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  1. Article ; Online: Patterns of Change in Nucleotide Diversity Over Gene Length.

    Ali, Farhan

    Genome biology and evolution

    2024  Volume 16, Issue 4

    Abstract: Nucleotide diversity at a site is influenced by the relative strengths of neutral and selective population genetic processes. Therefore, attempts to estimate Effective population size based on the diversity of synonymous sites demand a better ... ...

    Abstract Nucleotide diversity at a site is influenced by the relative strengths of neutral and selective population genetic processes. Therefore, attempts to estimate Effective population size based on the diversity of synonymous sites demand a better understanding of their selective constraints. The nucleotide diversity of a gene was previously found to correlate with its length. In this work, I measure nucleotide diversity at synonymous sites and uncover a pattern of low diversity towards the translation initiation site of a gene. The degree of reduction in diversity at the translation initiation site and the length of this region of reduced diversity can be quantified as "Effect Size" and "Effect Length" respectively, using parameters of an asymptotic regression model. Estimates of Effect Length across bacteria covaried with recombination rates as well as with a multitude of translation-associated traits such as the avoidance of mRNA secondary structure around translation initiation site, the number of rRNAs, and relative codon usage of ribosomal genes. Evolutionary simulations under purifying selection reproduce the observed patterns and diversity-length correlation and highlight that selective constraints on the 5'-region of a gene may be more extensive than previously believed. These results have implications for the estimation of effective population size, and relative mutation rates, and for genome scans of genes under positive selection based on "silent-site" diversity.
    MeSH term(s) Genetic Variation ; Evolution, Molecular ; Selection, Genetic ; Models, Genetic ; Nucleotides/genetics ; Codon Usage ; Peptide Chain Initiation, Translational
    Chemical Substances Nucleotides
    Language English
    Publishing date 2024-04-09
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2495328-3
    ISSN 1759-6653 ; 1759-6653
    ISSN (online) 1759-6653
    ISSN 1759-6653
    DOI 10.1093/gbe/evae078
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Patterns of change in nucleotide diversity over gene length.

    Ali, Farhan

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Nucleotide diversity at a site is influenced by the relative strengths of neutral and selective population genetic processes. Therefore, attempts to identify sites under positive selection require an understanding of the expected diversity in its absence. ...

    Abstract Nucleotide diversity at a site is influenced by the relative strengths of neutral and selective population genetic processes. Therefore, attempts to identify sites under positive selection require an understanding of the expected diversity in its absence. The nucleotide diversity of a gene was previously found to correlate with its length. In this work, I measure nucleotide diversity at synonymous sites and uncover a pattern of low diversity towards the translation initiation site (TIS) of a gene. The degree of reduction in diversity at the TIS and the length of this region of reduced diversity can be quantified as "Effect Size" and "Effect Length" respectively, using parameters of an asymptotic regression model. Estimates of Effect Length across bacteria covaried with recombination rates as well as with a multitude of fast-growth adaptations such as the avoidance of mRNA secondary structure around TIS, the number of rRNAs, and relative codon usage of ribosomal genes. Thus, the dependence of nucleotide diversity on gene length is governed by a combination of selective and non-selective processes. These results have implications for the estimation of effective population size and relative mutation rates based on "silent-site" diversity, and for pN/pS-based prediction of genes under selection.
    Language English
    Publishing date 2023-07-15
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.07.13.548940
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  3. Article ; Online: ICOP-Pharm: could the new paradigm bridge a gap in evidence raised by 2022 ESC guidelines on cardio-oncology?

    Yaseen, Israa Fadhil / Farhan, Hasan Ali

    European heart journal

    2022  Volume 44, Issue 11, Page(s) 912–915

    MeSH term(s) Humans ; Neoplasms/therapy ; Medical Oncology ; Cardiovascular Diseases/therapy
    Language English
    Publishing date 2022-12-02
    Publishing country England
    Document type Journal Article
    ZDB-ID 603098-1
    ISSN 1522-9645 ; 0195-668X
    ISSN (online) 1522-9645
    ISSN 0195-668X
    DOI 10.1093/eurheartj/ehac701
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  4. Article: Perceptions of the Cardiologists and Oncologists: Initial Step for Establishing Cardio-Oncology Service.

    Farhan, Hasan Ali / Yaseen, Israa Fadhil

    Frontiers in cardiovascular medicine

    2021  Volume 8, Page(s) 704029

    Abstract: Background: ...

    Abstract Background:
    Language English
    Publishing date 2021-11-24
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2781496-8
    ISSN 2297-055X
    ISSN 2297-055X
    DOI 10.3389/fcvm.2021.704029
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  5. Article: Cardiovascular drug interventions in the cardio-oncology clinic by a cardiology pharmacist: ICOP-Pharm study.

    Yaseen, Israa Fadhil / Farhan, Hasan Ali

    Frontiers in cardiovascular medicine

    2022  Volume 9, Page(s) 972455

    Abstract: Background: Cardio-oncology is a rapidly growing field that requires a novel service design to deal with the increasing number of patients. It is reported that the volume of patients at the cardio-oncology clinic in the United Kingdom is 535 patients/5 ... ...

    Abstract Background: Cardio-oncology is a rapidly growing field that requires a novel service design to deal with the increasing number of patients. It is reported that the volume of patients at the cardio-oncology clinic in the United Kingdom is 535 patients/5 years and in Canada is 779 patients/7 years. The pharmacist has a role in reducing the consultation time of physicians.
    Objective: To identify the role of a qualified cardiology pharmacist at the cardio-oncology clinic using a new paradigm based on complementary interventions with the cardiologist for the management of patients with cancer and cardiovascular risk factors and/or cardiovascular diseases (CVRF/CVD).
    Methods: A prospective observational study was conducted at the cardio-oncology clinic in the Medical City in Baghdad, Iraq between December 2020 and December 2021. Patients with CVRF/CVD were registered. The Iraqi Cardio-Oncology Program-Pharmacist (ICOP-Pharm) paradigm was designed to involve a qualified cardiology pharmacist for initial cardiovascular (CV) drug interventions.
    Results: Among 333 patients who attended our clinic over the 1-year interval, 200 (60%) CVRF/CVD cases were enrolled in the study, and of them 79 (40%) patients had CV drug interventions. A total of 196 interventions were done, including 147 (75%) cases performed by the cardiology pharmacist, and 92 (63%) of the latter were CV drug initiations. Among the total CVRF/CVD treated initially by the cardiology pharmacist, hypertension 32 (26%) and cancer therapy-related cardiac dysfunction 29 (24%) were the main types.
    Conclusion: The qualified cardiology pharmacist was responsible for three-quarters of the initial CV drug interventions at the cardio-oncology clinic in a complementary approach to the cardiologist. The role of the cardiology pharmacist in the ICOP-Pharm paradigm may be one of the reasons for the ability of the heart team to manage 3-fold of the patient volume when compared with those in the United Kingdom or Canada.
    Language English
    Publishing date 2022-09-29
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2781496-8
    ISSN 2297-055X
    ISSN 2297-055X
    DOI 10.3389/fcvm.2022.972455
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  6. Article ; Online: Spectrum sensing-focused cognitive radio network for 5G revolution

    Farhan Ali / He Yigang

    Frontiers in Environmental Science, Vol

    2023  Volume 11

    Abstract: The cognitive radio network (CRN), an instrumental part of the next-generation wireless communication systems, is mainly dependent on spectrum sensing to function properly. The radio spectrum can help in clean energy transition and load capacity factors ... ...

    Abstract The cognitive radio network (CRN), an instrumental part of the next-generation wireless communication systems, is mainly dependent on spectrum sensing to function properly. The radio spectrum can help in clean energy transition and load capacity factors by providing a more efficient and accurate spectrum utilization. By using it, the number of spectrums that is used for communication can be optimized, which can reduce the amount of energy consumed by the network. Additionally, 5G radio spectrum sensing can be used to identify and classify different types of signals, which can help reduce the amount of interference in the network and improve the efficiency of energy utilization. It can also allow for the digitization of clean energy infrastructure and facilitate better decision-making processes that take into account environmental impacts while optimizing energy use because of its efficient characteristics like non-linearity, detection, scalability, robustness, generalization, non-stationarity in wireless environments, dynamic entity, weighted sum of Gaussian functions centered at specific frequencies, and robustness against noise and interference. It can adapt to noise and interference by adjusting its parameters, and this allows accurate distinguishing between primary and secondary users in the wireless spectrum, which is why a radial basis function is a popular choice for spectrum sensing in 5G networks. Radial basis function networks (RBFNs) can work better in 5G spectrum sensing for better signal classification, dynamic adaptation, fast detection, faster decision-making, and improved noise and interference reduction. One of the most sought-after goals in the field of wireless research is the creation of spectrum-sensing technology that is dependable and intelligent because multilayer learning approaches are inappropriate for dealing with time-series data due to the higher misclassification rate and inherent computational complexity. To address this, the study proposed the radial basis function network that ...
    Keywords 5G ; spectrum sensing ; radial basis function ; energy detection ; cognitive radio network ; Environmental sciences ; GE1-350
    Subject code 600
    Language English
    Publishing date 2023-04-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
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  7. Article ; Online: Approval procedure for active substances in plant protection products - doubts of scientific certainty as a source of controversy. Analysis of systemic imperfections on the example of glyphosate

    Anna Gembicka / Jakub Ali Farhan

    Eastern European Journal of Transnational Relations, Vol 6, Iss

    2023  Volume 1

    Abstract: The purpose of this article is to examine the causes of recurring doubts regarding the safety of plant protection products used in the European Union. Plant protection products are a particular subject of regulation. All standards concerning them require ...

    Abstract The purpose of this article is to examine the causes of recurring doubts regarding the safety of plant protection products used in the European Union. Plant protection products are a particular subject of regulation. All standards concerning them require prior in-depth scientific research in the field of exact sciences. Achieving adequate safety of humans, animals and the environment in connection to the use of plant protection products requires not only good law, but a law based on representative research and scientific certainty. Bearing in mind the above, the authors undertook an analysis of what seems to be the cause of significant social doubts as to the actual achievement of the purposes of Regulation 1107/2009, i.e. inclusion of scientific research in the procedure of approval of active substances in plant protection products. First, the approval procedure for the active substance of the plant protection product was presented, and then the main shortcoming of the procedure was analyzed on the example of the approval of glyphosate. In the authors' opinion, guidance documents on literature review should be revised to reflect the best scientific practice, and their standards should be enforced, in particular, to ensure that there is no doubt about the objectivity of the literature review.
    Keywords active substance approval ; pesticides ; glyphosate ; Political science ; J ; Social Sciences ; H
    Subject code 340
    Language English
    Publishing date 2023-04-01T00:00:00Z
    Publisher University of Bialystok, Faculty of Law
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: The influence of meaningful work on the mental health of SME employees in the COVID-19 era

    Muhammad Farhan Jalil / Azlan Ali

    BMC Public Health, Vol 23, Iss 1, Pp 1-

    can coping strategies mediate the relationship?

    2023  Volume 20

    Abstract: Abstract Background Stress, depression, and anxiety are prevalent issues among SME employees during the COVID-19 pandemic. Even while having meaningful work that expressively contributes to individual growth has been related to improving mental health, ... ...

    Abstract Abstract Background Stress, depression, and anxiety are prevalent issues among SME employees during the COVID-19 pandemic. Even while having meaningful work that expressively contributes to individual growth has been related to improving mental health, employees’ work may also need to adopt coping strategies to increase outcomes. The purpose of this study was to examine the relationship between meaningful work (positive meaning, meaning-making, and greater good motivations) and mental health, as well as coping strategies (problem-focused and emotion-focused) as a mediator of this relationship. Methods Meaningful work, coping strategies, and mental health were evaluated in empirical research based on a sample of 462 SME employees working in Malaysia. Structured questionnaires were used to collect the data and analyze it through Structural Equation Modelling (SEM) using AMOS 21.0. Results The findings of the study show the importance of meaningful work in influencing the mental health of SME employees, particularly during a crisis like the COVID-19 pandemic. This suggests that the more they value and see their work as meaningful, the more capable they are of dealing with limitations and mental health problems associated with crises. The study also discovered a partial mediating role for coping strategies between employees’ mental health and meaningful work. Conclusion This study encourages employees to constantly feel connected and discover continued possibilities to work and learn even during crisis situations. In order to improve human resource efficiency in emerging markets, managers and owners of SMEs must implement the model developed by the researchers.
    Keywords Meaningful work ; Coping strategies ; Mental health ; SMEs ; Structure equation modelling ; COVID-19 ; Public aspects of medicine ; RA1-1270
    Subject code 360
    Language English
    Publishing date 2023-12-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: The influence of meaningful work on the mental health of SME employees in the COVID-19 era: can coping strategies mediate the relationship?

    Jalil, Muhammad Farhan / Ali, Azlan

    BMC public health

    2023  Volume 23, Issue 1, Page(s) 2435

    Abstract: Background: Stress, depression, and anxiety are prevalent issues among SME employees during the COVID-19 pandemic. Even while having meaningful work that expressively contributes to individual growth has been related to improving mental health, ... ...

    Abstract Background: Stress, depression, and anxiety are prevalent issues among SME employees during the COVID-19 pandemic. Even while having meaningful work that expressively contributes to individual growth has been related to improving mental health, employees' work may also need to adopt coping strategies to increase outcomes. The purpose of this study was to examine the relationship between meaningful work (positive meaning, meaning-making, and greater good motivations) and mental health, as well as coping strategies (problem-focused and emotion-focused) as a mediator of this relationship.
    Methods: Meaningful work, coping strategies, and mental health were evaluated in empirical research based on a sample of 462 SME employees working in Malaysia. Structured questionnaires were used to collect the data and analyze it through Structural Equation Modelling (SEM) using AMOS 21.0.
    Results: The findings of the study show the importance of meaningful work in influencing the mental health of SME employees, particularly during a crisis like the COVID-19 pandemic. This suggests that the more they value and see their work as meaningful, the more capable they are of dealing with limitations and mental health problems associated with crises. The study also discovered a partial mediating role for coping strategies between employees' mental health and meaningful work.
    Conclusion: This study encourages employees to constantly feel connected and discover continued possibilities to work and learn even during crisis situations. In order to improve human resource efficiency in emerging markets, managers and owners of SMEs must implement the model developed by the researchers.
    MeSH term(s) Humans ; Mental Health ; Stress, Psychological/psychology ; Pandemics ; COVID-19/epidemiology
    Language English
    Publishing date 2023-12-06
    Publishing country England
    Document type Journal Article
    ZDB-ID 2041338-5
    ISSN 1471-2458 ; 1471-2458
    ISSN (online) 1471-2458
    ISSN 1471-2458
    DOI 10.1186/s12889-023-17347-3
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  10. Article: The positive impact of COVID-19 on Tuberculosis endemic areas.

    Ali, Farhan / Ali, Kashif

    JPMA. The Journal of the Pakistan Medical Association

    2021  Volume 71, Issue 11, Page(s) 2686

    MeSH term(s) COVID-19 ; Endemic Diseases ; Humans ; SARS-CoV-2 ; Tuberculosis/complications ; Tuberculosis/epidemiology
    Language English
    Publishing date 2021-11-16
    Publishing country Pakistan
    Document type Journal Article
    ZDB-ID 603873-6
    ISSN 0030-9982
    ISSN 0030-9982
    DOI 10.47391/JPMA.013880
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