Predominance of MGMT promoter methylation among Pakistani glioblastoma patients.

BACKGROUND: Glioblastoma multiforme (GBM), the most prevalent subgroup of neuroepithelial tumors, is characterized by dismal overall survival (OS). Several studies have linked O6-methylguanine-DNA-methyltransferase (MGMT) promoter methylation to OS in GBM patients. However, MGMT methylation frequencies vary geographically and across ethnicities, with limited data for South Asian populations, including Pakistan. This study aimed to analyze MGMT promoter methylation in Pakistani GBM patients. METHODS: Consecutive primary GBM patients diagnosed ≥ 18 years-of-age, with no prior chemotherapy or radiotherapy history, were retrospectively selected. DNA was isolated from formalin-fixed-paraffin-embedded tissues. MGMT promoter methylation was analyzed using methylation-specific PCR. Clinical, pathological, and treatment data were assessed using Fisher's exact/Chi-squared tests. OS was calculated using Kaplan-Meier analysis in SPSS 27.0.1. RESULTS: The study included 48 GBM patients, comprising 38 (79.2%) males and 10 (20.8%) females. The median diagnosis age was 49.5 years (range 18-70). MGMT methylation was observed in 87.5% (42/48) of all cases. Patients with MGMT methylation undergoing radiotherapy or radiotherapy plus chemotherapy exhibited significantly improved median OS of 7.2 months (95% CI, 3.7-10.7; P < 0.001) and 16.9 months (95% CI, 15.9-17.9; P < 0.001), respectively, compared to those undergoing surgical resection only (OS: 2.2 months, 95% CI, 0.8-3.6). CONCLUSION: This is the first comprehensive study highlighting a predominance of MGMT methylation in Pakistani GBM patients. Furthermore, our findings underscore the association of MGMT methylation with improved OS across diverse treatment modalities. Larger studies are imperative to validate our findings for better management of Pakistani GBM patients.

Immune modulation of goat monocytes by Fasciola gigantica Legumain-1 protein (Fg-LGMN-1).

Legumains belonging to C_13 peptidase family of proteins, and are ubiquitously disseminated among all vertebrate and invertebrate organisms, and have been implicated in innumerable biological and cellular functionality. Herein, we characterized and evaluated immunoregulatory characteristics of Legumain-1 from Fasciola gigantica (Fg-LGMN-1) during its interaction with host immune cells. The isopropyl-ß-d-thiogalactopyranoside (IPTG) stimulated RFg-LGMN-1 protein was positively detected by rat serum containing anti-RFg-LGMN-1 polyclonal antibodies. Furthermore, the uptake of RFg-LGMN-1 by goat monocytes was successfully confirmed using Immunofluorescence Assay (IFA). The immunohistochemical analysis revealed the native localization of LGMN-1 protein on the periphery and internal structures such as suckers, pharynx, and genital pore of the adult parasite, thereby validating its presence in excretory-secretory (ES) products of F. gigantica. The RFg-LGMN-1 co-incubated with concanavalin-A (Con-A) stimulated the increase of interleukin 2 (IL-2), IL-10, and IL-17 in monocytes derived from peripheral blood mononuclear cells (PBMCs) in the concentration-dependent manner. However, the IL-4 cytokine in response to the RFg-LGMN-1 protein declined. These results illuminated the role of LGMN-1 during the parasite-host interface. Our findings elaborated additional evidence that Legumain protein play a role in the manipulating host immune responses during parasite infections. However, further evaluation of RFg-LGMN-1 protein in context of its immunomodulatory roles should be conducted to enhance our understandings of the mechanisms employed by F. gigantica to evade host immune responses.

Effects of dietary chromium supplementation on blood biochemical parameters in dairy cows: A multilevel meta-analytical approach.

Chromium (Cr) has been reported to modulate blood biochemistry in dairy cows. However, there is a discrepancy in the literature regarding the effects of dietary Cr supplementation on various blood parameters. This meta-analysis aimed to evaluate the effects of Cr supplementation in dairy cows on blood glucose, insulin, glucagon, nonesterified fatty acid (NEFA), cortisol, and serum total protein (STP) concentrations. Following relevant literature data extraction, a 3-level meta-analytical random effect model was fitted to the data expressed as standardized mean difference (SMD) of outcome measures of control versus Cr-supplemented cows (i.e., difference in mean between control and treatment group or pooled standard deviation). The SMD can be categorized as having a small effect (0.20), a moderate effect (0.50), and a large effect (0.80). The meta-regression identified the potential sources of heterogeneity, including the body weight of cows, experimental duration/duration of Cr supplementation, blood sampling time (3 wk before parturition until 4 wk after parturition categorized as the transition period, else as the nontransition period), and form of Cr complexes. Blood glucose did not differ significantly between control and Cr-supplemented cows with an estimated SMD of µ = 0.0071 (95% confidence interval [CI]: -0.212 to 0.226). The effect of Cr supplementation on blood insulin was also nonsignificant with an SMD of µ = 0.0007 (95% CI: -0.191 to 0.193). Cows receiving Cr supplements had significantly higher levels of glucagon than controls (95% CI: 0.116 to 0.489), with an estimated SMD = 0.303. Combined transition and nontransition data suggest Cr supplementation did not affect the concentration of NEFA. However, in transition cows, Cr supplementation significantly decreased blood NEFA levels as compared with controls (95% CI: -0.522 to -0.0039), with estimated SMD = -0.263. The estimated SMD was µ = -0.1983 (95% CI: -0.734 to 0.337) for cortisol and -0.0923 (95% CI: -0.316 to 0.131) for total protein. In summary, Cr supplementation in the transition cows decreased NEFA concentration. Blood glucose, insulin, cortisol, and STP concentrations were unaffected. However, Cr supplementation increased glucagon concentration.

Investigating the relationship between heat load and shade seeking behaviour in dairy buffaloes.

The study presented in this Research Communication aimed to investigate the relationship between physiological responses, body surface temperature and shade-seeking behaviour in Nili Ravi dairy buffaloes during summer months. We enrolled 60 buffaloes, and each animal was observed for three consecutive days starting before sunrise until they moved towards the shade structures. A repeated measures ANOVA was employed to assess the changes in physiological parameters and body surface temperature between the early morning and the occurrence of shade-seeking behaviour. The average temperature humidity index and heat load index during the behavioural monitoring period (0400 to 1200 h) were 81.3 ± 6.5 and 92.9 ± 17, respectively (mean ± sd). There was no significant difference in core body temperature between sunrise and the time of shade-seeking event. However, the buffaloes had a slightly higher respiration rate at the time of shade-seeking (19.2 vs. 22.4 breaths/min). In addition, body surface temperature, measured at the flank region, shoulder, base of the ear and forehead was significantly higher at the occurrence of shade-seeking behaviour compared to the early morning. On average, the buffaloes sought shade when the surface temperature was 2°C higher than the temperature recorded before sunrise. Overall, the current findings suggest that body surface temperature, rather than core body temperature was strongly associated with shade-seeking behaviour in dairy buffaloes. These findings could be useful in developing strategies to mitigate the effects of heat stress in dairy buffalo herds and thereby improve animal welfare.

Process optimization of adsorptive phytoremediation of mutagenic brilliant green dye for health risk management using chemically activated Symplocos racemosa agro-waste.

Textile industries use large amounts of water as well as dyes. These dyes containing water are then discharged into the water bodies causing a significant role in water pollution. Brilliant Green dye contributes to many harmful diseases related to the respiratory and gastrointestinal tract. In this study, Symplocos racemosa (SR) agro-waste was chemically treated with acid (SR-HCl) and base (SR-NaOH) and then used for removing Brilliant Green Dye (BGD) on the batch scale. They were characterized by SEM, EDX, FTIR, XRD, TGA and DSC. Optimized conditions were 30 °C temperature, pH 6, adsorbent dose of 0.10 g/25 ml dye solution, shaking speed of 100 revolutions per minute, initial dye concentration of 50 ppm and 35 min time for shaking adsorbent and dye solution. Adsorption data obtained were analyzed using isotherms. The experimental data was found to fit well with the Langmuir model and the maximum adsorption capacity (qmax) of BGD on the SR, SR-HCl, and SR-NaOH was revealed to be 62.90, 65.40, and 71 mg/g respectively. Kinetic data (pseudo-first-order and pseudo-second-order) were evaluated and adsorption tends to follow the pseudo-2nd-order, which indicated the chemisorption mechanism. The results revealed that Symplocos racemosa agro-waste can be considered as the potential biosorbent.

A Dynamic Framework for Internet-Based Network Time Protocol.

Time synchronization is vital for accurate data collection and processing in sensor networks. Sensors in these networks often operate under fluctuating conditions. However, an accurate timekeeping mechanism is critical even in varying network conditions. Consequently, a synchronization method is required in sensor networks to ensure reliable timekeeping for correlating data accurately across the network. In this research, we present a novel dynamic NTP (Network Time Protocol) algorithm that significantly enhances the precision and reliability of the generalized NTP protocol. It incorporates a dynamic mechanism to determine the Round-Trip Time (RTT), which allows accurate timekeeping even in varying network conditions. The proposed approach has been implemented on an FPGA and a comprehensive performance analysis has been made, comparing three distinct NTP methods: dynamic NTP (DNTP), static NTP (SNTP), and GPS-based NTP (GNTP). As a result, key performance metrics such as variance, standard deviation, mean, and median accuracy have been evaluated. Our findings demonstrate that DNTP is markedly superior in dynamic network scenarios, a common characteristic in sensor networks. This adaptability is important for sensors installed in time-critical networks, such as real-time industrial IoTs, where precise and reliable time synchronization is necessary.

Xylooligosaccharide supplementation in rice protein concentrate based diets: A comprehensive analysis of performance and health of Labeo rohita.

The primary aim of this study was to examine the impact of xylooligosaccharide (XOS) in rice protein concentrate (RPC) based diets on the growth performance, body composition, digestive enzymes, intestinal morphology and blood biochemistry of Labeo rohita fingerlings. Four different XOS levels (0%, 0.5%, 1% and 2%) were used at each RPC (75% and 100%) level. Twenty-five fish per tank with an average initial weight of 25 ± 0.05 g were randomly assigned (Randomised complete block design) to each of the 8 groups in triplicate aquaria (36 × 16 × 12″) and then fed with respective diets @ 3% body weight for 90 days. The results showed significant improvements in growth performance, such as increased weight gain %, specific growth rate, and protein efficiency ratio and improved feed conversion ratio in 1% XOS supplemented diet at 75% RPC. A significant decrease in serum alkaline phosphatase activity (ALP) and plasma melanodialdehyde (MDA) were observed at 1% XOS level in 75% RPC based diets, respectively. Meanwhile, the lowest total cholesterol and highest lysozyme activity were observed in 1% XOS supplemented diet at 75% RPC levels. Moreover, the serum (alanine aminotransferase and aspartate transaminase) and plasma (superoxide dismutase, triglyceride, high density and low density lipoprotein) activities showed nonsignificant effects among the treatments. Furthermore, the digestive enzymes (protease & lipase) and intestinal morphology were significantly influenced at 1% XOS in the 75% RPC-based diet. Polynomial regression analysis showed that 1.25% XOS is the optimum requirement for the growth of rohu fingerlings when fed at 75% RPC based diets. Overall, it was concluded that the 75% RPC diet was efficiently replaced by fishmeal along with 1% XOS addition in L. rohita fingerlings without any negative effect on growth performance and intestinal health.

Insights into the involvement of male Hyalomma anatolicum ticks in transmitting Anaplasma marginale, lumpy skin disease virus and Theileria annulata.

Ticks can transmit viruses, bacteria, and parasites to humans, livestock, and pet animals causing tick-borne diseases (TBDs) mechanically or biologically in the world. Lumpy skin disease virus, Anaplasma marginale, and Theileria annulata inflict severe infections in cattle, resulting in significant economic losses worldwide. The study investigated the potential transmissions of LSDV, A. marginale, and T. annulata through male Hyalomma anatolicum ticks in cattle calves. Two 6-month-old Holstein crossbred calves designated as A and B were used. On day 1, 15 uninfected female ticks (IIa) and infected batch of 40 male ticks (I) were attached on calf A for 11 days. Filial transmission of the infections was observed in female ticks (IIb) collected from calf A, where 8 female ticks had been co-fed with infected male ticks. The blood sample of calf B was found positive through PCR for the infections. The larvae and egg pools obtained from the infected ticks were also tested positive in PCR. The study confirmed the presence of these mixed pathogens and potential intra-stadial and transovarial transmissions of A. marginale, T. annulata, and LSDV in male and female ticks of H. anatolicum and experimental calves to establish the feasibility of infections through an in vivo approach.

Safety and Efficacy of High-Intensity Focused Ultrasound and Monopolar Radiofrequency Combination Therapy for Skin Tightening: A Retrospective Study in Malaysia.

Background: High-intensity focused ultrasound (HIFU) and monopolar radiofrequency (MRF) are common treatment modalities that have shown significant results in skin tightening. Nevertheless, the novel combination of these two treatments is new to the Malaysian landscape. Thus, this study aims to investigate the safety and efficacy of this novel combination treatment for the Malaysian population. Methods: This retrospective study included data on HIFU and MRF combination therapy for skin tightening collected from an aesthetic clinic in Johor Bahru, Malaysia from June 2018 to May 2021. Efficacy was assessed using the Global Aesthetic Improvement Scale (GAIS) and Glogau classification, while the safety of the treatment was analysed using pain scores and adverse events (AEs). Results: A total of 56 patients with a mean age of 47.7 years old (SD 10.00) were included in this study. The majority of the patients had Fitzpatrick skin types III and IV. Most of the patients were Chinese, followed by Malay, Indian and others. Most patients (96.4%) showed clinically significant improvement in skin tightening after treatment, with 15 patients scoring 1 (very much improved) and 39 scoring 2 (improved). All patients reported transient mild erythema, with no serious AEs, such as burn, swelling, numbness or muscle weakness. Among the patients, 80% reported a pain score of 5, while 10% reported pain scores of 4 and 6. Conclusion: Combining HIFU with MRF therapy improved GAIS scores by 96.4%, indicating a secure and efficient skin-tightening method. Transient erythema was shown to be the most common side effect of this combination.

In-silico analysis of heat shock transcription factor (OsHSF) gene family in rice (Oryza sativa L.).

BACKGROUND: One of the most important cash crops worldwide is rice (Oryza sativa L.). Under varying climatic conditions, however, its yield is negatively affected. In order to create rice varieties that are resilient to abiotic stress, it is essential to explore the factors that control rice growth, development, and are source of resistance. HSFs (heat shock transcription factors) control a variety of plant biological processes and responses to environmental stress. The in-silico analysis offers a platform for thorough genome-wide identification of OsHSF genes in the rice genome. RESULTS: In this study, 25 randomly dispersed HSF genes with significant DNA binding domains (DBD) were found in the rice genome. According to a gene structural analysis, all members of the OsHSF family share Gly-66, Phe-67, Lys-69, Trp-75, Glu-76, Phe-77, Ala-78, Phe-82, Ile-93, and Arg-96. Rice HSF family genes are widely distributed in the vegetative organs, first in the roots and then in the leaf and stem; in contrast, in reproductive tissues, the embryo and lemma exhibit the highest levels of gene expression. According to chromosomal localization, tandem duplication and repetition may have aided in the development of novel genes in the rice genome. OsHSFs have a significant role in the regulation of gene expression, regulation in primary metabolism and tolerance to environmental stress, according to gene networking analyses. CONCLUSION: Six genes viz; Os01g39020, Os01g53220, Os03g25080, Os01g54550, Os02g13800 and Os10g28340 were annotated as promising genes. This study provides novel insights for functional studies on the OsHSFs in rice breeding programs. With the ultimate goal of enhancing crops, the data collected in this survey will be valuable for performing genomic research to pinpoint the specific function of the HSF gene during stress responses.

Combined transcriptome and metabolome analysis reveals the effects of light quality on maize hybrids.

BACKGROUND: Heterosis, or hybrid vigor, refers to the phenotypic superiority of an F1 hybrid relative to its parents in terms of growth rate, biomass production, grain yield, and stress tolerance. Light is an energy source and main environmental cue with marked impacts on heterosis in plants. Research into the production applications and mechanism of heterosis has been conducted for over a century and a half, but little is known about the effect of light on plant heterosis. RESULTS: In this study, an integrated transcriptome and metabolome analysis was performed using maize (Zea mays L.) inbred parents, B73 and Mo17, and their hybrids, B73 × Mo17 (BM) and Mo17 × B73 (MB), grown in darkness or under far-red, red, or blue light. Most differentially expressed genes (73.72-92.50%) and differentially accumulated metabolites (84.74-94.32%) exhibited non-additive effects in BM and MB hybrids. Gene Ontology analysis revealed that differential genes and metabolites were involved in glutathione transfer, carbohydrate transport, terpenoid biosynthesis, and photosynthesis. The darkness, far-red, red, and blue light treatments were all associated with phenylpropanoid-flavonoid biosynthesis by Weighted Gene Co-expression Network Analysis and Kyoto Encyclopedia of Genes and Genomes enrichment analysis. Five genes and seven metabolites related to phenylpropanoid-flavonoid biosynthesis pathway were identified as potential contributors to the interactions between maize heterosis and light conditions. Consistent with the strong mid-parent heterosis observed for metabolites, significant increases in both fresh and dry weights were found in the MB and BM hybrids compared with their inbred parents. Unexpectedly, increasing light intensity resulted in higher biomass heterosis in MB, but lower biomass heterosis in BM. CONCLUSIONS: The transcriptomic and metabolomic results provide unique insights into the effects of light quality on gene expression patterns and genotype-environment interactions, and have implications for gene mining of heterotic loci to improve maize production.

Genomic diversity of aquaporins across genus Oryza provides a rich genetic resource for development of climate resilient rice cultivars.

BACKGROUND: Plant aquaporins are critical genetic players performing multiple biological functions, especially climate resilience and water-use efficiency. Their genomic diversity across genus Oryza is yet to be explored. RESULTS: This study identified 369 aquaporin-encoding genes from 11 cultivated and wild rice species and further categorized these into four major subfamilies, among which small basic intrinsic proteins are speculated to be ancestral to all land plant aquaporins. Evolutionarily conserved motifs in peptides of aquaporins participate in transmembrane transport of materials and their relatively complex gene structures provide an evolutionary playground for regulation of genome structure and transcription. Duplication and evolution analyses revealed higher genetic conservation among Oryza aquaporins and strong purifying selections are assisting in conserving the climate resilience associated functions. Promoter analysis highlighted enrichment of gene upstream regions with cis-acting regulatory elements involved in diverse biological processes, whereas miRNA target site prediction analysis unveiled substantial involvement of osa-miR2102-3p, osa-miR2927 and osa-miR5075 in post-transcriptional regulation of gene expression patterns. Moreover, expression patterns of japonica aquaporins were significantly perturbed in response to different treatment levels of six phytohormones and four abiotic stresses, suggesting their multifarious roles in plants survival under stressed environments. Furthermore, superior haplotypes of seven conserved orthologous aquaporins for higher thousand-grain weight are reported from a gold mine of 3,010 sequenced rice pangenomes. CONCLUSIONS: This study unveils the complete genomic atlas of aquaporins across genus Oryza and provides a comprehensive genetic resource for genomics-assisted development of climate-resilient rice cultivars.

Utilization of natural alleles for heat adaptability QTLs at the flowering stage in rice.

BACKGROUND: Heat stress threatens rice yield and quality at flowering stage. In this study, average relative seed setting rate under heat stress (RHSR) and genotypes of 284 varieties were used for a genome-wide association study. RESULTS: We identified eight and six QTLs distributed on chromosomes 1, 3, 4, 5, 7 and 12 in the full population and indica, respectively. qHTT4.2 was detected in both the full population and indica as an overlapping QTL. RHSR was positively correlated with the accumulation of heat-tolerant superior alleles (SA), and indica accession contained at least two heat-tolerant SA with average RHSR greater than 43%, meeting the needs of stable production and heat-tolerant QTLs were offer yield basic for chalkiness degree, amylose content, gel consistency and gelatinization temperature. Chalkiness degree, amylose content, and gelatinization temperature under heat stress increased with accumulation of heat-tolerant SA. Gel consistency under heat stress decreased with polymerization of heat-tolerant SA. The study revealed qHTT4.2 as a stable heat-tolerant QTL that can be used for breeding that was detected in the full population and indica. And the grain quality of qHTT4.2-haplotype1 (Hap1) with chalk5, wx, and alk was better than that of qHTT4.2-Hap1 with CHALK5, WX, and ALK. Twelve putative candidate genes were identified for qHTT4.2 that enhance RHSR based on gene expression data and these genes were validated in two groups. Candidate genes LOC_Os04g52830 and LOC_Os04g52870 were induced by high temperature. CONCLUSIONS: Our findings identify strong heat-tolerant cultivars and heat-tolerant QTLs with great potential value to improve rice tolerance to heat stress, and suggest a strategy for the breeding of yield-balance-quality heat-tolerant crop varieties.

Contribution of constitutional BRCA1 promoter methylation to early-onset and familial breast cancer patients from Pakistan.

PURPOSE: Constitutional BRCA1 promoter methylation has been identified as a potential risk factor for breast cancer (BC) in the Caucasian population. However, this data is lacking for BC patients of Asian origin. Therefore, we assessed the contribution of constitutional BRCA1 promoter methylation in Pakistani BC patients. METHODS: A total of 385 BRCA1/2-negative index BC patients (197 early-onset BC (≤ 30 years), 152 familial BC, 17 familial BC and ovarian cancer, 19 male BC) and 107 healthy controls were screened for the constitutional BRCA1 promoter methylation by methylation-sensitive high-resolution melting assay. Overall, 131 patients displayed triple-negative BC (TNBC) and 254 non-TNBC phenotypes. The prevalence of BRCA1 promoter methylation was calculated based on clinicopathological characteristics using univariable and multivariable logistic regression models. RESULTS: Constitutional BRCA1 promoter methylation was identified in 19.5% (75/385) of BC patients and 13.1% (14/107) of controls. The frequency of methylation was higher in early-onset BC (23.4% vs. 13.1%, P = 0.035) and TNBC patients (29.0% vs. 13.1%, P = 0.004) compared to controls. Methylation was also more prevalent in patients with high-grade than low-grade tumors (21.7% vs. 12.2%, P = 0.034) and progesterone receptor (PR)-negative than PR-positive tumors (26.0% vs. 13.9%, P = 0.004). Constitutional BRCA1 promoter methylation remained independently associated with TNBC phenotype (odds ratio 1.99; 95% CI 1.12-3.54; P = 0.02) after adjusting for BC diagnosis age, tumor grade, ER, and PR status. CONCLUSION: Constitutional BRCA1 promoter methylation is associated with TNBC and can serve as a non-invasive blood-based biomarker for Pakistani TNBC patients.

Complex high-risk percutaneous coronary intervention types, trends, and outcomes according to vascular access site.

BACKGROUND: Radial access is associated with improved outcomes following percutaneous coronary intervention (PCI); however, its role in complex, high-risk percutaneous coronary intervention (CHiP) remains poorly studied. METHODS: We studied retrospectively all registered patients's records from the British Cardiovascular Intervention Society dataset and compared the baseline characteristics, trends and outcomes of CHiP procedures performed electively between January 2006 and December 2017 according to the access site. RESULTS: Out of 137,785 CHiP procedures, 61,825 (44.9%) were undertaken via transradial access (TRA). TRA use increased over time (14.6% in 2006 to 67% in 2017). The TRA patients were older, with a greater prevalence of previous stroke, hypertension, peripheral vascular disease, and smokers. TRA was used more frequently in most CHiP procedures (elderly (51.6%), chronic renal failure (52.6%), poor left ventricular (LV) function (47.6%), left main PCI (48.0%), treatment for severe vascular calcification (50.3%); although transfemoral access (TFA) was used more commonly in those with prior history of coronary artery bypass graft surgery, and PCI to a chronic total occlusion and LV support patients. Following adjustment for differences in clinical and procedural characteristics, TFA was independently associated with higher odds for mortality [adjusted odds ratio (aOR): 1.3 (1.1-1.7)], major bleeding [aOR: 2.9 (2.3-3.4)], and MACCE (following propensity score matching) [aOR: 1.2 (1.1-1.4)]. The same was found with multiple accesses: mortality [aOR: 2.1 (1.5-2.8)], major bleeding [aOR: 5.5 (4.3-6.9)], and MACCE [aOR: 1.4 (1.2-1.7)]. CONCLUSION: TRA has become the predominant access site for CHiP procedures and is associated with significantly lower mortality, major bleeding and MACCE odds than TFA.

Genetic analysis of ACE2 peptidase domain in SARS-CoV-2-positive and SARS-CoV-2-negative individuals from Pakistan.

BACKGROUND: The outbreak of coronavirus disease 2019 (COVID-19) has emerged as a serious public health emergency of global concern. Angiotensin converting enzyme 2 (ACE2) peptidase domain is important for the cellular entry of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Germline variants in ACE2 peptidase domain may influence the susceptibility for SARS-CoV-2 infection and disease severity in the host population. ACE2 genetic analysis among Caucasians showed inconclusive results. This is the first Asian study investigating the contribution of ACE2 germline variants to SARS-CoV-2 infection in Pakistani population. METHODS: In total, 442 individuals, including SARS-CoV-2-positive (n = 225) and SARS-CoV-2-negative (n = 217) were screened for germline variants in ACE2 peptidase domain (exons 2, 3, 9, and 10) using high resolution melting and denaturing high-performance liquid chromatography analyses followed by DNA sequencing of variant fragments. The identified variant was analyzed by in silico tools for potential effect on ACE2 protein. RESULTS: A missense variant, p.Lys26Arg, was identified in one SARS-CoV-2-positive (1/225; 0.4%) and three SARS-CoV-2-negative (3/217; 1.4%) individuals. No significant difference in the minor allele frequency of this variant was found among SARS-CoV-2-positive and SARS-CoV-2-negative individuals (1/313; 0.3% versus 3/328; 0.9%; P = 0.624), respectively. The SARS-CoV-2-positive patient carrying p.Lys26Arg showed mild COVID-19 disease symptoms. It was predicted as benign variant by in silico tool. No variant was detected in ACE2 residues important for binding of SARS-CoV-2 spike protein. CONCLUSION: The p.Lys26Arg variant may have no association with SARS-CoV-2 susceptibility in Pakistani population. Whole ACE2 gene screening is warranted to clarify its role in SARS-CoV-2 infection.

Prevalence of BRCA1 and BRCA2 germline variants in an unselected pancreatic cancer patient cohort in Pakistan.

BACKGROUND: BRCA1 and BRCA2 (BRCA1/2) are the most frequently investigated genes among Caucasian pancreatic cancer patients, whereas limited reports are available among Asians. We aimed to investigate the prevalence of BRCA1/2 germline variants in Pakistani pancreatic cancer patients. METHODS: One hundred and fifty unselected and prospectively enrolled pancreatic cancer patients were comprehensively screened for BRCA1/2 germline variants using denaturing high-performance liquid chromatography and high-resolution melting analyses, followed by DNA sequencing of the variant fragments. The novel variants were analyzed for their pathogenic effect using in-silico tools. Potentially functional variants were further screened in 200 cancer-free controls. RESULTS: Protein truncating variant was detected in BRCA2 only, with a prevalence of 0.7% (1/150). A frameshift BRCA2 variant (p.Asp946Ilefs*14) was identified in a 71-year-old male patient of Pathan ethnicity, with a family history of abdominal cancer. Additionally, we found a novel variant in BRCA2 (p.Glu2650Gln), two previously reported variants in BRCA1 (p.Thr293Ser) and BRCA2 (p.Ile2296Leu) and a recurrent nonsense variant in BRCA2 (p.Lys3326Ter). These variants were classified as variants of uncertain significance (VUS). It is noteworthy that none of these VUS carriers had a family history of pancreatic or other cancers. CONCLUSIONS: In this first study, BRCA1/2 pathogenic variant is identified with a low frequency in pancreatic cancer patients from Pakistan. Comprehensive multigene panel testing is recommended in the Pakistani pancreatic cancer patients to enhance genetic understanding in this population.

Molecular detection of Toxoplasma gondii among commensal rodents from the Sahiwal division, Punjab, Pakistan.

Toxoplasmosis is a zoonotic disease in humans and animals caused by the protozoan parasite Toxoplasma gondii. Rodents not only act as intermediate hosts for T. gondii but are also a significant source of T. gondii infection for other hosts. There is limited information about the prevalence of this protozoan within rodents in Pakistan. The current study was conducted to determine the prevalence of T. gondii in commensal rodents as well as associated risk factors. A total of 236 rats including Rattus rattus and Rattus norvegicus were captured from three districts of the Sahiwal division in Punjab province, Pakistan. Brain samples were collected from each specimen. Data was gathered about rodent species, gender, age, location, districts, seasonality, and habitat type. PCR assays were used to screen for T. gondii from the brain samples. A Chi-square analysis was used to investigate the association between positive samples and risk factors. A total of 236 rodent spleen samples were examined for detection of the B1 and SAG3 genes of T. gondii DNA by conventional PCR, and 14 (5.9%) were positive. T. gondii prevalence was higher in R. norvegicus (8.2%) compared to R. rattus (4.6%). All risk factors were statistically non-significant. This study provides evidence of T. gondii in rodents in the Sahiwal division and indicates that other animals and humans are at risk of infection.

Comparative evaluation of cell-mediated immune response in calves immunized with live-attenuated and killed Theileria annulata vaccines.

Tropical theileriosis is a tick-borne disease caused by the protozoan Theileria annulata and transmitted by numerous species of Ixodid ticks of the genus Hyalomma. The main clinical signs are fever, lymphadenopathy, and anemia responsible for heavy economic losses, including mortality, morbidity, vaccination failure, and treatment cost. Development of poor cell-mediated immunity (CMI) has been observed in the case of many bovine pathogens (bacteria, viruses, and parasites). Quantification of CMI is a prerequisite for evaluating vaccine efficacy against theileriosis caused by T. annulata. The current study evaluated the CMI in calves administered with two types of T. annulata vaccine (live attenuated and killed). We prepared a live attenuated T. annulata vaccine by attenuation in a rabbit model and also prepared killed vaccine from non-attenuated T. annulata. For the evaluation of immune response in experimental groups including control, 20 calves were divided into four different groups (A, B, C, and D). They were either inoculated subcutaneously with live rabbit-propagated-Theileria-infected RBCs (5 × 106) (group A) or with killed T. annulata vaccine (2 × 109 schizonts) with Freund's adjuvant (group B), along with an infected group (group C) and a healthy control group (group D). The protection of vaccinated calves was estimated with challenge infection. Our results showed that with a single shot of live-attenuated and killed vaccine with a booster dose elicited cell-mediated immune responses in immunized calves. We observed a significant elevation in CD4 + and CD8 + T cells in immunized calves. A significant difference in the CD8 + T cell response between the post-challenge stage of killed and live vaccine (p < 0.0001) was observed, whereas no other difference was found at both pre- and post-immunization stages. A similar finding was recorded for the CD4 + T cells at a post-challenge stage, where a significant difference was seen between killed and live vaccine (p < 0.0001). Another significant difference was observed between the CD8 + T cells and CD4 + T cells at the post-challenge stage in the live vaccine group, where there was a significantly higher induction of CD4 + T cell response (p < 0.0001).

Algorithms and Techniques for the Structural Health Monitoring of Bridges: Systematic Literature Review.

Structural health monitoring (SHM) systems are used to analyze the health of infrastructures such as bridges, using data from various types of sensors. While SHM systems consist of various stages, feature extraction and pattern recognition steps are the most important. Consequently, signal processing techniques in the feature extraction stage and machine learning algorithms in the pattern recognition stage play an effective role in analyzing the health of bridges. In other words, there exists a plethora of signal processing techniques and machine learning algorithms, and the selection of the appropriate technique/algorithm is guided by the limitations of each technique/algorithm. The selection also depends on the requirements of SHM in terms of damage identification level and operating conditions. This has provided the motivation to conduct a Systematic literature review (SLR) of feature extraction techniques and pattern recognition algorithms for the structural health monitoring of bridges. The existing literature reviews describe the current trends in the field with different focus aspects. However, a systematic literature review that presents an in-depth comparative study of different applications of machine learning algorithms in the field of SHM of bridges does not exist. Furthermore, there is a lack of analytical studies that investigate the SHM systems in terms of several design considerations including feature extraction techniques, analytical approaches (classification/ regression), operational functionality levels (diagnosis/prognosis) and system implementation techniques (data-driven/model-based). Consequently, this paper identifies 45 recent research practices (during 2016-2023), pertaining to feature extraction techniques and pattern recognition algorithms in SHM for bridges through an SLR process. First, the identified research studies are classified into three different categories: supervised learning algorithms, neural networks and a combination of both. Subsequently, an in-depth analysis of various machine learning algorithms is performed in each category. Moreover, the analysis of selected research studies (total = 45) in terms of feature extraction techniques is made, and 25 different techniques are identified. Furthermore, this article also explores other design considerations like analytical approaches in the pattern recognition process, operational functionality and system implementation. It is expected that the outcomes of this research may facilitate the researchers and practitioners of the domain during the selection of appropriate feature extraction techniques, machine learning algorithms and other design considerations according to the SHM system requirements.