VPatho: a deep learning-based two-stage approach for accurate prediction of gain-of-function and loss-of-function variants.

Determining the pathogenicity and functional impact (i.e. gain-of-function; GOF or loss-of-function; LOF) of a variant is vital for unraveling the genetic level mechanisms of human diseases. To provide a 'one-stop' framework for the accurate identification of pathogenicity and functional impact of variants, we developed a two-stage deep-learning-based computational solution, termed VPatho, which was trained using a total of 9619 pathogenic GOF/LOF and 138 026 neutral variants curated from various databases. A total number of 138 variant-level, 262 protein-level and 103 genome-level features were extracted for constructing the models of VPatho. The development of VPatho consists of two stages: (i) a random under-sampling multi-scale residual neural network (ResNet) with a newly defined weighted-loss function (RUS-Wg-MSResNet) was proposed to predict variants' pathogenicity on the gnomAD_NV + GOF/LOF dataset; and (ii) an XGBOD model was constructed to predict the functional impact of the given variants. Benchmarking experiments demonstrated that RUS-Wg-MSResNet achieved the highest prediction performance with the weights calculated based on the ratios of neutral versus pathogenic variants. Independent tests showed that both RUS-Wg-MSResNet and XGBOD achieved outstanding performance. Moreover, assessed using variants from the CAGI6 competition, RUS-Wg-MSResNet achieved superior performance compared to state-of-the-art predictors. The fine-trained XGBOD models were further used to blind test the whole LOF data downloaded from gnomAD and accordingly, we identified 31 nonLOF variants that were previously labeled as LOF/uncertain variants. As an implementation of the developed approach, a webserver of VPatho is made publicly available at http://csbio.njust.edu.cn/bioinf/vpatho/ to facilitate community-wide efforts for profiling and prioritizing the query variants with respect to their pathogenicity and functional impact.

Management of Tomato Bacterial Canker Disease by the Green Fabricated Silver Nanoparticles.

Bacterial canker disease caused by Clavibacter michiganensis is a substantial threat to the cultivation of tomatoes, leading to considerable economic losses and global food insecurity. Infection is characterized by white raised lesions on leaves, stem, and fruits with yellow to tan patches between veins, and marginal necrosis. Several agrochemical substances have been reported in previous studies to manage this disease but these were not ecofriendly. Thus present study was designed to control the bacterial canker disease in tomato using green fabricated silver nanoparticles (AgNps). Nanosilver particles (AgNPs) were synthesized utilizing Moringa oleifera leaf extract as a reducing and stabilizing agent. Synthesized AgNPs were characterized using UV-visible spectroscopy, scanning electron microscopy (SEM), X-ray diffraction (XRD), energy-dispersive X-ray (EDX), and Fourier transform infrared spectrometry (FTIR). FTIR showed presence of bioactive compounds in green fabricated AgNPs and UV-visible spectroscopy confirmed the surface plasmon resonance (SPR) band in the range of 350 nm to 355 nm. SEM showed the rectangular segments fused together, and XRD confirmed the crystalline nature of the synthesized AgNPs. The presence of metallic silver ions was confirmed by an EDX detector. Different concentrations (10, 20, 30, and 40 ppm) of the green fabricated AgNPs were exogenously applied on tomato before applying an inoculum of Clavibacter michigensis to record the bacterial canker disease incidence at different day intervals. The optimal concentration of AgNPs was found to be 30 µg/mg that exhibited the most favorable impact on morphological (shoot length, root length, plant fresh and dry weights, root fresh and dry weights) and physiological parameters (chlorophyll contents, membrane stability index, and relative water content) as well as biochemical parameters (proline, total soluble sugar and catalase activity). These findings indicated a noteworthy reduction in biotic stress through the increase of both enzymatic and non-enzymatic activities by the green fabricated AgNPs. This study marks a first biocompatible approach in assessing the potential of green fabricated AgNPs in enhancing the well-being of tomato plants that affected with bacterial canker and establishing an effective management strategy against Clavibacter michiganensis. This is the first study suggests that low concentration of green fabricated nanosilvers (AgNPs) from leaf extract of Moringa oleifera against Clavibacter michiganensis is a promisingly efficient and eco-friendly alternative approach for management of bacterial canker disease in tomato crop.

Prediction of disease-associated nsSNPs by integrating multi-scale ResNet models with deep feature fusion.

More than 6000 human diseases have been recorded to be caused by non-synonymous single nucleotide polymorphisms (nsSNPs). Rapid and accurate prediction of pathogenic nsSNPs can improve our understanding of the principle and design of new drugs, which remains an unresolved challenge. In the present work, a new computational approach, termed MSRes-MutP, is proposed based on ResNet blocks with multi-scale kernel size to predict disease-associated nsSNPs. By feeding the serial concatenation of the extracted four types of features, the performance of MSRes-MutP does not obviously improve. To address this, a second model FFMSRes-MutP is developed, which utilizes deep feature fusion strategy and multi-scale 2D-ResNet and 1D-ResNet blocks to extract relevant two-dimensional features and physicochemical properties. FFMSRes-MutP with the concatenated features achieves a better performance than that with individual features. The performance of FFMSRes-MutP is benchmarked on five different datasets. It achieves the Matthew's correlation coefficient (MCC) of 0.593 and 0.618 on the PredictSNP and MMP datasets, which are 0.101 and 0.210 higher than that of the existing best method PredictSNP1. When tested on the HumDiv and HumVar datasets, it achieves MCC of 0.9605 and 0.9507, and area under curve (AUC) of 0.9796 and 0.9748, which are 0.1747 and 0.2669, 0.0853 and 0.1335, respectively, higher than the existing best methods PolyPhen-2 and FATHMM (weighted). In addition, on blind test using a third-party dataset, FFMSRes-MutP performs as the second-best predictor (with MCC and AUC of 0.5215 and 0.7633, respectively), when compared with the other four predictors. Extensive benchmarking experiments demonstrate that FFMSRes-MutP achieves effective feature fusion and can be explored as a useful approach for predicting disease-associated nsSNPs. The webserver is freely available at http://csbio.njust.edu.cn/bioinf/ffmsresmutp/ for academic use.

Pre-operative psoas muscle index, a surrogate for sarcopenia; as a predictor of post-esophagectomy complications.

BACKGROUND: Esophagectomy is the standard of care for curative esophageal cancer. However, it is associated with significant morbidity and mortality. Esophageal cancer is known to negatively affect the nutritional status of patients and many manifest cancer sarcopenia. At present, measures of sarcopenia involve complex and often subjective measurements. We assess whether the Psoas Muscle Index (PMI); an inexpensive, simple, validated method used to diagnose sarcopenia, can be used to predict adverse outcomes in patients after curative esophagectomy. METHODS: Multi-centre, retrospective cohort between 2010-2020, involving all consecutive patients undergoing curative esophagectomy for esophageal cancer in University Malaya Medical Centre, Sungai Buloh Hospital, and Sultanah Aminah Hospital. The cut-off value differentiating low and normal PMI is defined as 443mm2/m2 in males and 326326 mm2/m2 in females. Complications were recorded using the Clavien-Dindo Scale. RESULTS: There was no statistical correlation between PMI and major post-esophagectomy complications (p-value: 0.495). However, complication profile was different, and patients with low PMIs had higher 30-day mortality (21.7%) when compared with patients with normal PMI (8.1%) (p-value: 0.048). CONCLUSIONS: Although PMI did not significantly predict post-esophagectomy complications, low PMI correlates with higher 30-day mortality, reflecting a lower tolerance for complications among these patients. PMI is a useful, inexpensive tool to identify sarcopenia and aids the patient selection process. This alerts healthcare professionals to institute intensive physiotherapy and nutritional optimization prior to esophagectomy.

Myxobolus acanthogobii Hoshina, 1952 and Myxobolus selari n. sp. (Myxosporea: Myxobolidae) infecting brain of commercial fishes in Terengganu, Malaysia.

Myxosporean infection in marine water fishes has drawn less attention than in freshwater fishes, which resulted in a higher taxonomic variety in freshwater in Malaysia. This study aimed to address the gap by conducting a myxosporean survey on two commercially significant marine fish species, Nemipterus furcosus (Valenciennes) (Eupercaria incertae sedis: Nemipteridae) and Selar crumenophthalmus (Bloch) (Carangiformes: Carangidae), collected from the northeastern part of peninsular Malaysia. During the examination of the organs, two distinct Myxobolus Bütschli, 1882 species were discovered in the brain tissue of these fishes, despite the absence of any observable pathological signs. The two Myxobolus species were characterized through morphometry, morphology, and analysis of partial small subunit ribosomal RNA (18S rDNA) gene. As a result, Myxobolus acanthogobii Hoshina, 1952, which infects 2.3% of N. furcosus, is synonymous with a myxobolid species commonly found in Japanese waters, based on its morphological traits, tissue tropism, and molecular diagnostics. Furthermore, a novel species, Myxobolus selari n. sp., was described, infecting the brain of one (11%) individual S. crumenophthalmus. This unique species displayed distinctive features, placing it within a well-supported subclade primarily comprising brain-infecting myxobolids. Maximum likelihood analysis further revealed the close relationships among these brain-infecting myxobolids, underscoring the significance of tissue tropism and host taxonomy for myxobolids. This study represents the initial documentation of Myxobolus species within the southern South China Sea, shedding light on the potential diversity of marine myxosporean in this region. This article was registered in the Official Register of Zoological Nomenclature (ZooBank) as urn:lsid:zoobank.org:pub:7C400E35-7CB8-4DEE-92B7-F75FF3926441.

Delineation of a Human Mendelian Disorder of the DNA Demethylation Machinery: TET3 Deficiency.

Germline pathogenic variants in chromatin-modifying enzymes are a common cause of pediatric developmental disorders. These enzymes catalyze reactions that regulate epigenetic inheritance via histone post-translational modifications and DNA methylation. Cytosine methylation (5-methylcytosine [5mC]) of DNA is the quintessential epigenetic mark, yet no human Mendelian disorder of DNA demethylation has yet been delineated. Here, we describe in detail a Mendelian disorder caused by the disruption of DNA demethylation. TET3 is a methylcytosine dioxygenase that initiates DNA demethylation during early zygote formation, embryogenesis, and neuronal differentiation and is intolerant to haploinsufficiency in mice and humans. We identify and characterize 11 cases of human TET3 deficiency in eight families with the common phenotypic features of intellectual disability and/or global developmental delay; hypotonia; autistic traits; movement disorders; growth abnormalities; and facial dysmorphism. Mono-allelic frameshift and nonsense variants in TET3 occur throughout the coding region. Mono-allelic and bi-allelic missense variants localize to conserved residues; all but one such variant occur within the catalytic domain, and most display hypomorphic function in an assay of catalytic activity. TET3 deficiency and other Mendelian disorders of the epigenetic machinery show substantial phenotypic overlap, including features of intellectual disability and abnormal growth, underscoring shared disease mechanisms.

Modelling the impact of climate change on dengue outbreaks and future spatiotemporal shift in Pakistan.

Climate change has a significant impact on the intensity and spread of dengue outbreaks. The objective of this study is to assess the number of dengue transmission suitable days (DTSD) in Pakistan for the baseline (1976-2005) and future (2006-2035, 2041-2070, and 2071-2099) periods under Representative Concentration Pathway (RCP4.5 and RCP8.5) scenarios. Moreover, potential spatiotemporal shift and future hotspots of DTSD due to climate change were also identified. The analysis is based on fourteen CMIP5 models that have been downscaled and bias-corrected with quantile delta mapping technique, which addresses data stationarity constraints while preserving future climate signal. The results show a higher DTSD during the monsoon season in the baseline in the study area except for Sindh (SN) and South Punjab (SP). In future periods, there is a temporal shift (extension) towards pre- and post-monsoon. During the baseline period, the top ten hotspot cities with a higher frequency of DTSD are Karachi, Hyderabad, Sialkot, Jhelum, Lahore, Islamabad, Balakot, Peshawar, Kohat, and Faisalabad. However, as a result of climate change, there is an elevation-dependent shift in DTSD to high-altitude cities, e.g. in the 2020s, Kotli, Muzaffarabad, and Drosh; in the 2050s, Garhi Dopatta, Quetta, and Zhob; and in the 2080s, Chitral and Bunji. Karachi, Islamabad, and Balakot will remain highly vulnerable to dengue outbreaks for all the future periods of the twenty-first century. Our findings also indicate that DTSD would spread across Pakistan, particularly in areas where we have never seen dengue infections previously. The good news is that the DTSD in current hotspot cities is projected to decrease in the future due to climate change. There is also a temporal shift in the region during the post- and pre-monsoon season, which provides suitable breeding conditions for dengue mosquitos due to freshwater; therefore, local authorities need to take adaption and mitigation actions.

Is there an ideal method of reconstruction for proximal humerus osteosarcoma? A review of different reconstruction techniques.

Osteosarcoma is the commonest primary bone malignancy occurring in patients aged <20, and humerus is the third most common site affected by it. In the past, ablative surgery with poor functional outcomes was the only option, but due to advances in chemotherapy, medical imaging and surgical techniques, patient survivorship and the rate of limb salvage surgery has increased significantly. Over the decades many treatment options have been proposed for the reconstruction of the defect following extirpation of the tumour in the proximal humerus, with every procedure having its merits and demerits. However, there is no agreement on the preferred treatment even in similar age groups, and the best way to reconstruct the proximal humerus remains debatable because the restoration of the function of the shoulder girdle remains primarily dependant on the extent of muscle-loss during tumour resection, available surgical expertise and financial constraints in different health systems. The current narrative review was planned to discuss the various reconstruction techniques with their advantages and disadvantages, and a present general review of the relevant literature.

Mitigation of lead (Pb) toxicity in rice cultivated with either ground water or wastewater by application of acidified carbon.

Toxicity induced by a high concentration of lead (Pb) can significantly decrease plant's growth, gas exchange, and yield attributes. It can also causes cancer in humans. The use of organic amendments, especially biochar, can alleviate Pb toxicity in different crops. The application of biochar can decrease the uptake of Pb by plant roots. However, the high pH of thermo-pyrolyzed biochar makes it an unfit amendment for high pH soils. As Pb is an acute toxin and its uptake in rice is a major issue, the current experiment was conducted to explore the efficacy of chemically produced acidified carbon (AC) to mitigate Pb toxicity in rice. Lead was introduced in concentrations of 0, 15, and 30 mg kg-1 soil in combination with 0, 0.5, and 1% AC, underground water (GW) and wastewater (WW) in rice plants. The addition of 1% AC significantly improved the plant height (52 and 7%), spike length (66 and 50%), 1000 grains weight (144 and 71%) compared to 0% AC under GW and WW irrigation, respectively at 30 mg Pb kg-1 soil (30 Pb) toxicity. Similar improvements in the photosynthetic rate, transpiration rate and stomatal conductance also validated the effectiveness of 1% AC over 0% AC. A significant decrease in electrolyte leakage and plant Pb concentration by application of 0.5 and 1% AC validates the effectiveness of these treatments for mitigating 30 Pb toxicity in rice compared to 0% AC under GW or WW irrigation. In conclusion, 1% AC is an effective amendment in alleviating Pb toxicity in rice irrigated with GW or WW at 30 Pb.

Dietary patterns of Pakistani adults and their associations with sociodemographic characteristics-a community based study.

OBJECTIVE: To identify the dietary patterns and understand their association with sociodemographic characteristics among adults. METHODS: The community-based cross-sectional study was conducted in Islamabad, Lahore, Karachi, Peshawar and Quetta cities of Pakistan from March to November 2018, after approval from the National Bioethics Committee, Islamabad, and comprised adults of either gender. Data was collected using the food frequency questionnaire, and dietary patterns were identified using factor analysis. Multivariate regression analysis was used to assess the association of socio-demographic determinants with dietary patterns. Data was analysed using SPSS 21. Parallel Analysis criterion (Eigen values) was determined along with Monte Carlo simulation. RESULTS: Of the 448 subjects, 206(46%) were males and 242(54%) were females. The largest age group was 36-55 years 199(47.4%). Six dietary patterns were identified: "Vegetables", "Fruits", "Mixed Junk and Processed food", "Dairy and Fast food", "Discretionary" and "Fish". Regression analysis showed that those aged 36-55 years had higher scores for vegetables, fruit and fish pattern (p<0.05). Females scored more for vegetables, fish and fruits, and a significantly low score for discretionary diet pattern (p<0.05). Participants with high education level and socioeconomic status had raised scores for discretionary diet items (p<0.05). CONCLUSIONS: Six distinct dietary patterns among Pakistani adults were identified, showing significant association with sociodemographic characteristics.

A basis for prenatal diagnosis of Haemophilia-A in Pakistani patients.

Objective: To screen Haemophilia-A patients for five known recurrent F8 gene variants and to analyze CA repeats in intron 13 of F8 gene in the mother and the affected child pairs. Methods: In this descriptive cross sectional study, 80 unrelated pairs of "mother and son" affected by Haemophilia-A were recruited as subjects. After collection of samples DNA was extracted using the Chelex (Bio-Rad, USA) method. Five known F8 gene variants were screened in the mothers and the affected sons by the allele specific PCR. The amplified products were separated on 2% agarose gels.CA repeats in intron 13 of the F8 gene in the mother and the affected child pairs were analyzed by Sanger sequencing method. The CA repeat alleles were used to look for the feasibility of linkage based diagnosis of Haemophilia-A in the affected families. The data were analyzed using Statistical Package for Social Sciences (SPSS) version 22.0. Results: In the 80 subject "mother and son" pairs a recurrent F8 gene variant was found in 32 pairs (40%). The most recurrent variant c.6869G>A was seen in 12 (15%). Linkage based analysis of the CA repeats in intron 13 was found to be informative in 29 (36.2%) mother-son pairs. Conclusion: The five known Haemophilia-A disease causing variants were found in 40% of the Pakistani Haemophilia-A patients. The five recurrent F8 gene variants and the CA repeats in intron 13 of F8 gene can provide a comprehensive basis for carrying out prenatal diagnosis and carrier screening in majority of the Pakistani Haemophilia-A families.

Ex vivo and in vivo studies of Viola tricolor Linn. as potential cardio protective and hypotensive agent: Inhibition of voltage-gated Ca++ ion channels.

Viola tricolor Linn. is used as cardio-protective and anti-hypertensive agent in traditional medicine. Current study objective was to evaluate cardio-protective and hypotensive effects of Viola tricolor L. in vitro and in vivo studies. Viola tricolor L. crude extract (Vt.Cr) and its fractions (Aqueous and organic) were tested at rabbit atria and aorta coupled to Power Lab Data Acquisition System for cardio depressant and vasorelaxant effects in vitro whereas in vivo Blood Pressure was checked by invasive method in normotensive ketamine-diazepam anesthetized rats. Isoproterenol was employed for acute myocardial infarction (AMI) and left ventricular hypertrophy (LVH) development and cardioprotective effects of Vt.Cr were evaluated hemodynamically and histopathologically. Vt.Cr and its fractions decreased heart rate and contractile force in paired atria and relaxed Phenylephrine (1 µM) and K+ (80 mM) stimulated contractions in aorta possibly mediated through Voltage dependent L-type calcium channels blockage supported by in vivo hypotensive action. In LVH, Vt.Cr lowered Angiotensin Converting Enzymes and renin, increased cyclic Guanosine Monophosphate and nitric oxide levels, decreased cardiomyocytes size and fibrosis attributed to Gallic acid as detected by High Performance Liquid Chromatography. Partial positive results were seen hemodynamically and histologically in AMI Viola tricolor L. showed vasorelaxant, cardio-relaxant, hypotensive, and cardio protective effect validating traditional practice in cardiovascular disorders.

Causal variants in Maturity Onset Diabetes of the Young (MODY) - A systematic review.

BACKGROUND: Maturity Onset Diabetes of the Young (MODY) is an autosomal dominant type of diabetes. Pathogenic variants in fourteen genes are reported as causes of MODY. Its symptoms overlap with type 1 and type 2 diabetes. Reviews for clinical characteristics, diagnosis and treatments are available but a comprehensive list of genetic variants, is lacking. Therefore this study was designed to collect all the causal variants involved in MODY, reported to date. METHODS: We searched PubMed from its date of inception to December 2019. The search terms we used included disease names and name of all the known genes involved. The ClinVar database was also searched for causal variants in the known 14 MODY genes. RESULTS: The record revealed 1647 studies and among them, 326 studies were accessed for full-text. Finally, 239 studies were included, as per our inclusion criteria. A total of 1017 variants were identified through literature review and 74 unpublished variants from Clinvar database. The gene most commonly affected was GCK, followed by HNF1a. The traditional Sanger sequencing was used in 76 % of the cases and 65 % of the studies were conducted in last 10 years. Variants from countries like Jordan, Oman and Tunisia reported that the MODY types prevalent worldwide were not common in their countries. CONCLUSIONS: We expect that this paper will help clinicians interpret MODY genetics results with greater confidence. Discrepancies in certain middle-eastern countries need to be investigated as other genes or factors, like consanguinity may be involved in developing diabetes.

Psychological impact of polygamous marriage on women and children: a systematic review and meta-analysis.

BACKGROUND: Over the last two decades, there has been significant growth in public, political, and academic awareness of polygamy. Polygamous families have distinct household problems, usually stemming from jealousy between co-wives over the husband's affections and resources. This study aimed to ascertain the psychological impact of polygamous marriage on women and children worldwide. METHODS: A systematic search was performed in MEDLINE (PubMed), Scopus, CINAHL (EBSCOhost), Google Scholar, and ProQuest using search terms such as "marriage" and "polygamy." Studies published from the inception of the respective databases until April 2021 were retrieved to assess their eligibility for inclusion in this study. The Joanna Briggs Institute Critical Appraisal Checklist was used for data extraction and the quality assessment of the included studies. The generic inverse variance and odds ratios with 95% confidence intervals (CI) were calculated using RevMan software. RESULTS: There were 24 studies fulfilling the eligibility criteria, and 23 studies had a low risk of bias. The pooled meta-analysis showed women in polygamous marriages had a 2.25 (95% CI: 1.20, 4.20) higher chance of experiencing depression than in monogamous marriages. Children with polygamous parents had a significantly higher Global Severity Index with a mean difference of 0.21 (95% CI: 0.10, 0.33) than those with monogamous parents. CONCLUSIONS: The psychological impact of polygamous marriage on women and children was found to be relatively higher than monogamous marriage. Awareness of the proper practices for polygamy should be strengthened so that its adverse effects can be minimized. The agencies involved in polygamous practices should broaden and enhance their understanding of the correct practice of polygamy.

Analysis of treatment adherence and cost among patients with epilepsy: a four-year retrospective cohort study in Pakistan.

BACKGROUND: The adherence pattern of antiepileptic drugs (AEDs) among patients with epilepsy is relatively lower in the United States and different European countries. However, adherence and cost analysis of AEDs in Asian countries have not been thoroughly studied. Therefore, the present study aimed to analyze the cost and adherence of AEDs and its associated factors in patients followed in Pakistan. METHODS: Data from prescriptions collected from patients with epilepsy who have visited the Outpatient Department (OPD) of different tertiary care hospitals at the cosmopolitan city of Karachi, Pakistan from December 2015 to November 2019. The mean follow-up period for each participant was about 22 months. Pairwise comparisons from Cox regression/hazard ratios were used to assess the predictors of adherence. Direct costs of AEDs were calculated and presented as the annual cost of drugs. RESULTS: A total of 11,490 patients were included in this study, 51.2 % were male and 48.8 % were female with a mean age of 45.2 ± 15.8 y. Levetiracetam was found as the most prescribing AED in all study participants (32.9 %). Of them, 49.1 % of patients continued their initial recommended treatment. However, 31.3 % of patients have discontinued the therapy, while, 19.6 % were switched to other AED. Adherence with initial treatment was more profound in male (57.4 %) patients, compared to female with a mean age of 44.2 years. Lamotrigine users (60.6 %) showed a higher tendency to retain on initially prescribed drugs. The total cost of epilepsy treatment in the entire study cohort was 153280.5 PKR ($941.9). By applying the Cox regression analysis, it can be observed that the patients with increasing age (OR, 2.04), migraine (OR, 2.21), psychiatric disorders (OR, 4.28), other comorbidities (OR, 1.52) and users of other than top five prescribing AEDs (2.35) were at higher risk of treatment discontinuation. However, levetiracetam (OR, 0.69), valproic acid (OR, 0.52), carbamazepine (OR, 0.81), lamotrigine (OR, 0.80) or lacosamide (OR, 0.65) users have more chances to continue their initial therapy. CONCLUSIONS: Similar to western countries, the majority of patients with epilepsy exhibited low adherence with AEDs. Various associated factors for improving adherence were identified in this study.

Community-Based Assessment of Knowledge, Attitude, Practices and Risk Factors Regarding COVID-19 Among Pakistanis Residents During a Recent Outbreak: A Cross-Sectional Survey.

Exceptional precautionary measures have been adopted to stop the transmission and control of COVID-19 through the world and Pakistan is facing lockdown in this scenario. Public loyalty to precautionary measures is affected by their knowledge, attitude, risk factors and practices (KAP) towards COVID-19. The present study was conducted among the Pakistani residents to observe the knowledge, attitude, practices and risk factors towards COVID-19 outbreak in Pakistan. A questionnaire was designed, and a cross-sectional survey was conducted among participants of the study area. Participants were asked the questions regarding knowledge, attitude, practices and risk factors towards COVID-19. Data were analyzed by SPSS and t/F test and correlation was applied among the knowledge, attitude, risk factors and practices. A total of 1060 questionnaires were received. 1004 were included while 56 were excluded. The highest representation was from Punjab province (65.6%), female (63%) and age group of 21-30 years (62.1%). Most participants were single (85%), Muslim (99.4%), Urdu speaking (45.6%) and were graduates (51.5%). Most of the participants were students (52.9%) and were from economically middle-class families (40.8%). The knowledge was positively correlated with attitude and practices whereas negatively correlated with risk factors (P < 0.05). The attitude was negatively correlated with risk factor and positively correlated with practices. The risk factors and practices were positively correlated with each other. Health education program to improve the COVID-19 knowledge, attitude, practices and risk factors should be initiated to combat current health challenge.

TiO2 nanoparticles dose, application method and phosphorous levels influence genotoxicity in Rice (Oryza sativa L.), soil enzymatic activities and plant growth.

The present study focused on investigating the effect of titanium dioxide nanoparticles (TiO2NPs) on rice (Oryza sativa L.) growth and changes in soil health in two contrasting soil textures (silt-loam and clay). Moreover, response of rice to different methods of TiO2NPs application and phosphorous fertilizer levels were also evaluated. For toxicity assessment, pot experiment was carried out. TiO2NPs (0, 500, 750 mg kg-1) were applied and plants were grown till vegetative stage. After harvesting, physiological parameters, stress assay, soil microbial and enzymatic activities were determined. Based on the results of toxicity study, impact of three methods of TiO2NPs application (foliar, irrigation, soil) and four phosphorous fertilizer levels (0, 10, 20, 40 mg kg-1) on rice growth were assessed. During the 1st phase, results showed an adverse effect of TiO2NPs on plant growth and soil microorganisms in both soil textures at 750 mg kg-1. The H2O2 production, lipid peroxidation and leaf membrane injury index were increased by 4.3-, 2.4-, and 1.9-folds in clay soil upon 750 mg kg-1 TiO2NPs application. Likewise, at the same level of TiO2NPs; microbial biomass, dehydrogenase, and respiration were decreased by 0.91-, 0.79-, and 0.78- folds respectively. In 2nd phase, maximum shoot length, biomass, phosphorous uptake and rice grain protein content were observed under application of TiO2NPs (500 mg kg-1) through irrigation method in combination with 40 mg P kg-1. However, 20 and 40 mg P kg-1 performed equally well upon TiO2NPs application and the results were not statistically significant. The results suggest that 750 mg kg-1 of TiO2NPs negatively affect plant growth and soil enzymatic activities. Moreover, combined application of TiO2NPs (500 mg kg-1) through irrigation and 20 mg P kg-1 is recommended to be the optimum for growth of rice plant.

Advanced Nanoscale Surface Characterization of CuO Nanoflowers for Significant Enhancement of Catalytic Properties.

In this work, advanced nanoscale surface characterization of CuO Nanoflowers synthesized by controlled hydrothermal approach for significant enhancement of catalytic properties has been investigated. The CuO nanoflower samples were characterized by field-emission scanning electron microscopy (FE-SEM), X-ray powder diffraction (XRD), X-ray photoelectron spectroscopy (XPS), Raman spectroscopy, high-resolution transmission electron microscopy (HR-TEM), selected-area electron diffraction (SAED), high-angular annular dark field scanning transmission electron microscopy (HAADF-STEM) with elemental mapping, energy dispersive spectroscopy (STEM-EDS) and UV-Vis spectroscopy techniques. The nanoscale analysis of the surface study of monodispersed individual CuO nanoflower confirmed the fine crystalline shaped morphology composed of ultrathin leaves, monoclinic structure and purified phase. The result of HR-TEM shows that the length of one ultrathin leaf of copper oxide nanoflower is about ~650-700 nm, base is about ~300.77 ± 30 nm and the average thickness of the tip of individual ultrathin leaf of copper oxide nanoflower is about ~10 ± 2 nm. Enhanced absorption of visible light ~850 nm and larger value of band gap energy (1.68 eV) have further supported that the as-grown material (CuO nanoflowers) is an active and well-designed surface morphology at the nanoscale level. Furthermore, significant enhancement of catalytic properties of copper oxide nanoflowers in the presence of H2O2 for the degradation of methylene blue (MB) with efficiency ~96.7% after 170 min was obtained. The results showed that the superb catalytic performance of well-fabricated CuO nanoflowers can open a new way for substantial applications of dye removal from wastewater and environment fields.

Organochlorine pesticide residues in raw milk samples collected from dairy farms and urban areas of Lahore district, Pakistan.

The current study was employed to investigate the organochlorine pesticides (OCP) concentrations in milk, as the milk we consume, has residues of these notorious pesticides. The residual concentrations of OCP in milk have numerous harmful effects on health especially the children. Therefore, milk was analyzed using gas chromatography equipped with µECD for seven OCP residues, namely α-endosulfan, ß-endosulfan, Endosulfan-sulphate, DDE, γ-HCH, Dieldrin, and DDT. Three hundred and sixty raw milk samples were collected from urban areas (10 areas of Lahore N = 300) and Dairy Farms (10 farms in Lahore N = 60) from September 2012 to September 2013. Samples were collected after an interval of 2 months, for 12 months. Mean values of OCPs in milk samples from urban areas were reported as α-endosulfan, ß-endosulfan, Endosulfan-sulphate, DDE, γ-HCH, and Dieldrin with concentration of 17.44 ± 3.99, 35.74 ± 7.50, 20.28 ± 3.95, 2.51 ± 0.55, 0.93 ± 0.16 and 1.12 ± 0.18 µg kg-1, respectively, while the milk samples from dairy farms with concentration of 26.94 ± 4.63, 59.88 ± 6.76, 32.07 ± 4.51, 4.64 ± 0.48, 1.20 ± 0.17 and 1.93 ± 0.18 µg kg-1, respectively. None of the samples analyzed were found positive for the presence of DDT, just as none of the samples from area milk shops exceeded the Maximum Residual Limits (MRLs). γ-HCH and ß-endosulfan were found higher in dairy farm milk samples than the MRLs. Conclusively, these pesticide residues are present in milk available in Lahore in enough quantity (some exceeding the MRLs) to threaten human health, particularly the infant and children.

Screening of phytochemical constituents and potential antioxidant, antibacterial and anticancerous activities of Carpesium nepalense seeds oil.

The pharmacological importance and ecofriendly nature of medicinal plants holding a unique edge in the arena of pharmaceutical industries. Therefore, the current research was aimed to evaluate the phytochemical constituents and potential antioxidant, in vitro anticancer and antibacterial activity of Carpesium nepalense seeds essential oil. The analysis performed through Gas chromatography/Mass spectroscopy confirmed the presence of different types of biologically active compounds. At the concentration of 500µg/mL, n-hexane fraction of C. nepalense showed highly significant (P<0.001) antioxidant activity in 2,2-diphenyl-1-picrylhydrazyl, 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid and superoxide assays with the percentage inhibitions of 86.60±1.6%, 82.55±1.0% and 80.50±1.0% respectively. The extract also produced highly significant anticancerous activity against different cell lines at 500µg/mL. The significant antibacterial activity of extract was observed against bacterial strains with the zone of inhibitions of 24.3±0.8, 28.20±0.10, 22.33±0.11 and 33.22±0.10 mm respectively. The significant damage in bacterial cell membranes was also observed in atomic force microscopic analysis. In the light of obtained findings, it is concluded that C. nepalence proved to be a potential candidate as an alternative medicinal agent.