intelligence-enabled Internet of Medical Things (AI-IoMT) envisions the connectivity of medical devices encompassing advanced computing technologies to empower large-scale intelligent healthcare networks. The AI-IoMT continuously monitors patients' health and vital computations via IoMT sensors with enhanced resource utilization for providing progressive medical care services. However, the security concerns of these autonomous systems against potential threats are still underdeveloped. Since these IoMT sensor networks carry a bulk of sensitive data, they are susceptible to unobservable False Data Injection Attacks (FDIA), thus jeopardizing patients' health. This paper presents a novel threat-defense analysis framework that establishes an experience-driven approach based on a deep deterministic policy gradient to inject false measurements into IoMT sensors, computing vitals, causing patients' health instability. Subsequently, a privacy-preserved and optimized federated intelligent FDIA detector is deployed to detect malicious activity. The proposed method is parallelizable and computationally efficient to work collaboratively in a dynamic domain. Compared to existing techniques, the proposed threat-defense framework is able to thoroughly analyze severe systems' security holes and combats the risk with lower computing cost and high detection accuracy along with preserving the patients' data privacy.

Minimizing Viral Transmission in COVID-19 Like Pandemics: Technologies, Challenges, and Opportunities

Coronavirus (COVID-19) pandemic has incurred huge loss to human lives throughout the world. Scientists, researchers, and doctors are trying their best to develop and distribute the COVID-19 vaccine throughout the world at the earliest. In current circumstances, different tracking systems are utilized to control or stop the spread of the virus till the whole population of the world gets vaccinated. To track and trace patients in COVID-19 like pandemics, various tracking systems based on different technologies are discussed and compared in this paper. These technologies include, cellular, cyber, satellite-based radio navigation and low range wireless technologies. The main aim of this paper is to conduct a comprehensive survey that can overview all such tracking systems, which are used in minimizing the spread of COVID-19 like pandemics. This paper also highlights the shortcoming of each tracking systems and suggests new mechanisms to overcome such limitations. In addition, the authors propose some futuristic approaches to track patients in prospective pandemics, based on artificial intelligence and big data analysis. Potential research directions, challenges, and the introduction of next-generation tracking systems for minimizing the spread of prospective pandemics, are also discussed at the end.