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Genomic Epidemiology of SARS-CoV-2 in Pakistan

Genomics, Proteomics & Bioinformatics 2021年第5期19卷 727-740页

作者： Shuhui Song Cuiping Li Lu Kang Dongmei Tian Nazish Badar Wentai Ma Shilei Zhao Xuan Jiang Chun Wang Yongqiao Sun Wenjie Li Meng Lei Shuangli Li Qiuhui Qi Aamer Ikram Muhammad Salman Massab Umair Huma Shireen fatima Batool Bing Zhang Hua Chen Yun-Gui Yang Amir ali Abbasi Mingkun Li Yongbiao Xue Yiming Bao China National Center for Bioinformation Beijing 100101China National Genomics Data Center Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China CAS Key Laboratory of Genomic and Precision Medicine Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China Department of Virology and Immunology National Institute of HealthIslamabad 45500Pakistan National Center for Bioinformatics Programme of Comparative and Evolutionary GenomicsFaculty of Biological SciencesQuaid-i-Azam UniversityIslamabad 45320Pakistan Center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunming 650223China State Key Laboratory of Plant Cell and Chromosome Engineering Institute of Genetics and Developmental BiologyThe Innovation Academy of Seed DesignChinese Academy of SciencesBeijing 100101China

COVID-19 has swept globally and Pakistan is no *** investigate the initial introductions and transmissions of the SARS-CoV-2 in Pakistan,we performed the largest genomic epidemiology study of COVID-19 in Pakistan and generated 150 complete SARS-CoV-2 genome sequences from samples collected from March 16 to June 1,*** identified a total of 347 mutated positions,31 of which were over-represented in ***,we found over 1000 intra-host single-nucleotide variants(iSNVs).Several of them occurred concurrently,indicating possible interactions among them or *** of the high-frequency iSNVs in Pakistan were not observed in the global population,suggesting strong purifying *** genomic epidemiology revealed five distinctive spreading *** largest cluster consisted of 74 viruses which were derived from different geographic locations of Pakistan and formed a deep hierarchical structure,indicating an extensive and persistent nation-wide transmission of the virus that was probably attributed to a signature mutation(G8371T in ORF1ab)of this ***,28 putative international introductions were identified,several of which are consistent with the epidemiological *** all,this study has inferred the possible pathways of introductions and transmissions of SARS-CoV-2 in Pakistan,which could aid ongoing and future viral surveillance and COVID-19 control.

关键词： SARS-CoV-2 Virus Molecular evolution Haplotype network Pakistan

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Vitamin E in ataxia and neurodegenerative diseases:A review

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World Journal of Neuroscience 2012年第4期2卷 217-222页

作者： fatima Imounan Naima Bouslam Jehanne Aasfara Kaoutar El Alaoui Wafa Regragui El Hachmia Ait Benhaddou Ahmed Bouhouche ali Benomar Mohamed Yahyaoui Mohammed V Souissi University CHU Ibn SinaNeurology B and Neurogenetics DepartmentHopital des SpecialitesRabatMorocco Mohammed V Souissi University Faculte de Medecine et de Pharmacie RabatCentre de Recherche en Epidemiologie Clinique et Essais Therapeutiques(CRECET)RabatMorocco

Vitamin E is one of the most important lipid-soluble antioxidants. It is essential for the neurological function but its role in the central nervous system has not fully been elucidated. It is known that tocopherol acts in protecting cell membranes from oxidative damage and it can act as an anti-in?ammatory agent, which may also be neuroprotective, as well as regulating speci?c enzymes. There is growing evidence that oxidative stress plays a key role in the pathophysiology of several neurodegenerative disorders. These diseases are defined by the progressive loss of speci?c neuronal cell populations and are associated with protein aggregates. We reviewed some aspects related to the role of antioxidant properties of Vitamin E in preventing and/or curing neurodegenerative disorders such as the Alzheimer’s disease, Parkinson’s disease, amyotrophic lateral sclerosis, ataxia, tardive dyskinesia and Huntington’s disease.

关键词： Vitamin E Neurodegenerative Diseases Ataxia with Vitamin E Deficiency

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A remotely sensed tracking of forest cover and associatedtemperature change in Margalla hills

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International Journal of Digital Earth 2019年第10期12卷 1133-1150页

作者： Noora Khalid Saleem Ullah Sheikh Saeed Ahmad Asad ali Farrukh Chishtie Department of Space Science Institute of Space TechnologyIslamabadPakistan Department of Environmental Sciences Fatima Jinnah Women UniversityRawalpindiPakistan

Worldwide, forest degradation is a serious environmental issue, and inPakistan, forest wealth is depleting at the highest rate in South Asia. Toensure sustainable development goals of environmental stewardship,social development and economic growth, a sound monitoring andregulatory mechanism is essential for tracking forest cover changes. Thisstudy aims to quantify the decline of forest reserves and associatedtemperature variations in a relatively unexplored biodiversity hotspot ofIslamabad, Margalla Hills National Park (MHNP). Imagery acquired byLandsat TM (Thematic Mapper) for the year 1992, 2000 and 2011 areused to assess the spatial and temporal changes occurred over the lasttwo decades (from 1992 to 2011). A robust hybrid-classification routineis implemented to monitor the changes in forest cover and ANOVAalong with Tukey’s HSD (Honestly Significant Difference) test is used totest the significance of temperature variation associated with a shift inland cover classes. The results showed a significant growth insettlements, agricultural area and barren soil whereas water body, lowervegetation, scrub and pine forest are diminishing. In both decades, thetemperature alteration associated with a change in land cover classesare statistically significant (confirmed by ANOVA and Tukey’s HSD tests)for most of the land use/land cover classes. Based on these findings, thisstudy concludes that forests are dwindling at MHNP and the degradingcondition of the forest is below par and necessitates the promotion ofconservation practices to minimize ecological disturbances.

关键词： Margalla hills Landsat thematic mapper(Landsat TM) forest cover change hybrid classification land cover classes ANOVA Tukey’s HSD

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Determinants of Health Care Seeking Behaviors in Puerperal Sepsis in Rural Sindh, Pakistan: A Qualitative Study

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Open Journal of Preventive Medicine 2020年第9期10卷 255-266页

作者： Shabina Ariff fatima Mir Farhana Tabassum Farrukh Raza Atif Habib ali Turab Amnesty LeFevre Linda A. Bartlett Sajid Bashir Soofi Zulfiqar A. Bhutta Department of Paediatric and Child Health Aga Khan University Karachi Pakistan Center of Excellence in Women & Child Health Aga Khan University Karachi Pakistan Department of International Health Johns Hopkins Bloomberg School of Public Health Baltimore MD USA

Background: Puerperal sepsis (PS) is one of the major causes of maternal death, contributing to 26,000 deaths per year in developing countries. Early recognition and treatment are essential to managing PS, but numerous social, cultural and technical barriers prevent or delay access to care and necessary medical attention. Through this qualitative study, we identified barriers to care seeking for puerperal sepsis among recently delivered women in Matiari, Pakistan. Methods: We conducted 20 in-depth interviews among recently delivered women with and without sepsis and their family members in September 2012. Key informant interviews were conducted with 14 healthcare providers and traditional birth attendants. The themes used for content analysis were knowledge of danger signs, factors affecting care seeking and local treatment practices for postpartum sepsis. Results: A total of 34 interviews were conducted. Recently delivered women, their family members and traditional birth attendants were unaware of the word PS or the local translated term for PS. However, they were familiar with most of the individual symptoms associated with PS. Healthcare providers were aware of the condition and the associated symptoms. The healthcare providers’ understanding of the seriousness of PS was directly proportional their age and clinical experience. The most common barriers to care seeking was the division of labor within the household, obtaining permission from the primary decision maker, access to transportation, lack of financial resources and support from family members. Conclusion: To improve maternal care seeking behaviors for PS, interventions focusing on increasing knowledge of PS, addressing gender inequality, implementing an affordable community transport service and enhancing TBA’s knowledge and skills to manage PS need to be implemented.

关键词： Puerperal Sepsis Qualitative Care Seeking Barrier Maternal Health

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A Comparative Study of Fungal and Some Aflatoxin Contents of Freshly Fried and Stored SallahMeat from Danbatta Local Government Area of Kano State, Nigeria

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Open Journal of Medical Microbiology 2020年第2期10卷 71-88页

作者： fatima S. Abdullahi Amin O. Igwegbe Bello A. Bello Mamudu H. Badau Sani Abashe Imaan U. Igwegbe Zainab ali Department of Food Science and Technology Federal University Dutsin-ma Dutsin-ma Nigeria Department of Food Science and Technology University of Maiduguri Maiduguri Nigeria Department of Biochemistry Federal University Dutse Dutse Nigeria Department of Medical Microbiology University of Maiduguri Teaching Hospital (UMTH) Miaduguri Nigeria Department of Animal of Science University of Maiduguri Maiduguri Nigeria

A comparative study of Fungi (yeast and moulds) and their toxic metabolites was carried out on offal and muscles of freshly fried and stored Sallah meats from rams, bulls, goats and camels slaughtered for sacrifice in Danbatta Local Government Area, Kano State, Nigeria. The objective was to determine the effects of frying and four weeks storage at ambient temperatures on the mycological loads of the fried and stored meats. A total of seventy two (72) samples of muscles and offal were collected from six different and randomly selected households that slaughtered and fried any of the four animals during that period. The samples were analyzed immediately as freshly fried, and then stored for a period of four weeks during which analyses were conducted at the second and fourth weeks. An analysis of variance (ANOVA) was used to compare between the fungal loads and the toxin contents in the stored meat. Results revealed the presence of Mucor, Rhizopus stolonifer, Aspergillus niger, Saccharomycetes, Penicilium spp and Aspergillus flavus;and that, Aspergillus flavus and

关键词： Danbatta Sallah Meat Aflatoxin Metabolites Fried Meat

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Activity and Selectivity of Bimetallic Catalysts Based on SBA-15 for Nitrate Reduction in Water

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Materials Sciences and Applications 2023年第2期14卷 78-93页

作者： Mouhamad Rachini Mira Jaafar Nabil Tabaja Sami Tlais Rasha Hamdan fatima Al ali Ola Haidar ali Jaber Mohammad Kassem Eugene Bychkov Lucette Tidahy Renaud Cousin Dorothée Dewaele Tayssir Hamieh Joumana Toufaily Laboratory of Materials Catalysis Environment and Analytical Methods (MCEMA) EDST FS Lebanese University Hariri Campus Hadath Lebanon Université du Littoral Cô te d’Opale (ULCO) LPCA EA 4493 F-59140 Dunkerque France Laboratory of Applied Studies for Sustainable Development and Renewable Energy (LEADDER) EDST Lebanese University Hariri Campus Hadath Lebanon College of Engineering and Technology American University of the Middle East Kuwait Kuwait Department of Chemistry American University of Beirut Riad El-Solh Beirut Lebanon Laboratoire de Recherche et Développement des Médicaments et des Produits Naturels RDMPN Faculty of Pharmacy Lebanese University Hariri Campus Hadath Lebanon Université du Littoral Cô te d’Opale UCEIV Unité de Chimie Environnementale et Interactions sur le Vivant EA 4492 SFR Condorcet FR CNRS 3417 Dunkerque France Centre Commun de Mesures Université du Littoral C&ocircte d’Opale Dunkerque France Faculty of Science and Engineering Maastricht University Maastricht The Netherlands

Nitrate from the application of nitrogen-based fertilizers in intensive agriculture is a notorious waste product, though it lacks cost-effective solutions for its removal from potential drinking water resources. Catalytic reduction appears to be a promising technique for converting nitrates to benign nitrogen gas. Mesoporous silica SBA-15 is a frequently used catalyst support that has large surface areas and highly ordered nanopores. In this work, mesoporous silica SBA-15 bimetallic catalysts for nitrate reduction were investigated. The catalyst was optimized for the selection of promoter metal (Sn and Cu), noble metal (Pd and Pt) and loading ratios of these metals at different temperatures and reduction conditions. The catalysts prepared were characterized by FT-IR, N2 physisorption, XRD, SEM, and ICP. All catalysts showed the presence of cylindrical mesoporous channels and uniform pore structures that remained even after metals loading. In the presence of a CO2 buffer, the catalysts 4Pd-1Cu/SBA-15 and 1Pt-1Cu/SBA-15 reduced at 100?C under H2 and 1Pd-1Cu/SBA-15 reduced at 200°C under H2 demonstrated very high nitrate conversion. Furthermore, the forementioned Pd catalysts had higher N2 selectivity (88% - 87%) compared to Pt catalyst (80%). Nitrate conversion by the 4Pd-1Cu/SBA-15 catalyst was significantly decreased to 81% in the absence of CO2.

关键词： Bimetallic Catalyst Heterogeneous Catalyst Nitrate Reduction SBA-15 XRD BET SEM FTIR ICP

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Assessment of Retreatment Tuberculosis Cases amongst All Tuberculosis Cases Notification in District Swat 2015-2017: A Retrospective Cohort Review

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Journal of Tuberculosis Research 2019年第1期7卷 11-18页

作者： Zahir Shah Maqsood ali Khan Hina Najmi Razia fatima Aashifa Yaqoob Abdul Ghafoor Ahmed Wali Amjad Khan Shah Hasan Khan Ghulam Mustafa Halepota Provincial Tuberculosis Control Program Swat Khyber Pakhtunkhwa Pakistan Sukh Initiative Aman Health Care Services Karachi Pakistan National Tuberculosis Control Program Islamabad Pakistan Provincial Tuberculosis Control Program Quetta Pakistan Pakistan Kidney and Liver Institute & Research Center Lahore Pakistan

Retreatment Tuberculosis (TB) has long been a neglected area in global TB control. To determine the notification of re-treatment Tuberculosis TB cases among all enrolled TB patients, we conducted a retrospective cohort review of routine program data from 2015-2017. A total of 8663 tuberculosis cases (all new and old forms) were registered at the study site. Of these, 1916 (22%) were pulmonary bacteriological confirmed;3498 (40.37%) were pulmonary clinical diagnosed and 3396 (39.20%) were clinically or bacteriological confirmed extra-pulmonary tuberculosis cases. Retreatment cases trend was found to be increased from 1% in 2015 to 1.6% in 2017. Majority of re-treatment cases were in the age group 18 - 43 years and only 7 patients were under the age of 15 years. This concludes that notification of re-treatment cases is very low among all enrolled TB patients and this could be possibly due to the fact that most of the re-treatment cases were registered as new cases or misdiagnosed. There is need and space to increase retreatment cases. Most of the re-treatment cases were usually converted to MDR-TB (Multi-Drug Resistant Tuberculosis) as noted in PMDT (Programmatic management of Drugs resistant tuberculosis) site. Therefore, proper history and diagnosis should be encouraged at the time of case notification.

关键词： Retreatment TB Cases Retrospective Cohort Swat Pakistan

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Estimating Ecological Characteristics and Carbon Stock in Uneven-Aged Plantations of Acacia senegal L. in the Savannah Woodlands of Sudan

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Journal of Environmental Protection 2023年第5期14卷 404-418页

作者： fatima Elhassan Awadalla Abass Safa Salaheldine Mubarak Khugali Nagla Abdelmounaim Mohammed Ahmed Ahmed Laamrani Elsadig Agabna Elhadi Ahmed ali Hassabelkareem Siddig Edouard Konan Kouassi Department of Soil and Environmental Science Faculty of Agriculture University of Khartoum (UofK) Khartoum Sudan African Center of Excellence in Climate Change Biodiversity & Sustainable Agriculture (CEA-CCBAD) University Felix Houphou&eumlt-Boigny Abidjan C&ocircte d’Ivoire Centre for Remote Sensing Applications (CRSA) Mohammed VI University (UM6P) Ben Guerir Morocco Environmental and Natural Resources and Desertification Institute National Center for Research (NCR) Khartoum Sudan Institute of Environmental Studies University of Khartoum Khartoum Sudan Department of Forest Conservation and Protection Faculty of Forestry University of Khartoum (UofK) Khartoum Sudan

The aim of this study was to assess Acacia senegal trees’ characteristics as well as evaluate the carbon stock under a variety of ages in the El Demokeya forest in Sudan, where the Gum Arabic belt is located. 12 sample plots, in 2021 were randomly distributed to represent the entire area of the forest prior to the required measurements. The sample was designed as squire plots with one hectare. In each sample plot, all trees were counted, their height (m), and Diameters Breast Height (DBH in cm), respectively. The results showed the highest number of trees per ha at age 20 years old and the lowest number at age 47 years, while the highest values of DBH and volume were found at age 47 years old. As a result, the maximum and minimum values of the aboveground biomass were found in the age 47 years old and 16 years, accounting for 19.87 tons and 1.9 tons respectively. Thus, the amount of carbon stock was 11.92 tons/ha in the 35-years-old and 1.19 tons/ha in the 21-year stands. Furthermore, the average carbon stock in all plots was estimated as 18.70 tons/ha and hence the total carbon stock in the El Demokeya forest is equal to 620.11 tons. Conclusively, the characteristics of trees, amount of aboveground biomass and carbon stock in the El Demokeya forest varied among the uneven-aged plantation groups. The study recommends and encourages the protection of A. senegal in order to increase the carbon sink as well as protect the environment in the era of climatic changes.

关键词： Aboveground Biomass Soil Organic Carbon Dry Lands Forest Climate Change Mitigation Carbon

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Enhancing Childhood TB Notifications by Strengthening Linkages with Large Hospitals in Pakistan —Childhood TB in Large Hospitals, Pakistan

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Journal of Tuberculosis Research 2018年第1期6卷 63-67页

作者： ali Saeed Mirza Razia fatima Aashifa Yaqoob Ejaz Qadeer Ahmed Wali Afshan Khurshid Mahboob Ul Haq Ajay M. V. Kumar National TB Control Program Islamabad Pakistan Provincial TB Control Program Quetta Pakistan Provincial TB Control Program Sindh Pakistan International Union against Tuberculosis and Lung Disease Paris France International Union against Tuberculosis and Lung Disease South-East Asia Office New Delhi India

To improve childhood Tuberculosis management, the National Tuberculosis Program implemented a package of interventions Hospital DOTS linkages (HDL) in 2015 in 144 tertiary and secondary care hospitals across Pakistan. This included systematic engagement of hospital administration and all specialist doctors, staff training and regular facility-based review meetings. HDL was associated with 35% increase in childhood TB notifications in 2015 (versus 2014) in HDL sites as compared to 16% increase in non-HDL sites. The increase was seen across provinces, age-groups and sexes, but did not correlate with presence of Xpert MTB/RIF®?or “screeners” (health workers deployed to screen children for TB).

关键词： Tuberculosis Childhood Tuberculosis Hospital DOTS Linkages Pakistan SORT IT

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Current Status of Withania somnifera(L.) Dunal: An Endangered Medicinal Plant from Himalaya

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American Journal of Plant Sciences 2017年第5期8卷 1159-1169页

作者： Sumaira Aslam Naveed Iqbal Raja Mubashir Hussain Muhammad Iqbal Muhammad Ejaz Danish Ashfaq Hira fatima Muhammad ali Shah Abd-Ur-Rehman Maria Ehsan Department of Botany PMAS Arid Agriculture University Rawalpindi Pakistan Department of Botany University of Sargodha Sargodha Pakistan Department of Biological Sciences University of Lahore Sargodha Pakistan Department of Biotechnology University of Azad Jammu & Kashmir Muzaffarabad Pakistan

Withania somnifera is highly medicinal plant species of Pakistan floristically placed in the Western Himalayan Province, Himalaya Range of Azad Jammu and Kashmir and in the Soon valley (Salt Range) of Punjab Pakistan. It grows in high altitude of 5500 feet in the Himalayas. Its English name is Winter Cherry and its Urdu name is Asghand/Kutilal. It is the low lying shrub of about 1.50 m in height with erect branching. It grows in dry arid regions of Pakistan, India, China and Bangladesh. Its flowers are bisexual, small, axillary, greenish, solitary and few-flowered cymes. Chemical analysis of Ashwagandha showed that it has alkaloids and steroidal lactones (withanolides) as the main chemical constituent. W. somnifera has not yet been assessed for the IUCN Red List. However, in Pakistan, W. somnifera is falling under criteria A of endangered category. Asghand (W. somnifera) acquires much therapeutic potential which include sedative, narcotic, thyroid stimulation, anti-inflammatory, hypnotic, anti-stress, general tonic, diuretic, antimicrobial, and antitumor activities. There are number of threats responsible for the decrease of W. somnifera number in western Himalayan range and salt range of Punjab Pakistan which may include deforestation over exploitation and climatic changes. Conservation strategies need to be adopted for improving the population pool of W. somnifera. There is also the dire need to conserve this important medicinal plant species with some standard biotechnological approaches and conservation strategies in future.

关键词： Withania somnifera Endangered Antimicrobial Antitumor Conservation

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