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  1. Article: Validation and Development of Discharge Equations for 3D Printed Flumes for Flow Monitoring

    Akhter, Farhana / McMaine, John / McLemore, Alex J. / Hurst, Morghan J.

    Transactions of the ASABE. , v. 64, no. 6

    2021  

    Abstract: HighlightsTwo different configurations of 3D printed flumes of two different materials were tested for accuracy and variability.Discharge equations were developed for 3D printed 0.122 m HS and 0.102 m Palmer-Bowlus flumes.3D flumes are accurate and show ... ...

    Abstract HighlightsTwo different configurations of 3D printed flumes of two different materials were tested for accuracy and variability.Discharge equations were developed for 3D printed 0.122 m HS and 0.102 m Palmer-Bowlus flumes.3D flumes are accurate and show no statistical variability between prints, providing a low-cost flow measurement tool.Abstract. Flumes are specially shaped, engineered structures that have been used widely for measuring flow. Flumes are typically fabricated from aluminum or fiberglass; however, these types of flumes can be costly if purchased commercially and may lack machine precision if custom fabricated. This limits availability for widespread monitoring by smaller municipalities, engineering firms, or researchers with limited budgets. Using 3D printing technology (additive manufacturing) to produce flumes is very cost-effective, but variability between flumes and materials has not been tested, and discharge equations have not been developed for 3D printed flumes. In this study, a laboratory-scale setup was used to develop discharge equations for two types of 3D printed flumes (0.122 m HS flume and 0.102 m Palmer-Bowlus flume) made from two 3D printing materials: polylactic acid (PLA) and polyethylene terephthalate glycol modified (PETG). Variability between the same type of flume and between different materials for the same type of flume was analyzed to evaluate the consistency of the discharge equation with flumes of the same type. Eight models were developed to fit each dataset (PLA, PETG, and combined PLA and PETG) for both flume types and evaluated for goodness-of-fit and information criteria (AIC and BIC for model parsimony) to select the discharge equation for each flume type. Discharge equations were consistent for the same type of flume across each print and across different print materials. The discharge equations of 3D printed 0.122 m HS flumes and 0.102 m Palmer-Bowlus flumes are Q = 0.45624 × H2.351 and Q = 0.0001176 + 1.309 × (H - 0.0174625)2.235, respectively. The discharge equations of both flume types had R2adj values greater than 97% for the measured data of each individual flume. Both 3D printed flumes were consistent in measuring flow and are suitable for hydrologic monitoring. Keywords: 3D printing, Additive manufacturing, Discharge equation, Flume, Hydrologic monitoring.
    Keywords aluminum ; cost effectiveness ; data collection ; equations ; fiberglass ; hydraulic flumes ; hydrology ; polyethylene terephthalates ; polylactic acid ; three-dimensional printing
    Language English
    Size p. 1921-1928.
    Publishing place American Society of Agricultural and Biological Engineers (ASABE)
    Document type Article
    ZDB-ID 2232767-8
    ISSN 2151-0032
    ISSN 2151-0032
    DOI 10.13031/trans.14365
    Database NAL-Catalogue (AGRICOLA)

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  2. Article: Designing an effective therapeutic siRNA to silence RdRp gene of SARS-CoV-2

    Shawan, Mohammad Mahfuz Ali Khan / Sharma, Ashish Ranjan / Bhattacharya, Manojit / Mallik, Bidyut / Akhter, Farhana / Shakil, Md. Salman / Hossain, Md. Mozammel / Banik, Subrata / Lee, Sang-Soo / Hasan, Md. Ashraful / Chakraborty, Chiranjib

    Infection, genetics, and evolution. 2021 Sept., v. 93

    2021  

    Abstract: The devastating outbreak of COVID-19 has spread all over the world and has become a global health concern. There is no specific therapeutics to encounter the COVID-19. Small interfering RNA (siRNA)-based therapy is an efficient strategy to control human ... ...

    Abstract The devastating outbreak of COVID-19 has spread all over the world and has become a global health concern. There is no specific therapeutics to encounter the COVID-19. Small interfering RNA (siRNA)-based therapy is an efficient strategy to control human viral infections employing post-transcriptional gene silencing (PTGS) through neutralizing target complementary mRNA. RNA-dependent RNA polymerase (RdRp) encoded by the viral RdRp gene as a part of the replication-transcription complex can be adopted as an acceptable target for controlling SARS-CoV-2 mediated infection. Therefore, in the current study, accessible siRNA designing tools, including significant algorithms and parameters, were rationally used to design the candidate siRNAs against SARS-COV-2 encoded RdRp. The designed siRNA molecules possessed adequate nucleotide-based and other features for potent gene silencing. The targets of the designed siRNAs revealed no significant matches within the whole human genome, ruling out any possibilities for off-target silencing by the siRNAs. Characterization with different potential parameters of efficacy allowed selecting the finest siRNA among all the designed siRNA molecules. Further, validation assessment and target site accessibility prediction also rationalized the suitability of this siRNA molecule. Molecular docking study between the selected siRNA molecule and component of RNA interference (RNAi) pathway gave an excellent outcome. Molecular dynamics of two complexes: siRNA and argonaute complex, guide RNA, and target protein complex, have shown structural stability of these proteins. Therefore, the designed siRNA molecule might act as an effective therapeutic agent against the SARS-CoV-2 at the genome level and can prevent further outbreaks of COVID-19 in humans.
    Keywords COVID-19 infection ; RNA interference ; RNA-directed RNA polymerase ; Severe acute respiratory syndrome coronavirus 2 ; evolution ; genes ; humans ; infection ; molecular dynamics ; prediction ; therapeutics
    Language English
    Dates of publication 2021-09
    Publishing place Elsevier B.V.
    Document type Article
    Note NAL-AP-2-clean
    ZDB-ID 2037068-4
    ISSN 1567-1348
    ISSN 1567-1348
    DOI 10.1016/j.meegid.2021.104951
    Database NAL-Catalogue (AGRICOLA)

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  3. Article ; Online: Designing an effective therapeutic siRNA to silence RdRp gene of SARS-CoV-2.

    Shawan, Mohammad Mahfuz Ali Khan / Sharma, Ashish Ranjan / Bhattacharya, Manojit / Mallik, Bidyut / Akhter, Farhana / Shakil, Md Salman / Hossain, Md Mozammel / Banik, Subrata / Lee, Sang-Soo / Hasan, Md Ashraful / Chakraborty, Chiranjib

    Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases

    2021  Volume 93, Page(s) 104951

    Abstract: The devastating outbreak of COVID-19 has spread all over the world and has become a global health concern. There is no specific therapeutics to encounter the COVID-19. Small interfering RNA (siRNA)-based therapy is an efficient strategy to control human ... ...

    Abstract The devastating outbreak of COVID-19 has spread all over the world and has become a global health concern. There is no specific therapeutics to encounter the COVID-19. Small interfering RNA (siRNA)-based therapy is an efficient strategy to control human viral infections employing post-transcriptional gene silencing (PTGS) through neutralizing target complementary mRNA. RNA-dependent RNA polymerase (RdRp) encoded by the viral RdRp gene as a part of the replication-transcription complex can be adopted as an acceptable target for controlling SARS-CoV-2 mediated infection. Therefore, in the current study, accessible siRNA designing tools, including significant algorithms and parameters, were rationally used to design the candidate siRNAs against SARS-COV-2 encoded RdRp. The designed siRNA molecules possessed adequate nucleotide-based and other features for potent gene silencing. The targets of the designed siRNAs revealed no significant matches within the whole human genome, ruling out any possibilities for off-target silencing by the siRNAs. Characterization with different potential parameters of efficacy allowed selecting the finest siRNA among all the designed siRNA molecules. Further, validation assessment and target site accessibility prediction also rationalized the suitability of this siRNA molecule. Molecular docking study between the selected siRNA molecule and component of RNA interference (RNAi) pathway gave an excellent outcome. Molecular dynamics of two complexes: siRNA and argonaute complex, guide RNA, and target protein complex, have shown structural stability of these proteins. Therefore, the designed siRNA molecule might act as an effective therapeutic agent against the SARS-CoV-2 at the genome level and can prevent further outbreaks of COVID-19 in humans.
    MeSH term(s) Argonaute Proteins/chemistry ; Argonaute Proteins/genetics ; Argonaute Proteins/metabolism ; Base Composition ; Coronavirus RNA-Dependent RNA Polymerase/genetics ; Coronavirus RNA-Dependent RNA Polymerase/metabolism ; Gene Silencing ; Genome, Human ; Humans ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; RNA, Small Interfering/chemistry ; RNA, Small Interfering/genetics ; SARS-CoV-2/genetics ; Sequence Alignment
    Chemical Substances Argonaute Proteins ; RNA, Messenger ; RNA, Small Interfering ; Coronavirus RNA-Dependent RNA Polymerase (EC 2.7.7.48)
    Language English
    Publishing date 2021-06-02
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2037068-4
    ISSN 1567-7257 ; 1567-1348
    ISSN (online) 1567-7257
    ISSN 1567-1348
    DOI 10.1016/j.meegid.2021.104951
    Database MEDical Literature Analysis and Retrieval System OnLINE

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