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  1. Book ; Online: Hierarchical deep learning-based adaptive time-stepping scheme for multiscale simulations

    Hamid, Asif / Rafiq, Danish / Nahvi, Shahkar Ahmad / Bazaz, Mohammad Abid

    2023  

    Abstract: Multiscale is a hallmark feature of complex nonlinear systems. While the simulation using the classical numerical methods is restricted by the local \textit{Taylor} series constraints, the multiscale techniques are often limited by finding heuristic ... ...

    Abstract Multiscale is a hallmark feature of complex nonlinear systems. While the simulation using the classical numerical methods is restricted by the local \textit{Taylor} series constraints, the multiscale techniques are often limited by finding heuristic closures. This study proposes a new method for simulating multiscale problems using deep neural networks. By leveraging the hierarchical learning of neural network time steppers, the method adapts time steps to approximate dynamical system flow maps across timescales. This approach achieves state-of-the-art performance in less computational time compared to fixed-step neural network solvers. The proposed method is demonstrated on several nonlinear dynamical systems, and source codes are provided for implementation. This method has the potential to benefit multiscale analysis of complex systems and encourage further investigation in this area.
    Keywords Mathematics - Dynamical Systems ; Computer Science - Machine Learning
    Subject code 000
    Publishing date 2023-11-10
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article: Evaluation and prediction of COVID-19 in India: A case study of worst hit states.

    Rafiq, Danish / Suhail, Suhail Ahmad / Bazaz, Mohammad Abid

    Chaos, solitons, and fractals

    2020  Volume 139, Page(s) 110014

    Abstract: In this manuscript, system modeling and identification techniques are applied in developing a prognostic yet deterministic model to forecast the spread of COVID-19 in India. The model is verified with the historical data and a forecast of the spread for ... ...

    Abstract In this manuscript, system modeling and identification techniques are applied in developing a prognostic yet deterministic model to forecast the spread of COVID-19 in India. The model is verified with the historical data and a forecast of the spread for 30-days is presented in the 10 most affected states of India. The major results suggest that our model can very well capture the disease variations with high accuracy. The results also show a steep rise in the total cumulative cases and deaths in the coming weeks.
    Keywords covid19
    Language English
    Publishing date 2020-06-19
    Publishing country England
    Document type Journal Article
    ZDB-ID 2003919-0
    ISSN 1873-2887 ; 0960-0779
    ISSN (online) 1873-2887
    ISSN 0960-0779
    DOI 10.1016/j.chaos.2020.110014
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Epigenetic‐based control of flowering and seed development in plants: A review

    Ibrar, Danish / Ahmad, Rafiq / Hasnain, Zuhair / Gul, Safia / Rais, Afroz / K̲h̲ān, Shahbāz

    Plant Breeding. 2023 Dec., v. 142, no. 6, p. 732-744

    2023  , Page(s) 732–744

    Abstract: Plants grown at different latitudes perceive and interpret seasonal variations in day length (photoperiod) and exposure to cold winter temperatures (vernalization). These factors control the expression of various genes involved in flowering, depending on ...

    Abstract Plants grown at different latitudes perceive and interpret seasonal variations in day length (photoperiod) and exposure to cold winter temperatures (vernalization). These factors control the expression of various genes involved in flowering, depending on the variations in photoperiod and vernalization. Epigenetic regulatory systems have evolved in plants to process environmental signals. Gene expression is modified through chromatin remodelling and small RNAs in response to seasonal changes in both annual and perennial plants. Key regulators of flowering, such as FLOWERING LOCUS C (FLC) and FLOWERING LOCUS T (FT), interact with other floral regulatory factors and undergo chromatin remodelling in response to seasonal cues. The Polycomb repressive complex (PRC) controls the expression of flowering‐related genes in photoperiodic flowering regulation. FLC acts as a potent suppressor by down‐regulating the expression of genes that promote flowering. Methylation, particularly in the context of CHG, CG and CHH, plays a critical role in embryogenesis. This review briefly explores and describes the regulation of flowering mechanisms in response to day‐length variations, cold exposure (vernalization) and seed development in plants.
    Keywords chromatin ; cold ; cold stress ; embryogenesis ; epigenetics ; gene expression ; loci ; methylation ; photoperiod ; seed development ; vernalization
    Language English
    Dates of publication 2023-12
    Size p. 732-744
    Publishing place John Wiley & Sons, Ltd
    Document type Article ; Online
    Note REVIEW
    ZDB-ID 232853-7
    ISSN 0179-9541
    ISSN 0179-9541
    DOI 10.1111/pbr.13148
    Database NAL-Catalogue (AGRICOLA)

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  4. Article ; Online: Three months of COVID-19: A systematic review and meta-analysis.

    Rafiq, Danish / Batool, Asiya / Bazaz, M A

    Reviews in medical virology

    2020  Volume 30, Issue 4, Page(s) e2113

    Abstract: The pandemic of 2019 novel coronavirus (SARS-CoV-2019), reminiscent of the 2002-SARS-CoV outbreak, has completely isolated countries, disrupted health systems and partially paralyzed international trade and travel. In order to be better equipped to ... ...

    Abstract The pandemic of 2019 novel coronavirus (SARS-CoV-2019), reminiscent of the 2002-SARS-CoV outbreak, has completely isolated countries, disrupted health systems and partially paralyzed international trade and travel. In order to be better equipped to anticipate transmission of this virus to new regions, it is imperative to track the progress of the virus over time. This review analyses information on progression of the pandemic in the past 3 months and systematically discusses the characteristics of SARS-CoV-2019 virus including its epidemiologic, pathophysiologic, and clinical manifestations. Furthermore, the review also encompasses some recently proposed conceptual models that estimate the spread of this disease based on the basic reproductive number for better prevention and control procedures. Finally, we shed light on how the virus has endangered the global economy, impacting it both from the supply and demand side.
    MeSH term(s) Adaptive Immunity ; Antiviral Agents/therapeutic use ; Basic Reproduction Number ; Betacoronavirus/classification ; Betacoronavirus/genetics ; Betacoronavirus/pathogenicity ; Betacoronavirus/physiology ; COVID-19 ; COVID-19 Testing ; Clinical Laboratory Techniques ; Commerce ; Coronavirus Infections/diagnosis ; Coronavirus Infections/drug therapy ; Coronavirus Infections/epidemiology ; Coronavirus Infections/transmission ; Coronavirus Infections/virology ; Economics ; Genome, Viral ; Humans ; Models, Theoretical ; Pandemics ; Pneumonia, Viral/diagnosis ; Pneumonia, Viral/epidemiology ; Pneumonia, Viral/transmission ; Pneumonia, Viral/virology ; SARS-CoV-2 ; Virus Replication
    Chemical Substances Antiviral Agents
    Keywords covid19
    Language English
    Publishing date 2020-05-18
    Publishing country England
    Document type Journal Article ; Meta-Analysis ; Research Support, Non-U.S. Gov't ; Systematic Review
    ZDB-ID 1086043-5
    ISSN 1099-1654 ; 1052-9276
    ISSN (online) 1099-1654
    ISSN 1052-9276
    DOI 10.1002/rmv.2113
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Cross talk of tumor protein D52 (TPD52) with KLF9, PKCε, and MicroRNA 223 in ovarian cancer.

    Khan, Khushbukhat / Zafar, Sameen / Badshah, Yasmin / Ashraf, Naeem Mahmood / Rafiq, Mehak / Danish, Lubna / Shabbir, Maria / Trembley, Janeen H / Afsar, Tayyaba / Almajwal, Ali / Razak, Suhail

    Journal of ovarian research

    2023  Volume 16, Issue 1, Page(s) 202

    Abstract: Background: Gynecologic cancers comprise malignancies in the female reproductive organs. Ovarian cancer ranks sixth in terms of incidence rates while seventh in terms of mortality rates. The stage at which ovarian cancer is diagnosed mainly determines ... ...

    Abstract Background: Gynecologic cancers comprise malignancies in the female reproductive organs. Ovarian cancer ranks sixth in terms of incidence rates while seventh in terms of mortality rates. The stage at which ovarian cancer is diagnosed mainly determines the survival outcomes of patients. Various screening approaches are presently employed for diagnosing ovarian cancer; however, these techniques have low accuracy and are non-specific, resulting in high mortality rates of patients due to this disease. Hence, it is crucial to identify improved screening and diagnostic markers to overcome this cancer. This study aimed to find new biomarkers to facilitate the prognosis and diagnosis of ovarian cancer.
    Methods: Bioinformatics approaches were used to predict the tertiary structure and cellular localization along with phylogenetic analysis of TPD52. Its molecular interactions were determined through KEGG analysis, and real-time PCR-based expression analysis was performed to assess its co-expression with another oncogenic cellular pathway (miR-223, KLF9, and PKCε) proteins in ovarian cancer.
    Results: Bioinformatics analysis depicted the cytoplasmic localization of TPD52 and the high conservation of its coiled-coil domains. Further study revealed that TPD52 mRNA and miRNA-223 expression was elevated, while the expression of KLF 9 and PKCε was reduced in the blood of ovarian cancer patients. Furthermore, TPD52 and miR-223 expression were upregulated in the early stages of cancer and non-metastatic cancers.
    Conclusion: TPD52, miR-223, PKCε, and KLF9, can be used as a blood based markers for disease prognosis, metastasis, and treatment response. The study outcomes hold great potential to be translated at the clinical level after further validation on larger cohorts.
    MeSH term(s) Female ; Humans ; Kruppel-Like Transcription Factors/genetics ; MicroRNAs/genetics ; Neoplasm Proteins/genetics ; Ovarian Neoplasms/genetics ; Ovarian Neoplasms/pathology ; Phylogeny ; Protein Kinase C-epsilon/genetics
    Chemical Substances KLF9 protein, human ; Kruppel-Like Transcription Factors ; MicroRNAs ; MIRN223 microRNA, human ; Neoplasm Proteins ; Protein Kinase C-epsilon (EC 2.7.11.13) ; TPD52 protein, human
    Language English
    Publishing date 2023-10-13
    Publishing country England
    Document type Journal Article
    ZDB-ID 2455679-8
    ISSN 1757-2215 ; 1757-2215
    ISSN (online) 1757-2215
    ISSN 1757-2215
    DOI 10.1186/s13048-023-01292-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Evaluation and prediction of COVID-19 in India

    Rafiq, Danish / Suhail, Suhail Ahmad / Bazaz, Mohammad Abid

    Chaos, Solitons & Fractals

    A case study of worst hit states

    2020  Volume 139, Page(s) 110014

    Keywords General Mathematics ; covid19
    Language English
    Publisher Elsevier BV
    Publishing country us
    Document type Article ; Online
    ZDB-ID 2003919-0
    ISSN 1873-2887 ; 0960-0779
    ISSN (online) 1873-2887
    ISSN 0960-0779
    DOI 10.1016/j.chaos.2020.110014
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Three months of COVID ‐19

    Rafiq, Danish / Batool, Asiya / Bazaz, M. A.

    Reviews in Medical Virology

    A systematic review and meta‐analysis

    2020  Volume 30, Issue 4

    Keywords Virology ; Infectious Diseases ; covid19
    Language English
    Publisher Wiley
    Publishing country us
    Document type Article ; Online
    ZDB-ID 1086043-5
    ISSN 1099-1654 ; 1052-9276
    ISSN (online) 1099-1654
    ISSN 1052-9276
    DOI 10.1002/rmv.2113
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article: Covert nail injury to the back: A case report.

    Kathia, Usama Muhammad / Rafiq, Iqra / Hussain, Bilal / Fatima, Tausief / Khan, Anwar Zeb / Ali, Danish

    JPMA. The Journal of the Pakistan Medical Association

    2021  Volume 71, Issue 6, Page(s) 1679–1681

    Abstract: Occupational trauma in carpentry is common in our society due to lack of awareness on occupational safety and poor availability and adherence towards protective equipment. Given below is an unusual case of a young carpenter who presented in the ... ...

    Abstract Occupational trauma in carpentry is common in our society due to lack of awareness on occupational safety and poor availability and adherence towards protective equipment. Given below is an unusual case of a young carpenter who presented in the orthopaedic outpatient department with complaint of difficulty in walking for the last four days. On examination, restricted movement of the hip joint on extension was observed. On further work up in the form of radiological investigations, a long iron nail was discovered as incidental finding in the back in close proximity to the ascending colon and duodenum in the retroperitoneum. Elective laparotomy was performed to remove the nail, after which the patient improved clinically and his presenting complaints were completely resolved on further follow up. This demonstrates the unusual way in which such a case can present in the outpatient department instead of the emergency department and with symptoms that may prompt one to think of anything but foreign body trauma, emphasising the need for proper history and meticulous relevant clinical examination, as covert foreign body injury can occur to the back, especially in patients involved in such occupations.
    MeSH term(s) Eye Injuries, Penetrating ; Foreign Bodies/complications ; Foreign Bodies/diagnostic imaging ; Foreign Bodies/surgery ; Humans ; Occupational Injuries
    Language English
    Publishing date 2021-06-10
    Publishing country Pakistan
    Document type Case Reports
    ZDB-ID 603873-6
    ISSN 0030-9982
    ISSN 0030-9982
    DOI 10.47391/JPMA.
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Application of machine learning for identification of heterotic groups in sunflower through combined approach of phenotyping, genotyping and protein profiling.

    Ibrar, Danish / Khan, Shahbaz / Raza, Mudassar / Nawaz, Muhammad / Hasnain, Zuhair / Kashif, Muhammad / Rais, Afroz / Gul, Safia / Ahmad, Rafiq / Gaafar, Abdel-Rhman Z

    Scientific reports

    2024  Volume 14, Issue 1, Page(s) 7333

    Abstract: Application of machine learning in plant breeding is a recent concept, that has to be optimized for precise utilization in the breeding program of high yielding crop plants. Identification and efficient utilization of heterotic grouping pattern aided ... ...

    Abstract Application of machine learning in plant breeding is a recent concept, that has to be optimized for precise utilization in the breeding program of high yielding crop plants. Identification and efficient utilization of heterotic grouping pattern aided with machine learning approaches is of utmost importance in hybrid cultivar breeding as it can save time and resources required to breed a new plant hybrid/variety. In the present study, 109 genotypes of sunflower were investigated at morphological, biochemical (SDS-PAGE) and molecular levels (through micro-satellites (SSR) markers) for heterotic grouping. All the three datasets were combined, scaled, and subjected to unsupervised machine learning algorithms, i.e., Hierarchical clustering, K-means clustering and hybrid clustering algorithm (hierarchical + K-means) for assessment of efficiency and resolution power of these algorithms in practical plant breeding for heterotic grouping identification. Following the application of machine learning unsupervised clustering approach, two major groups were identified in the studied sunflower germplasm, and further classification revealed six smaller classes in each major group through hierarchical and hybrid clustering approach. Due to high resolution, obtained in hierarchical clustering, classification achieved through this algorithm was further used for selection of potential parents. One genotype from each smaller group was selected based on the maximum seed yield potential and hybridized in a line  ×  tester mating design producing 36 F
    MeSH term(s) Hybrid Vigor ; Hybridization, Genetic ; Helianthus/genetics ; Genotype ; Plant Breeding ; Asteraceae ; Machine Learning
    Language English
    Publishing date 2024-03-27
    Publishing country England
    Document type Journal Article
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-024-58049-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: Green synthesis and application of GO nanoparticles to augment growth parameters and yield in mungbean (

    Mirza, Faisal Shafiq / Aftab, Zill-E-Huma / Ali, Muhammad Danish / Aftab, Arusa / Anjum, Tehmina / Rafiq, Hamza / Li, Guihua

    Frontiers in plant science

    2022  Volume 13, Page(s) 1040037

    Abstract: Plant growth promotion has long been a challenge for growers all over the world. In this work, we devised a green nanomaterial-assisted approach to boost plant growth. It has been reported that carbon nanomaterials are toxic to plants because they can ... ...

    Abstract Plant growth promotion has long been a challenge for growers all over the world. In this work, we devised a green nanomaterial-assisted approach to boost plant growth. It has been reported that carbon nanomaterials are toxic to plants because they can inhibit the uptake of nutrients if employed in higher concentrations, however this study shows that graphene oxide (GO) can be used as a regulator tool to improve plant growth and stability. Graphene oxide in different concentrations was added to the soil of mungbean. It is proved that when a suitable amount of graphene oxide was applied, it had a good influence on plant growth by enhancing the length of roots and shoots, number of leaves, number of root nodules per plant, number of pods, and seeds per pod. We presume that the use of bio-fabricated graphene oxide as a strategy would make it possible to boost both plant growth and the significant increase in the number of seeds produced by each plant.
    Language English
    Publishing date 2022-11-10
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2613694-6
    ISSN 1664-462X
    ISSN 1664-462X
    DOI 10.3389/fpls.2022.1040037
    Database MEDical Literature Analysis and Retrieval System OnLINE

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