Biology subjects

Zafar, M.

Publications and source records attributed to Zafar, M..

12 recordsLinked to original sources

bioRxiv2026

A robust and scalable image analysis framework for phenotyping human thoracic aorta

Large-scale phenotyping of the thoracic aorta requires a workflow in which every step, from segmentation to phenotype extraction, runs without manual intervention. We present a robust and scalable framework that converts contrast-enhanced CT into anatomical landmarks, a patient-specific quadrilateral mesh, a wall-stress field and regional phenotypes of the thoracic aorta. Four nnU-Net segmentation tasks delineate the aorta, its anatomical regions and two partitions of the aortic root. A surface-curve-point procedure derives the annulus, the sinotubular junction, the ostia of the supra-aortic branches, the cusp nadirs and the commissures from the interfaces between segmented regions. We fit a structured template of 24,882 quadrilateral elements to the segmented aortic surface by staged, differentiable mesh deformation and compute the transmural mean wall stress with PyTorch-FEA. The structured mesh provides node-to-node correspondence across patients, anchored to the anatomy by the landmarks, from which the framework extracts regional morphological and biomechanical phenotypes.

bioengineering↗

bioRxiv2026

Patient-specific zebrafish models reveal a complex phenotypic spectrum in NBAS-associated Atypical Osteogenesis Imperfecta

Neuroblastoma amplified sequence gene (NBAS) variants are associated with short stature, optic atrophy, and Pelger-Huet anomaly (SOPH) syndrome. We previously identified compound heterozygous variants in NBAS to cause atypical Osteogenesis Imperfecta (OI), with these patients presenting with short stature, developmental delay and recurrent long-bone fractures. However, skeletal disease progression due to these variants and the disease mechanisms underlying NBAS-associated OI remain poorly understood. Here, we provide a clinical update on previously identified patients and investigate the role of NBAS during skeletal development using zebrafish knockout and patient-specific missense variant zebrafish models. Homozygous knockout larvae exhibited delayed operculum development, reduced bone ossification, and defects in Meckels cartilage morphology and its underlying cellular structure. Homozygous missense larvae displayed milder cartilage defects without any major defects to early skeletal structures. Seemingly opposing phenotypes were observed in compound heterozygous zebrafish carrying the knockout and missense alleles in trans, with no obvious phenotypes seen in the Meckels cartilage and accelerated operculum development observed. Together, our results demonstrate that different nbas variants differentially affect skeletal development, suggesting complex spectrums of phenotypic and pathogenic mechanisms in NBAS-associated atypical OI.

genetics↗

bioRxiv2024

A 3D Image Segmentation Study of U-Net on CT Images of the Human Aorta with Morphologically Diverse Anatomy

For the machine learning -assisted diagnosis of cardiac diseases, such as thoracic aortic aneurysm, the geometries of the heart and blood vessels need to be reconstructed from medical images, which is usually done by image segmentation followed by meshing. In this study, we applied U-Net (2D and 3D versions), a deep neural network with a U-shaped architecture, to segment human aorta from CT images. From our experiments, we have the following observations: (1) 2D U-Net, which segments each of the 2D slices of a 3D CT image independently, produced erroneous fragments (e.g., missing part of the aorta) and boundaries (i.e., aortic walls) in 3D; (2) 3D U-Net, which does segmentation in 3D regions of a 3D CT image, performed much better than 2D U-Net. We also observe the major weakness of the 3D U-Net: the reconstructed geometries of the aortic wall had large errors (measured by HD95) for some cases. The 3D U-Net in this study serves as a baseline for developing more advanced architectures of deep neural networks for more accurate geometry reconstruction of human aorta.

bioengineering↗

bioRxiv2024

Neurological Research in 47 Asian Countries

Neurology research in the Asian region has seen significant growth and development over the past decade, yet comprehensive analyses of its progress remain scarce. This study aims to address this gap by providing a detailed examination of neurology research in 47 Asian countries from 2013 to 2022. Data was extracted from the Scopus database, encompassing scholarly output, citations, and citation impact metrics. Findings reveal a total of 128,306 research documents published with 1,725,678 total citations, demonstrating a commendable level of research activity. However, disparities exist among countries, with China, Japan, and Australia emerging as leading contributors in terms of both quantity and citation impact. Despite this, a substantial number of countries and universities have published fewer than 100 papers, indicating room for improvement and the need for targeted capacity-building efforts.

neuroscience↗

bioRxiv2024

Multiparameter Quantitative Analyses of Diagnostic Cells in Brain Tissues from Tuberous Sclerosis Complex

The advent of high-dimensional imaging approaches offers innovative opportunities to molecularly characterize diagnostic cells in disorders that have previously relied on histopathological definitions. One example of such disorders is tuberous sclerosis complex (TSC), a developmental disorder characterized by systemic growth of benign tumors. Within resected brain tissues from patients with TSC, detection of abnormally enlarged balloon cells (BCs) is pathognomonic for this disorder. Though BCs can be identified by an expert neuropathologist, little is known about the specificity and broad applicability of protein markers for these cells, complicating classification of proposed BCs identified in experimental models of this disorder. Here, we report the development of a customized machine-learning workflow (Balloon Identifier; BAIDEN) that was trained to prospectively identify BCs in tissue sections using a histological stain compatible with high-dimensional cytometry. This approach was coupled to a custom antibody panel and 36-parameter imaging mass cytometry (IMC) to explore the expression of multiple previously proposed BC markers and develop a descriptor of BC features conserved across multiple tissue samples from patients with TSC. These findings comprise a toolbox and dataset for understanding the abundance, structure, and signaling activity of these histopathologically abnormal cells, and an example case of how such tools can be developed and applied within human tissues.

neuroscience↗

bioRxiv2024

Heterologous expression and characterization of mutant cellulase from indigenous strain of Aspergillus niger

The current study highlights the effect of mutagenesis on endoglucanase B activity of indigenous strain of Aspergillus niger and its heterologous expression studies in the pET28a+ vector. The physical and chemical mutagens were employed to incorporate mutations in A. niger. For determination of mutations, mRNA was isolated followed by cDNA synthesis and cellulase gene was amplified, purified and sequenced both from native and mutant A. niger. On comparison of gene sequences, it was observed that 5 nucleotide base pairs have been replaced in the mutant cellulase. The mutant recombinant enzyme showed 4.5 times higher activity (428.5 {micro}mol/mL/min) as compared to activity of native enzyme (94 {micro}mol/mL/min). The mutant gene was further investigated using Phyre2 and I-Tesser tools which exhibited 71% structural homology with Endoglucanase B of Thermoascus aurantiacus. The root mean square deviation (RMSD), root mean square fluctuation (RMSF), solvent accessible surface area (SASA), radius of gyration (Rg) and hydrogen bonds analysis were carried at 35 {degrees}C and 50 {degrees}C to explore the integrity of structure of recombinant mutant endoglucanase B which corresponded to its optimal temperature. Hydrogen bonds analysis showed more stability of recombinant mutant endoglucanase B as compared to native enzyme. Both native and mutant endoglucanase B genes were expressed in pET 28a+ and purified with nickel affinity chromatography. Theoretical masses determined through ExPaSy Protparam were found 38.7 and 38.5 kDa for native and mutant enzymes, respectively. The optimal pH and temperature values for the mutant were 5.0 and 50 {degrees}C while for native these were found 4.0 and 35 {degrees}C, respectively. On reacting with carboxy methyl cellulose (CMC) as substrate, the mutant enzyme exhibited less Km (0.452 mg/mL) and more Vmax (50.25 {micro}mol/ml/min) as compared to native having 0.534 mg/mL as Km and 38.76 {micro}mol/ml/min as Vmax. Among metal ions, Mg2+ showed maximum inducing effect (200 %) on cellulase activity at 50 mM concentration followed by Ca2+ (140%) at 100 mM concentration. Hence, expression of a recombinant mutant cellulase from A. niger significantly enhanced its cellulytic potential which could be employed for further industrial applications at pilot scale.

biochemistry↗

bioRxiv2024

Sterol O-acyltransferase (SOAT/ACAT) activity is required to form cholesterol crystals in hepatocyte lipid droplets

ObjectiveExcess unesterified (free) cholesterol can induce formation of cholesterol crystals in hepatocyte lipid droplets. Presence of such crystal distinguishes metabolic dysfunction associated steatohepatitis (MASH) from simple steatosis and may underlie its pathogenesis by causing cell damage that triggers liver inflammation. The mechanism linking cholesterol excess to its crystallization in lipid droplets is unclear. As cholesteryl esters localize to and accumulate in lipid droplets much more readily than free cholesterol, we investigated whether cholesterol esterification by sterol O-acyltransferase (SOAT), also known as acyl co-A cholesterol acyltransferase (ACAT) is required for hepatocyte lipid droplet crystal formation. MethodCholesterol crystals were measured in cholesterol loaded Hep3B hepatocytes, RAW264.7 macrophages and mouse liver using polarizing light microscopy. We examined the effect of blocking SOAT activity on crystal formation and compared these results to cholesterol metabolism and the progression to intracellular crystal deposits. ResultsCholesterol loading of Hep3B cells caused robust levels of lipid droplet localized crystal formation in a dose- and time-dependent manner. Co-treatment with SOAT inhibitors and genetic ablation of SOAT1 blocked crystal formation. SOAT inhibitor also blocked crystal formation in low density lipoprotein (LDL) treated Hep3B cells, acetylated LDL treated RAW 264.7 macrophages, and in the liver of mice genetically predisposed to hepatic cholesterol overload and in mice fed a cholesterol enriched, MASH-promoting diet for 24 weeks. ConclusionSOAT1-mediated esterification may underlie cholesterol crystals associated with MASH by concentrating it in lipid droplets. These findings imply that inhibiting hepatocyte SOAT1 may alleviate cholesterol associated MASH. Moreover, that a lipid droplet localized cholesteryl ester hydrolase may be required for cholesterol crystal formation or, instead, that the crystals are composed of cholesteryl ester. Funding SourcesGrants supporting this research were awarded to SBW from the Natural Sciences and Engineering Research Council of Canada (NSERC). SBW was supported by a National New Investigator Award and McDonald Scholarship from the Heart and Stroke Foundation of Canada. UN and MA were supported by a James Regan Cardiology Research scholarship from University of Saskatchewans College of Medicine.

molecular biology↗

bioRxiv2024

Four Years of COVID-19: Saudi Arabia, Egypt and Pakistan Have the Highest Research Growth Rates From 2020-2023

We tried to assess the global research scholarly output after COVID-19 (from 2020 to 2023). Based on Scopus record, the world has produced 15, 041, 579 publications with 86, 165, 933 citations. We analyzed those countries, which have published at least 150, 000 research papers. For each country, we retrieved total number of publications, % growth rate, total citations, citations per paper, Field Weighted Citation Impact (FWCI), and % international collaboration. Twenty-seven (n=27) countries were found to be highly productive, with China leading the way in number of publications. Citation metrics are dominated by the USA, China, and European countries. Specifically, Switzerland, Netherlands, and Australia are notable for their high impact and influence. Saudi Arabia achieved the highest growth rate of 53.5%, and highest international collaboration (76.5%). Infact Saudi Arabia also attained high citations per article (8.8), and an FWCI of 1.63. While, Pakistan exhibited an 8.4 citations per article, FWCI of 1.54, growth rate of 34.9%, and collaborative percentage of 64.9%. Egypt also attained the 2nd highest growth rate (n=36.1). Based on four (n=4) distinct performance metrics, Pakistan and Saudi Arabia were in the top ten group.

scientific communication and education↗

bioRxiv2022

Anatomical and Palynological Investigation within flora of Family Asteraceae

A comprehensive microscopic investigation of the leaf epidermis, as well as anatomical and palynological research of selected Asteraceae species from the flora of Havali (Kahutta) Azad Jammu and Kashmir (AJK) Pakistan, was carried out. This study includes 11 plant species comprising of Senecio jacobea, Leucanthemum vulgare, Halianthus annuus, Erigeron bonariensis, Achillea millifolium, Halianthus Linnaeus, Taraxacum officinale, Anaphalius nepalensis, Erigeron Canadensis, and Tagetes erecta. All the species studied were amphistomatic, with four different forms of stomata i.e tetracytic, anomocytic, anisocytic, and tricytic. The main stomatal type was tetracytic, followed by anomocytic. The abaxial epidermis has a higher stomatal density than the adaxial epidermis. Highest stomatal density was present Tagetes erecta while lowest is present in Conyza canadensis. In lower epidermis stomatal index was higher in Taraxacum officinale followed by Halianthus annuus and Tagetes erecta while in upper epidermis highest index was shown by Halianthus annuus. For this study species of family Acteraceae were properly collected. Furthermore, variation in pollen can be seen. List of palynomorph which includes family name, botanical name, local name, English name, flower colour, season and pollen description for the logical arrangement of these species. The logical ordering of these species was guided by dust characteristics such as form and pollen morphology. Palynological data has been found to be too big for taxonomists to calculate and make appropriate observations on their findings.

plant biology↗

bioRxiv2021

Acid sphingomyelinase deactivation post-ischemia/ reperfusion promotes cerebral angiogenesis and brain remodeling via small extracellular vesicles

Functional inhibitors of acid sphingomyelinase are clinically used as anti-depressants since [~]60 years. Here, we show that acid sphingomyelinase inhibition by the antidepressants amitriptyline, fluoxetine and desipramine protects from ischemia/reperfusion and elicits a profound brain remodeling response with increased angiogenesis, improved blood-brain barrier integrity, reduced brain leukocyte infiltration and increased neuronal survival. Angiogenesis is promoted by small extracellular vesicles with bona fide characteristics of exosomes, which are released from endothelial cells and which constitute an elegant target for the amplification of stroke recovery.

neuroscience↗

bioRxiv2020

Clarithromycin Exerts an Antibiofilm Effect against Salmonella typhimurium rdar Biofilm Formation, and Transforms the Physiology towards an Apparent Oxygen-depleted Energy and Carbon Metabolism

Upon biofilm formation, production of extracellular matrix components and alteration in physiology and metabolism allows bacteria to build up multicellular communities which can facilitate nutrient acquisition during unfavorable conditions and provide protection towards various forms of environmental stresses to individual cells. Thus, bacterial cells become tolerant against antimicrobials and the immune system within biofilms. In the current study, we evaluated the antibiofilm activity of the macrolides clarithromycin and azithromycin. Clarithromycin showed antibiofilm activity against rdar (red, dry and rough) biofilm formation of the gastrointestinal pathogen Salmonella typhimurium ATCC14028 Nalr at 1.56 M subinhibitory concentration in standing culture and dissolved cell aggregates at 15 M in a microaerophilic environment suggesting that the oxygen level affects the activity of the drug. Treatment with clarithromycin significantly decreased transcription and production of the rdar biofilm activator CsgD, with biofilm genes such as csgB and adrA to be consistently downregulated. While fliA and other flagellar regulon genes were upregulated, apparent motility was downregulated. RNA sequencing showed a holistic cell response upon clarithromycin exposure, whereby not only genes involved in the biofilm-related regulatory pathways, but also genes that likely contribute to intrinsic antimicrobial resistance, and the heat shock stress response were differentially regulated. Most significantly, clarithromycin exposure shifts the cells towards an apparent oxygen- and energy-depleted status, whereby the metabolism that channels into oxidative phosphorylation is downregulated, and energy gain by degradation of propane 1,2-diol, ethanolamine and L-arginine catabolism is upregulated. This initial analysis will allow the subsequent identification of novel intrinsic antimicrobial resistance determinants.

microbiology↗

bioRxiv2019

KCND3 is a novel susceptibility locus for early repolarization

The presence of an early repolarization pattern (ERP) on the surface electrocardiogram (ECG) is associated with risk of ventricular fibrillation and sudden cardiac death. Family studies have shown that ERP is a highly heritable trait but molecular genetic determinants are unknown. We assessed the ERP in 12-lead ECGs of 39,456 individuals and conducted a two-stage meta-analysis of genome-wide association studies (GWAS). In the discovery phase, we included 2,181 cases and 23,641 controls from eight European ancestry studies and identified 19 genome-wide significant (p<5E-8) variants in the KCND3 (potassium voltage gated channel subfamily D member 3) gene with a p-value of 4.6E-10. Replication of two loci in four additional studies including 1,124 cases and 12,510 controls confirmed the association at the KCND3 gene locus with a pooled odds ratio of 0.82, p=7.7E-12 (rs1545300 minor allele T). A subsequent GWAS meta-analysis combining all samples did not reveal additional loci. The lead SNP of the discovery stage (rs12090194) was in strong linkage disequilibrium with rs1545300 (r2=0.96, D=1). Summary statistics based conditional analysis did not reveal any secondary signals. Co-localization analyses indicate causal effects of KCND3 gene expression levels on ERP in both the left ventricle of the heart and in tibial artery.\n\nIn this study we identified for the first time a genome-wide significant association of a genetic variant with ERP. Our findings of a locus in the KCND3 gene not only provide insights into the genetic determinants but also into the pathophysiological mechanism of ERP, revealing a promising candidate for functional studies.

genetics↗