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Novel Analysis of Fuzzy Fractional Emden-Fowler Equations within New Iterative Transform Method

M. Mossa Al-Sawalha, Naila Amir, Rasool Shah, Muhammad Yar, Muhammad Gulzar
2022 Journal of Function Spaces  
The analytical behavior of fractional differential equations is often puzzling and difficult to predict under uncertainty. It is crucial to develop a robust, extensive, and extremely successful theory to address these problems. An application of fuzzy fractional differential equations can be found in applied mathematics and engineering. Using the iterative transform technique, the study determines the analytic solution of fractional fuzzy Emden-Fowler equation in the sense of the Caputo
more » ... , which is applied to evaluate the physical model range in several scientific and engineering disciplines. The derived solutions to the fractional fuzzy Emden-Fowler equations are more generic and applicable to a broader range of problems. Through the translation of fractional fuzzy differential equations into equivalent crisp systems of fractional differential equations, we obtain a parametric description of the solutions. The graphical and numerical representation demonstrates the symmetry among the upper and lower fuzzy solution representations in their simplest form, which may aid in the comprehension of artificial intelligence, control system models, computer science, image processing, quantum optics, medical science, physics, measure theory, stochastic optimization theory, biology, mathematical finance, and other domains, as well as nonfinancial evaluation.
doi:10.1155/2022/7731135 fatcat:54xlnqylibhuhdajf6m3tqfibq

BioCompute Objects to communicate a viral detection pipeline with potential for use in a regulatory environment [article]

Naila Gulzar, Jonathon Keeney, Jack B. Baker, Ondrej Klempir, Geoffrey Hannigan, Danny A. Bitton, Julia M Maritz, Charles Hadley S. King, Janisha A. Patel, Paul Duncan, Raja Mazumder
2021 bioRxiv   pre-print
AbstractThe volume of nucleic acid sequence data has exploded in recent years, and with it, the challenge of finding and transforming relevant data into meaningful information. Processing the abundance of data can require a dynamic ecosystem of customized tools. As analysis pipelines become more complex, there is an increased difficulty in communicating analysis details in a way that is understandable yet of sufficient detail to make informed decisions about results or repeat the analysis. This
more » ... may be of particular interest to institutions and private companies that need to communicate complex computations in a regulatory environment. To meet this need for standard reporting, the open source BioCompute framework was developed as a standardized mechanism for communicating the details of an analysis in a concise and organized way, and other tools and interfaces were subsequently developed according to the standard. The goal of BioCompute is to streamline the process of communicating computational analyses. Reports that conform to the BioCompute standard are called BioCompute Objects (BCOs). Here, a comprehensive suite of BCOs is presented, representing interconnected elements of a computation that is modeled after those that might be found in a regulatory submission, but which can be shared publicly. Because BCOs are human and machine readable, they can be displayed in customized ways to further improve their utility, and an example of a collapsible format is shown. The work presented here serves as a real world implementation that imitates actual submissions, providing concrete examples. As an example, a pipeline designed to identify viral contaminants in biological manufacturing, such as for vaccines, is developed and rigorously tested to establish a rate of false positive detection, and is described in a BCO report. That pipeline relies on a specially curated database for alignment, and a set of synthetic reads for testing, both of which are also descriptively packaged in their own BCOs. All of the sufficiently complex processes associated with this analysis are therefore represented as BCOs that can be cross-referenced, demonstrating the modularity of BCOs, their ability to organize tremendous complexity, and their use in a lifelike regulatory environment.
doi:10.1101/2021.10.19.465010 fatcat:of72i6y54zg2zc2o2d3bcbbcv4

BioXpress: an integrated RNA-seq-derived gene expression database for pan-cancer analysis

Quan Wan, Hayley Dingerdissen, Yu Fan, Naila Gulzar, Yang Pan, Tsung-Jung Wu, Cheng Yan, Haichen Zhang, Raja Mazumder
2015 Database: The Journal of Biological Databases and Curation  
Citation details: Wan,Q.,Dingerdissen,H.,Fan,Y., et al. BioXpress: an integrated RNA-seq-derived gene expression database for pan-cancer analysis. Abstract BioXpress is a gene expression and cancer association database in which the expression levels are mapped to genes using RNA-seq data obtained from The Cancer Genome Atlas, International Cancer Genome Consortium, Expression Atlas and publications. The BioXpress database includes expression data from 64 cancer types, 6361 patients and 17 469
more » ... nes with 9513 of the genes displaying differential expression between tumor and normal samples. In addition to data directly retrieved from RNA-seq data repositories, manual biocuration of publications supplements the available cancer association annotations in the database. All cancer types are mapped to Disease Ontology terms to facilitate a uniform pan-cancer analysis. The BioXpress database is easily searched using HUGO Gene Nomenclature Committee gene symbol, UniProtKB/ RefSeq accession or, alternatively, can be queried by cancer type with specified significance filters. This interface along with availability of pre-computed downloadable files containing differentially expressed genes in multiple cancers enables straightforward retrieval and display of a broad set of cancer-related genes. Database URL: http://hive.biochemistry.gwu.edu/tools/bioxpress V C The Author(s)
doi:10.1093/database/bav019 pmid:25819073 pmcid:PMC4377087 fatcat:icbyogkhkrecjozhrwd5iy2qy4

Baseline human gut microbiota profile in healthy people and standard reporting template [article]

Charles Hadley King, Hiral Desai, Allison C. Sylvetsky, Jonathan LoTempio, Shant Ayanyan, Jill Carrie, Keith Crandall, Brian Fochtman, Lusine Gasparyan, Naila Gulzar, Paul Howell, Najy Issa (+11 others)
2018 bioRxiv   pre-print
A comprehensive knowledge of the types and ratios of microbes that inhabit the healthy human gut is necessary before any kind of pre-clinical or clinical study can be performed that attempts to alter the microbiome to treat a condition or improve therapy outcome. To address this need we present an innovative scalable comprehensive analysis workflow, a healthy human reference microbiome list and abundance profile (GutFeelingKB), and a novel Fecal Biome Population Report (FecalBiome) with
more » ... applicability. GutFeelingKB provides a list of 157 organisms (8 phyla, 18 classes, 23 orders, 38 families, 59 genera and 109 species) that forms the baseline biome and therefore can be used as healthy controls for studies related to dysbiosis. The incorporation of microbiome science into routine clinical practice necessitates a standard report for comparison of an individual's microbiome to the growing knowledgebase of "normal" microbiome data. The FecalBiome and the underlying technology of GutFeelingKB address this need. The knowledgebase can be useful to regulatory agencies for the assessment of fecal transplant and other microbiome products, as it contains a list of organisms from healthy individuals. In addition to the list of organisms and abundances the study also generated a list of contigs of metagenomics dark matter. In this study, metagenomic dark matter represents sequences that cannot be mapped to any known sequence but can be assembled into contigs of 10,000 nucleotides or higher. These sequences can be used to create primers to study potential novel organisms. All data is freely available from https://hive.biochemistry.gwu.edu/gfkb and NCBI's Short Read Archive.
doi:10.1101/445353 fatcat:cfovmxejprfpnd3j3e7xkyoyzi

Streamlined Subpopulation, Subtype, and Recombination Analysis of HIV-1 Half-Genome Sequences Generated by High-Throughput Sequencing

Bhavna Hora, Naila Gulzar, Yue Chen, Konstantinos Karagiannis, Fangping Cai, Chang Su, Krista Smith, Vahan Simonyan, Sharaf Ali Shah, Manzoor Ahmed, Ana M. Sanchez, Mars Stone (+5 others)
2020 mSphere  
High-throughput sequencing (HTS) has been widely used to characterize HIV-1 genome sequences. There are no algorithms currently that can directly determine genotype and quasispecies population using short HTS reads generated from long genome sequences without additional software. To establish a robust subpopulation, subtype, and recombination analysis workflow, we amplified the HIV-1 3′-half genome from plasma samples of 65 HIV-1-infected individuals and sequenced the entire amplicon (∼4,500
more » ... by HTS. With direct analysis of raw reads using HIVE-hexahedron, we showed that 48% of samples harbored 2 to 13 subpopulations. We identified various subtypes (17 A1s, 4 Bs, 27 Cs, 6 CRF02_AGs, and 11 unique recombinant forms) and defined recombinant breakpoints of 10 recombinants. These results were validated with viral genome sequences generated by single genome sequencing (SGS) or the analysis of consensus sequence of the HTS reads. The HIVE-hexahedron workflow is more sensitive and accurate than just evaluating the consensus sequence and also more cost-effective than SGS. IMPORTANCE The highly recombinogenic nature of human immunodeficiency virus type 1 (HIV-1) leads to recombination and emergence of quasispecies. It is important to reliably identify subpopulations to understand the complexity of a viral population for drug resistance surveillance and vaccine development. High-throughput sequencing (HTS) provides improved resolution over Sanger sequencing for the analysis of heterogeneous viral subpopulations. However, current methods of analysis of HTS reads are unable to fully address accurate population reconstruction. Hence, there is a dire need for a more sensitive, accurate, user-friendly, and cost-effective method to analyze viral quasispecies. For this purpose, we have improved the HIVE-hexahedron algorithm that we previously developed with in silico short sequences to analyze raw HTS short reads. The significance of this study is that our standalone algorithm enables a streamlined analysis of quasispecies, subtype, and recombination patterns from long HIV-1 genome regions without the need of additional sequence analysis tools. Distinct viral populations and recombination patterns identified by HIVE-hexahedron are further validated by comparison with sequences obtained by single genome sequencing (SGS).
doi:10.1128/msphere.00551-20 pmid:33055255 fatcat:6algpve565gxvkhaysutuocpr4

Baseline human gut microbiota profile in healthy people and standard reporting template

Charles H. King, Hiral Desai, Allison C. Sylvetsky, Jonathan LoTempio, Shant Ayanyan, Jill Carrie, Keith A. Crandall, Brian C. Fochtman, Lusine Gasparyan, Naila Gulzar, Paul Howell, Najy Issa (+12 others)
2019 PLoS ONE  
A comprehensive knowledge of the types and ratios of microbes that inhabit the healthy human gut is necessary before any kind of pre-clinical or clinical study can be performed that attempts to alter the microbiome to treat a condition or improve therapy outcome. To address this need we present an innovative scalable comprehensive analysis workflow, a healthy human reference microbiome list and abundance profile (GutFeelingKB), and a novel Fecal Biome Population Report (FecalBiome) with
more » ... applicability. GutFeelingKB provides a list of 157 organisms (8 phyla, 18 classes, 23 orders, 38 families, 59 genera and 109 species) that forms the baseline biome and therefore can be used as healthy controls for studies related to dysbiosis. This list can be expanded to 863 organisms if closely related proteomes are considered. The incorporation of microbiome science into routine clinical practice necessitates a standard report for comparison of an individual's microbiome to the growing knowledgebase of "normal" microbiome data. The FecalBiome and the underlying technology of GutFeelingKB address this need. The knowledgebase can be useful to regulatory agencies for the assessment of fecal transplant and other microbiome products, as it contains a list of organisms from healthy individuals. In addition to the list of organisms and their abundances, this study also generated a collection of assembled contiguous sequences (contigs) of metagenomics dark matter. In this study, metagenomic dark matter represents sequences that cannot be mapped to any known sequence but can be assembled into contigs of 10,000 nucleotides or higher. These sequences can be used to create primers to study potential novel organisms. All data is freely available from https://hive.biochemistry.gwu.edu/gfkb and NCBI's Short Read Archive.
doi:10.1371/journal.pone.0206484 pmid:31509535 pmcid:PMC6738582 fatcat:mf2chvyyajdedm76pmcuictuuy

High-performance integrated virtual environment (HIVE): a robust infrastructure for next-generation sequence data analysis

Vahan Simonyan, Konstantin Chumakov, Hayley Dingerdissen, William Faison, Scott Goldweber, Anton Golikov, Naila Gulzar, Konstantinos Karagiannis, Phuc Vinh Nguyen Lam, Thomas Maudru, Olesja Muravitskaja, Ekaterina Osipova (+14 others)
2016 Database: The Journal of Biological Databases and Curation  
Citation details: Simonyan,V., Chumakov,K., Dingerdissen,H. et al. High-performance integrated virtual environment (HIVE): a robust infrastructure for next-generation sequence data analysis. Abstract The High-performance Integrated Virtual Environment (HIVE) is a distributed storage and compute environment designed primarily to handle next-generation sequencing (NGS) data. This multicomponent cloud infrastructure provides secure web access for authorized users to deposit, retrieve, annotate and
more » ... compute on NGS data, and to analyse the outcomes using web interface visual environments appropriately built in collaboration with research and regulatory scientists and other end users. Unlike many massively parallel computing environments, HIVE uses a cloud control server which virtualizes services, not processes. It is both very robust and flexible due to the abstraction layer introduced between computational requests and operating system processes. The novel paradigm of moving computations to the data, instead of moving data to computational nodes, has proven to be significantly less taxing for both hardware and network infrastructure. The honeycomb data model developed for HIVE integrates metadata into an object-oriented model. Its distinction from other object-oriented databases is in the additional implementation of a unified application program interface to search, view and manipulate data of all types. This model simplifies the introduction of new data types, thereby minimizing the need for database restructuring and streamlining the development of new V C The Author(s) integrated information systems. The honeycomb model employs a highly secure hierarchical access control and permission system, allowing determination of data access privileges in a finely granular manner without flooding the security subsystem with a multiplicity of rules. HIVE infrastructure will allow engineers and scientists to perform NGS analysis in a manner that is both efficient and secure. HIVE is actively supported in public and private domains, and project collaborations are welcomed. Database URL: https://hive.
doi:10.1093/database/baw022 pmid:26989153 pmcid:PMC4795927 fatcat:6fzlwvktpnafnlgtyy6ryf2uri

A Technique For Perceiving Abusive Bangla Comments

Md Gulzar Hussain, Tamim Al Mahmud
2019 Zenodo  
Prothom Alo [22] , Mashrafe Bin Mortaza [23] , Shakib Al Hasan [24] , SalmoN TheBrownFish [25] , Naila Nayem [26] and Prothom Alo News Portal [27] .  ...  Md Gulzar Hussain is with the Computer Science & Engineering, Green University of Bangladesh, Dhaka, Bangladesh.  ...  Gulzar Hussain was born in  ... 
doi:10.5281/zenodo.3544582 fatcat:rnvjppffhvff7cdbxnowj5pnaa

Allelopathy and Agricultural Sustainability: Implication in weed management and crop protection—an overview

Zahir Muhammad, Naila Inayat, Abdul Majeed, Hazrat Ali, Kaleem Ullah, Rehmanullah
2019 European Journal of Ecology  
biomass Kahliq et al. (2010) S. bicolor, H. annus, and others Rice weeds Growth, biomass and chlorophyll contents suppression Khaliq et al. (2013) Eclipta alba Cassia tora, Cassia sophera Gulzar  ... 
doi:10.2478/eje-2019-0014 fatcat:5dac4jmrbjaytjsycbyyrdrr5i

A Study on Aligarh Muslim University, Aligarh, Uttar Pradesh, Indiaal Culture and its Impact on Employee Performance: A Case Study of State Bank of India

Ms. Naila Zia, Prof. Nafees. A. Khan
2019 International Journal of Trend in Scientific Research and Development  
Fakhar, Zahid and Muhammad gulzar (2013) surveyed about the overall impact of the organizational culture on the job performance of the employees either directly or indirectly.  ... 
doi:10.31142/ijtsrd23374 fatcat:adowgxyywncczfyddq7muimevu

Generating a focused view of disease ontology cancer terms for pan-cancer data integration and analysis

T.-J. Wu, L. M. Schriml, Q.-R. Chen, M. Colbert, D. J. Crichton, R. Finney, Y. Hu, W. A. Kibbe, H. Kincaid, D. Meerzaman, E. Mitraka, Y. Pan (+5 others)
2015 Database: The Journal of Biological Databases and Curation  
Acknowledgements The authors thank COSMIC, TCGA, ICGC, TARGET, IntOGen and EDRN for providing the data and Naila Gulzar, Pascale Gaudet and Yu Hu for their suggestions and comments.  ... 
doi:10.1093/database/bav032 pmid:25841438 pmcid:PMC4385274 fatcat:uifubwm7qjbzxcittpu3xxg4ba

Cancer Preventive and Therapeutic Compounds: Gift From Mother Nature

Muhammad Zahid, Qureshi Postdoctrate
2017 unpublished
Gulzareen Gulzar Identification of animal species through DNA from hair samples 2014 27.  ...  Naila Islam Analysis of Δ 9 -tetrahydrocannabinol (cannabis sativa) in hair of chronic abusers. 2014 26.  ... 
fatcat:ljzxz6mfrrhqrg6xkswwsrvgca

Prevalence And Severity of Restless Legs Syndrome Among Physiotherapy Students Farkhunda Rasheed Choudhary, Saba Rasheed Benefits And Survival of Vascularized Fibular Graft in Young Population With Avascular Necrosis Hip Rizwan Aslam

Benish Khanzada, Tehmina Rehman, Saba Mansoor, Falak Siyar, Raheel Khan, Mukarram Hussain, Zahid Anwar, Muhammad Zahid, Hussain S6, Muhammad Saleem, Nasir Mehmood Wattu, Ahmed Khan (+132 others)
2017 Asad Maqbool   unpublished
Objective: To determine the frequency of endometrial hyperplasia in histopathology of endometrial curettings in perimenopausal women with abnormal uterine bleeding. Study Design: Prospective case series study. Place and Duration of Study: Conducted in obstetric and gynae department of Dow University of Health and Sciences/Lyari General Hospital, from Jul 2009 to Jan 2010. Material and Methods: Two hundred and eighty one perimenopausal women with abnormal uterine bleeding were included with age
more » ... ange between 40 to 55 years. Dilatation and curettage were carried out, under general anesthesia and endometrial samples were taken by scrapping walls of the uterus. Collected samples were fixed in 10% formalin and sent to histopathology department, Dow Medical College Karachi. Histopathology report of each patient was studied for hyperplasia and frequency of hyperplasia and its relation with type of abnormal uterine bleeding (menorrhagia, polymenorrhagea and menometrorrhagia) was determined. Results: Mean age (± SD) was 44.13 ± 3.7 years with age range of 40-55 years. Most common type of abnormal uterine bleeding (AUB) was menorrhagia found in 211 (75.08%) women followed by menometrorrhagia in 40 (14.23%) and polymenorrhagea in 30 (10.67%) women. Endometrial hyperplasia was found in 37 (13.17%) women. Most common pattern of abnormal uterine bleeding associated with hyperplasia was polymenorrhagea 5 out of 30 (16.6%) women. Conclusion: In this study frequency of endometrial hyperplasia was 13.17% in perimenopausal women with abnormal uterine bleeding. Abnormal uterine bleeding occurring in perimenopausal age is alarming and needs thorough evaluation including endometrial sampling, as it could be the only clinical manifestation of endometrial hyperplasia, a precursor of endometrial cancer.
fatcat:irnkypz42jg3jn77shzhwcoyjq

E Ed di it to or ri ia al l C Co om mm mi it tt te ee e Chief Editor Joint Editor Assistant Editors National (Extra-Organizational) National (Organizational) PAKISTAN ARMED FORCES MEDICAL JOURNAL

Muhammad Riaz, Aziz Ahmed, Muhammad Mukarram Bashir, Mushtaq Ahmed, Javaid Malik, Nabeel Khan, Afridi, Suhaib Ahmed, Ahmed Khan, Nadir Ali, Shan-E Rauf, Muhammad Siddiqui (+75 others)
2016 unpublished
Nighat Jamal 857 P Pe er rs so on na al li it ty y T Ty yp pe e A An nd d W Wo or rk k F Fa am mi il ly y C Co on nf fl li ic ct t i in n F Fe em ma al le e D Do oc ct to or rs s Mehreen Gulzar  ... 
fatcat:cyehsjtp65gxzi5o7qi6a5yy6q

A Reference Viral Database (RVDB) To Enhance Bioinformatics Analysis of High-Throughput Sequencing for Novel Virus Detection

Norman Goodacre, Aisha Aljanahi, Subhiksha Nandakumar, Mike Mikailov, Arifa S. Khan, Michael J. Imperiale
2018 mSphere  
We are grateful to Raja Mazumder, Naila Gulzar, and Robel Kahsay for making the RVDB available to the public through the George Washington University HIVE and to Debbie Sieff and her staff at the FDA for  ... 
doi:10.1128/mspheredirect.00069-18 pmid:29564396 pmcid:PMC5853486 fatcat:bi6jnuapi5hjxir2aju46bn2fy
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