Displaying publications 141 - 160 of 576 in total

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  1. Fulltext Computational approaches: discovery of GTPase HRas as prospective drug target for 1,3-diazine scaffolds
    Kumar S, Sharma D, Narasimhan B, Ramasamy K, Shah SAA, Lim SM, et al.
    BMC Chem, 2019 Dec;13(1):96.
    PMID: 31355369 DOI: 10.1186/s13065-019-0613-8
    Heterocyclic 1,3-diazine nucleus is a valuable pharmacophore in the field of medicinal chemistry and exhibit a wide spectrum of biological activities. PharmMapper, a robust online tool used for establishing the target proteins based on reverse pharmacophore mapping. PharmMapper study is carried out to explore the pharmacological activity of 1,3-diazine derivatives using reverse docking program. PharmMapper, an open web server was used to recognize for all the feasible target proteins for the developed compounds through reverse pharmacophore mapping. The results were analyzed via molecular docking with maestro v11.5 (Schrodinger 2018-1) using GTPase HRas as possible target. The molecular docking studies displayed the binding behavior of 1,3-diazine within GTP binding pocket. From the docking study compounds s3 and s14 showed better docked score with anticancer potency against cancer cell line (HCT116). Hence, the GTPase HRas may be the possible target of 1,3-diazine derivatives for their anticancer activity where the retrieved information may be quite useful for developing rational drug designing. Furthermore the selected 1,3-diazine compounds were evaluated for their in vitro anticancer activity against murine macrophages cell line. 1,3-Diazine compounds exhibited good selectivity of the compounds towards the human colorectal carcinoma cell line instead of the murine macrophages. The toxicity study of the most active compounds was also performed on non cancerous HEK-293 cell line.
  2. Fulltext Molecular docking, synthesis and biological significance of pyrimidine analogues as prospective antimicrobial and antiproliferative agents
    Kumar S, Kaushik A, Narasimhan B, Shah SAA, Lim SM, Ramasamy K, et al.
    BMC Chem, 2019 Dec;13(1):85.
    PMID: 31384832 DOI: 10.1186/s13065-019-0601-z
    Pyrimidine nucleus is a significant pharmacophore that exhibited excellent pharmacological activities. A series of pyrimidine scaffolds was synthesized and its chemical structures were confirmed by physicochemical and spectral analysis. The synthesized compounds were evaluated for their antimicrobial potential towards Gram positive and negative bacteria as well as fungal species. They were also assessed for their anticancer activity toward a human colorectal carcinoma cell line (HCT116). Whilst results of antimicrobial potential revealed that compounds Ax2, Ax3, Ax8 and Ax14 exhibited better activity against tested microorganisms, the results of antiproliferative activity indicated that compounds Ax7 and Ax10 showed excellent activity against HCT116. Further, the molecular docking of pyrimidine derivatives Ax1, Ax9 and Ax10 with CDK8 (PDB id: 5FGK) protein indicated that moderate to better docking results within the binding pocket. Compounds Ax8 and Ax10 having significant antimicrobial and anticancer activities may be selected as lead compounds for the development of novel antimicrobial and anticancer agent, respectively.
  3. Fulltext Reverse pharmacophore mapping and molecular docking studies for discovery of GTPase HRas as promising drug target for bis-pyrimidine derivatives
    Kumar S, Singh J, Narasimhan B, Shah SAA, Lim SM, Ramasamy K, et al.
    Chem Cent J, 2018 Oct 22;12(1):106.
    PMID: 30345469 DOI: 10.1186/s13065-018-0475-5
    BACKGROUND: Pyrimidine is an important pharmacophore in the field of medicinal chemistry and exhibit a broad spectrum of biological potentials. A study was carried out to identify the target protein of potent bis-pyrimidine derivatives using reverse docking program. PharmMapper, a robust online tool was used for identifying the target proteins based on reverse pharmacophore mapping. The murine macrophage (RAW 264.7) and human embryonic kidney (HEK-293) cancer cell line used for selectivity and safety study.

    METHODS: An open web server PharmMapper was used to identify the possible target of the developed compounds through reverse pharmacophore mapping. The results were analyzed and validated through docking with Schrodinger v9.6 using 10 protein GTPase HRas selected as possible target. The docking studies with Schrödinger validated the binding behavior of bis-pyrimidine compounds within GTP binding pocket. MTT and sulforhodamine assay were used as antiproliferative activity.

    RESULTS AND DISCUSSION: The protein was found one of the top scored targets of the compound 18, hence, the GTPase HRas protein was found crucial to be targeted for competing cancer. Toxicity study demonstrated the significant selectivity of most active compounds, 12, 16 and 18 showed negligible cell toxicity at their IC50 concentration.

    CONCLUSION: From the results, we may conclude that GTPase HRas as a possible target of studied bis-pyrimidine derivatives where the retrieved information may be quite useful for rational drug designing.

  4. Synthesis, molecular docking and biological potentials of new 2-(4-(2-chloroacetyl) piperazin-1-yl)-N-(2-(4-chlorophenyl)-4-oxoquinazolin-3(4H)-yl)acetamide derivatives
    Mehta S, Kumar S, Marwaha RK, Narasimhan B, Ramasamy K, Lim SM, et al.
    BMC Chem, 2019 Dec;13(1):113.
    PMID: 31517312 DOI: 10.1186/s13065-019-0629-0
    In the present study, a series of 2-(4-(2-chloroacetyl)piperazin-1-yl)-N-(2-(4-chlorophenyl)-4-oxoquinazolin-3(4H)-yl)acetamide derivatives was synthesized and its chemical structures were confirmed by physicochemical and spectral characteristics. The synthesized compounds were evaluated for their in vitro antimicrobial (tube dilution technique) and anticancer (MTT assay) activities along with molecular docking study by Schrodinger 2018-1, maestro v11.5. The antimicrobial results indicated that compounds 3, 8, 11 and 12 displayed the significant antimicrobial activity and comparable to the standards drugs (ciprofloxacin and fluconazole). The anticancer activity results indicated that compound 5 have good anticancer activity among the synthesized compounds but lower active than the standard drugs (5-fluorouracil and tomudex). Molecular docking study demonstrated that compounds 5 and 7 displayed the good docking score with better anticancer potency within the binding pocket and these compounds may be used as a lead for rational drug designing for the anticancer molecules.
  5. Fulltext Past, present, and future of sustainable finance: insights from big data analytics through machine learning of scholarly research
    Kumar S, Sharma D, Rao S, Lim WM, Mangla SK
    Ann Oper Res, 2022 Jan 04.
    PMID: 35002001 DOI: 10.1007/s10479-021-04410-8
    Sustainable finance is a rich field of research. Yet, existing reviews remain limited due to the piecemeal insights offered through a sub-set rather than the entire corpus of sustainable finance. To address this gap, this study aims to conduct a large-scale review that would provide a state-of-the-art overview of the performance and intellectual structure of sustainable finance. To do so, this study engages in a review of sustainable finance research using big data analytics through machine learning of scholarly research. In doing so, this study unpacks the most influential articles and top contributing journals, authors, institutions, and countries, as well as the methodological choices and research contexts for sustainable finance research. In addition, this study reveals insights into seven major themes of sustainable finance research, namely socially responsible investing, climate financing, green financing, impact investing, carbon financing, energy financing, and governance of sustainable financing and investing. To drive the field forward, this study proposes several suggestions for future sustainable finance research, which include developing and diffusing innovative sustainable financing instruments, magnifying and managing the profitability and returns of sustainable financing, making sustainable finance more sustainable, devising and unifying policies and frameworks for sustainable finance, tackling greenwashing of corporate sustainability reporting in sustainable finance, shining behavioral finance on sustainable finance, and leveraging the power of new-age technologies such as artificial intelligence, blockchain, internet of things, and machine learning for sustainable finance.
  6. Hazardous heavy metals contamination of vegetables and food chain: Role of sustainable remediation approaches - A review
    Kumar S, Prasad S, Yadav KK, Shrivastava M, Gupta N, Nagar S, et al.
    Environ Res, 2019 12;179(Pt A):108792.
    PMID: 31610391 DOI: 10.1016/j.envres.2019.108792
    This review emphasizes the role of toxic metal remediation approaches due to their broad sustainability and applicability. The rapid developmental processes can incorporate a large quantity of hazardous and unseen heavy metals in all the segments of the environment, including soil, water, air and plants. The released hazardous heavy metals (HHMs) entered into the food chain and biomagnified into living beings via food and vegetable consumption and originate potentially health-threatening effects. The physical and chemical remediation approaches are restricted and localized and, mainly applied to wastewater and soils and not the plant. The nanotechnological, biotechnological and genetical approaches required to more rectification and sustainability. A cellular, molecular and nano-level understanding of the pathways and reactions are responsible for potentially toxic metals (TMs) accumulation. These approaches can enable the development of crop varieties with highly reduced concentrations of TMs in their consumable foods and vegetables. As a critical analysis by authors observed that nanoparticles could provide very high adaptability for both in-situ and ex-situ remediation of hazardous heavy metals (HHMs) in the environment. These methods could be used for the improvement of the inbuilt genetic potential and phytoremediation ability of plants by developing transgenic. These biological processes involve the transfer of gene of interest, which plays a role in hazardous metal uptake, transport, stabilization, inactivation and accumulation to increased host tolerance. This review identified that use of nanoremediation and combined biotechnological and, transgenic could help to enhance phytoremediation efficiency in a sustainable way.
  7. Facile synthesis and characterization of tailor-made pectin-gellan gum-bionanofiller composites as intragastric drug delivery shuttles
    Bera H, Kumar S, Maiti S
    Int J Biol Macromol, 2018 Oct 15;118(Pt A):149-159.
    PMID: 29932998 DOI: 10.1016/j.ijbiomac.2018.06.085
    Olive oil-entrapped diethanolamine-modified high-methoxyl pectin (DMP)-gellan gum (GG)-bionanofiller composites were developed for controlled intragastric delivery of metformin HCl (MFM). DMP had a degree of amidation of 48.7% and was characterized further by FTIR, XRD and DSC analyses. MFM-loaded composites were subsequently accomplished by green synthesis via ionotropic gelation technique using zinc acetate as cross-linker. The thermal, X-ray and infrared analyses suggested an environment in the composites compatible with the drug, except certain degree of attenuation in drug's crystallinity. Scanning electron microscopy revealed almost spherical shape of the composites. Depending upon the mass ratios of GG:DMP, types of nanofiller (neusilin/bentonite/Florite) and oil inclusion, the composites exhibited variable drug encapsulation efficiency (DEE, 50-85%) and extended drug release behaviours (Q8h, 69-94%) in acetate buffer (pH 4.5). The optimized oil-entrapped Florite R NF/GG: DMP (1:1) composites eluted MFM via case-II transport mechanism and its drug release data was best fitted in zero-order kinetic model. The optimized formulation demonstrated excellent gastroretentive properties and substantial hypoglycemic effect in streptozotocin-induced diabetic rats. These novel hybrid matrices were thus found suitable for controlled intragastric delivery of MFM for the management of type 2 diabetes.
  8. In silico identification and validation of a novel hypothetical protein in Cryptosporidium hominis and virtual screening of inhibitors as therapeutics
    Shrivastava AK, Kumar S, Sahu PS, Mahapatra RK
    Parasitol Res, 2017 May;116(5):1533-1544.
    PMID: 28389892 DOI: 10.1007/s00436-017-5430-1
    Computational approaches to predict structure/function and other biological characteristics of proteins are becoming more common in comparison to the traditional methods in drug discovery. Cryptosporidiosis is a major zoonotic diarrheal disease particularly in children, which is caused primarily by Cryptosporidium hominis and Cryptosporidium parvum. Currently, there are no vaccines for cryptosporidiosis and recommended drugs are ineffective. With the availability of complete genome sequence of C. hominis, new targets have been recognized for the development of effective and better drugs and/or vaccines. We identified a unique hypothetical protein (TU502HP) in the C. hominis genome from the CryptoDB database. A three-dimensional model of the protein was generated using the Iterative Threading ASSEmbly Refinement server through an iterative threading method. Functional annotation and phylogenetic study of TU502HP protein revealed similarity with human transportin 3. The model is further subjected to a virtual screening study form the ZINC database compound library using the Dock Blaster server. A docking study through AutoDock software reported N-(3-chlorobenzyl)ethane-1,2-diamine as the best inhibitor in terms of docking score and binding energy. The reliability of the binding mode of the inhibitor is confirmed by a complex molecular dynamics simulation study using GROMACS software for 10 ns in the water environment. Furthermore, antigenic determinants of the protein were determined with the help of DNASTAR software. Our findings report a great potential in order to provide insights in the development of new drug(s) or vaccine(s) for treatment and prophylaxis of cryptosporidiosis among humans and animals.
  9. Fulltext On Comparison of Heat Treated and Non-Heat-Treated LOM Manufactured Sample for Poly(lactic)acid: Mechanical and Morphological View Point
    Singh I, Kumar S, R Koloor SS, Kumar D, Yahya MY, Mago J
    Polymers (Basel), 2022 Nov 24;14(23).
    PMID: 36501501 DOI: 10.3390/polym14235098
    This work reports the comparison of heat-treated and non-heat-treated laminated object-manufactured (LOM) 3D-printed specimens from mechanical and morphological viewpoints. The study suggests that heat treatment of the FDM-printed specimen may have a significant impact on the material characteristics of the polymer. The work has been performed at two stages for the characterization of (a) non-heat-treated samples and (b) heat-treated samples. The results for stage 1 (non-heat-treated samples) suggest that the infill density: 70%, infill pattern: honeycomb, and six number of discs in a single LOM-manufactured sample is the optimized condition with a compression strength of 42.47 MPa. The heat treatment analysis at stage 2 suggests that a high temperature: 65 °C, low time interval: 10 min, works equally well as the low temperature: 55 °C, high time interval: 30 min. The post-heat treatment near Tg (65 °C) for a time interval of 10 min improved the compressive strength by 105.42%.
  10. Bcp1 Is the Nuclear Chaperone of Rpl23 in Saccharomyces cerevisiae
    Ting YH, Lu TJ, Johnson AW, Shie JT, Chen BR, Kumar S S, et al.
    J Biol Chem, 2017 Jan 13;292(2):585-596.
    PMID: 27913624 DOI: 10.1074/jbc.M116.747634
    Eukaryotic ribosomes are composed of rRNAs and ribosomal proteins. Ribosomal proteins are translated in the cytoplasm and imported into the nucleus for assembly with the rRNAs. It has been shown that chaperones or karyopherins responsible for import can maintain the stability of ribosomal proteins by neutralizing unfavorable positive charges and thus facilitate their transports. Among 79 ribosomal proteins in yeast, only a few are identified with specific chaperones. Besides the classic role in maintaining protein stability, chaperones have additional roles in transport, chaperoning the assembly site, and dissociation of ribosomal proteins from karyopherins. Bcp1 has been shown to be necessary for the export of Mss4, a phosphatidylinositol 4-phosphate 5-kinase, and required for ribosome biogenesis. However, its specific function in ribosome biogenesis has not been described. Here, we show that Bcp1 dissociates Rpl23 from the karyopherins and associates with Rpl23 afterward. Loss of Bcp1 causes instability of Rpl23 and deficiency of 60S subunits. In summary, Bcp1 is a novel 60S biogenesis factor via chaperoning Rpl23 in the nucleus.
  11. Fulltext Potential Factors Influencing Repeated SARS Outbreaks in China
    Sun Z, Thilakavathy K, Kumar SS, He G, Liu SV
    Int J Environ Res Public Health, 2020 Mar 03;17(5).
    PMID: 32138266 DOI: 10.3390/ijerph17051633
    Within last 17 years two widespread epidemics of severe acute respiratory syndrome (SARS) occurred in China, which were caused by related coronaviruses (CoVs): SARS-CoV and SARS-CoV-2. Although the origin(s) of these viruses are still unknown and their occurrences in nature are mysterious, some general patterns of their pathogenesis and epidemics are noticeable. Both viruses utilize the same receptor-angiotensin-converting enzyme 2 (ACE2)-for invading human bodies. Both epidemics occurred in cold dry winter seasons celebrated with major holidays, and started in regions where dietary consumption of wildlife is a fashion. Thus, if bats were the natural hosts of SARS-CoVs, cold temperature and low humidity in these times might provide conducive environmental conditions for prolonged viral survival in these regions concentrated with bats. The widespread existence of these bat-carried or -released viruses might have an easier time in breaking through human defenses when harsh winter makes human bodies more vulnerable. Once succeeding in making some initial human infections, spreading of the disease was made convenient with increased social gathering and holiday travel. These natural and social factors influenced the general progression and trajectory of the SARS epidemiology. However, some unique factors might also contribute to the origination of SARS in Wuhan. These factors are discussed in different scenarios in order to promote more research for achieving final validation.
  12. Fulltext Human Mesenchymal Stem Cells Expressing Erythropoietin Enhance Survivability of Retinal Neurons Against Oxidative Stress: An In Vitro Study
    Shirley Ding SL, Kumar S, Ali Khan MS, Ling Mok P
    Front Cell Neurosci, 2018;12:190.
    PMID: 30108483 DOI: 10.3389/fncel.2018.00190
    Retinal degeneration is a prominent feature in ocular disorders. In exploring possible treatments, Mesenchymal Stem Cells (MSCs) have been recognized to yield therapeutic role for retinal degenerative diseases. Studies have also displayed that erythropoietin (EPO) administration into degenerative retina models confers significant neuroprotective actions in limiting pathological cell death. In this study, we aimed to use MSCs to deliver EPO and to evaluate the ability of EPO to rescue retinal neurons from dying upon reactive oxidative stress induction. We derived human MSCs from Wharton's jelly (hWJMSCs) of the umbilical cord and cells were transduced with lentivirus particles encoding EPO and a reporter gene of green fluorescent protein (GFP). The supernatants of both transduced and non-transduced cells were collected and used as a pre-conditioning medium for Y79 retinoblastoma cells (retinal neuron cell line) following exposure to glutamate induction. Retinal cells exposed to glutamate showed reduced mitochondrial depolarization and enhanced improvement in cell viability when incubated with pre-conditioned media of transduced cells. Our results established a proof-of-concept that MSCs could be used as a candidate for the delivery of EPO therapeutic gene in the treatment of retinal degenerations.
  13. Absolute Photoabsorption Cross-Sections of Methanol for Terrestrial and Astrophysical Relevance
    Lange E, Lozano AI, Jones NC, Hoffmann SV, Kumar S, Śmiałek MA, et al.
    J Phys Chem A, 2020 Sep 30.
    PMID: 32941031 DOI: 10.1021/acs.jpca.0c06615
    We investigate the methanol absorption spectrum in the range 5.5-10.8 eV to provide accurate and absolute cross-sections values. The main goal of this study is to provide a comprehensive analysis of methanol electronic-state spectroscopy by employing high-resolution vacuum ultraviolet (VUV) photoabsorption measurements together with state-of-the-art quantum chemical calculation methods. The VUV spectrum reveals several new features that are not previously reported in literature, for n > 3 in the transitions (nsσ(a') ← (2a″)) (1A' ← X̃1A') and (nsσ, npσ, npσ', ndσ ← (7a')) (1A' ← X̃1A'), and with particular relevance to vibrational progressions of the CH3 rocking mode, v11'(a″), mode in the (3pπ(a″) ← (2a″)) (21A' ← X̃1A') absorption band at 8.318 eV. The measured absolute photoabsorption cross-sections have subsequently been used to calculate the photolysis lifetime of methanol in the Earth's atmosphere from the ground level up to the limit of the stratosphere (50 km altitude). This shows that solar photolysis plays a negligible role in the removal of methanol from the lower atmosphere compared with competing sink mechanisms. Torsional potential energy scans, as a function of the internal rotation angle for the ground and first Rydberg states, have also been calculated as part of this investigation.
  14. Fulltext Factors influencing COVID-19 vaccination intention among university students: A cross-sectional study in Malaysia
    Wong CY, Tham JS, Foo CN, Ng FL, Shahar S, Zahary MN, et al.
    Biosaf Health, 2023 Feb;5(1):37-44.
    PMID: 36588928 DOI: 10.1016/j.bsheal.2022.12.005
    Vaccination is crucial in controlling the spread of the coronavirus disease 2019 (COVID-19) that triggered the pandemic, but herd immunity can only work with high vaccination coverage in the population. This study aims to measure the COVID-19 knowledge level and determine the factors influencing COVID-19 vaccination intention among university students in Malaysia. A cross-sectional online survey was carried out with 1,274 Malaysian university students in July 2021. Univariate and multivariate analyses were employed to examine the relationships between the study variables. Results showed that the majority of university students had an acceptable level of knowledge of COVID-19. The knowledge, risk perception of COVID-19, social norms, and perceived benefit of COVID-19 vaccination were positively associated with vaccination intention. However, perceived trust in information sources of COVID-19 vaccination and the government's response to COVID-19 did not affect the university students' desire to receive the vaccination. These findings are essential for health policymakers and healthcare providers to implement evidence-based interventions to increase COVID-19 vaccination uptake among university students.
  15. Facile synthesis of graphene oxide-silver nanocomposite and its modified electrode for enhanced electrochemical detection of nitrite ions
    Ikhsan NI, Rameshkumar P, Pandikumar A, Mehmood Shahid M, Huang NM, Vijay Kumar S, et al.
    Talanta, 2015 Nov 1;144:908-14.
    PMID: 26452907 DOI: 10.1016/j.talanta.2015.07.050
    In this report, silver nanoparticles (Ag NPs) were successfully deposited on graphene oxide (GO) sheets to form GO-Ag nanocomposite using garlic extract and sunlight and the nanocomposite modified glassy carbon (GC) electrode was applied as an electrochemical sensor for the detection of nitrite ions. The formation of GO-Ag nanocomposite was confirmed by using UV-visible absorption spectroscopy, TEM, XRD and FTIR spectroscopy analyses. Further, TEM pictures showed a uniform distribution Ag on GO sheets with an average size of 19 nm. The nanocomposite modified electrode produced synergistic catalytic current in nitrite oxidation with a negative shift in overpotential. The limit of detection (LOD) values were found as 2.1 µM and 37 nM, respectively using linear sweep voltammetry (LSV) and amperometric i-t curve techniques. The proposed sensor was stable, reproducible, sensitive and selective toward the detection nitrite and could be applied for the detection of nitrite in real water sample.
  16. Early Diagnosis of Intrahepatic Pseudoaneurysm during Radiofrequency Ablation using Contrast-Enhanced Ultrasound
    Kumar SK, Oon OK, Horgan P, Leen E
    Malays J Med Sci, 2015 Nov;22(6):58-62.
    PMID: 28223887
    Radiofrequency ablation is one of the more established forms of local treatment in patients with unresectable tumours, including colorectal hepatic metastases. Complications associated with this method of intervention include thermal and mechanical injuries, including vascular insults resulting in haemorrhage or pseudoaneurysm formation. This is the first case demonstrating the detection of post-ablation acute pseudoaneurysm formation identified on the table using contrast-enhanced ultrasound (CEUS) and the subsequent successful management.
  17. Study of structural properties and defects of Ni-doped SnO2 nanorods as ethanol gas sensors
    Inderan V, Arafat MM, Kumar S, Haseeb ASMA, Jiang ZT, Altarawneh M, et al.
    Nanotechnology, 2017 Jun 30;28(26):265702.
    PMID: 28593932 DOI: 10.1088/1361-6528/aa731c
    An ethanol gas sensor with enhanced sensor response was fabricated using Ni-doped SnO2 nanorods, synthesized via a simple hydrothermal method. It was found that the response (R = R 0/R g) of a 5.0 mol% Ni-doped SnO2 (5.0Ni:SnO2) nanorod sensor was 1.4 × 104 for 1000 ppm C2H5OH gas, which is about 13 times higher than that of pure SnO2 nanorods, (1.1 × 103) at the operating temperature of 450 °C. Moreover, for 50 ppm C2H5OH gas, the 5.0Ni:SnO2 nanorod sensor still recorded a significant response reading, namely 2.0 × 103 with a response time of 30 s and recovery time of 10 min. To investigate the effect of Ni dopant (0.5-5.0 mol%) on SnO2 nanorods, structural characterizations were demonstrated using field emission scanning electron microscopy, high-resolution transmission electron microscopy, Fourier transform infrared spectroscopy, x-ray diffraction (XRD) analysis, x-ray photoelectron spectroscopy and an ultraviolet-visible spectrometer. XRD results confirmed that all the samples consisted of tetragonal-shaped rutile SnO2 nanorods. It was found that the average diameter and length of the nanorods formed in 5.0Ni:SnO2 were four times smaller (∼6 and ∼35 nm, respectively) than those of the nanorods formed in pure SnO2 (∼25 and 150 nm). Interestingly, both samples had the same aspect ratio, ∼6. It is proposed that the high response of the 5.0Ni:SnO2 nanorod sensor can be attributed to the particle size, which causes an increase in the thickness of the charge depletion layer, and the presence of oxygen vacancies within the matrix of SnO2 nanorods.
  18. Fulltext Multi-platform discovery of haplotype-resolved structural variation in human genomes
    Chaisson MJP, Sanders AD, Zhao X, Malhotra A, Porubsky D, Rausch T, et al.
    Nat Commun, 2019 04 16;10(1):1784.
    PMID: 30992455 DOI: 10.1038/s41467-018-08148-z
    The incomplete identification of structural variants (SVs) from whole-genome sequencing data limits studies of human genetic diversity and disease association. Here, we apply a suite of long-read, short-read, strand-specific sequencing technologies, optical mapping, and variant discovery algorithms to comprehensively analyze three trios to define the full spectrum of human genetic variation in a haplotype-resolved manner. We identify 818,054 indel variants (<50 bp) and 27,622 SVs (≥50 bp) per genome. We also discover 156 inversions per genome and 58 of the inversions intersect with the critical regions of recurrent microdeletion and microduplication syndromes. Taken together, our SV callsets represent a three to sevenfold increase in SV detection compared to most standard high-throughput sequencing studies, including those from the 1000 Genomes Project. The methods and the dataset presented serve as a gold standard for the scientific community allowing us to make recommendations for maximizing structural variation sensitivity for future genome sequencing studies.
  19. A defect in DNA topoisomerase II activity in ataxia-telangiectasia cells
    Mohamed R, Pal Singh S, Kumar S, Lavin MF
    Biochem Biophys Res Commun, 1987 Nov 30;149(1):233-8.
    PMID: 2825700
    DNA topoisomerase type I and II activities were determined by serial dilution in nuclear extracts from control and ataxia-telangiectasia lymphoblastoid cells. Topoisomerase I activity, assayed by relaxation of supercoiled plasmid DNA, was found to be approximately the same in both cell types. In order to remove interference from topoisomerase I, the activity of topoisomerase II was measured by the unknotting of knotted P4 phage DNA in the presence of ATP. The activity of topoisomerase II was markedly reduced in two ataxia-telangiectasia cell lines, AT2ABR and AT8ABR, compared to controls. This reduction in activity was detected with increasing concentration of protein and in time course experiments at a single protein concentration. A third cell line, AT3ABR, did not have a detectably lower activity of topoisomerase II when assayed under these conditions. The difference in topoisomerase II activity in the ataxia-telangiectasia cell lines examined may reflect to some extent the heterogeneity observed in this syndrome.
  20. Fulltext Efficacy of combined formulations of fungicides with different modes of action in controlling botrytis gray mold disease in chickpea
    Rashid MH, Hossain MA, Kashem MA, Kumar S, Rafii MY, Latif MA
    ScientificWorldJournal, 2014;2014:639246.
    PMID: 24723819 DOI: 10.1155/2014/639246
    Botrytis gray mold (BGM) caused by Botrytis cinerea Pers. Ex. Fr. is an extremely devastating disease of chickpea (Cicer arietinum L.) and has a regional as well as an international perspective. Unfortunately, nonchemical methods for its control are weak and ineffective. In order to identify an effective control measure, six fungicides with different modes of action were evaluated on a BGM susceptible chickpea variety BARIchhola-1 at a high BGM incidence location (Madaripur) in Bangladesh for three years (2008, 2009, and 2010). Among the six fungicides tested, one was protectant [Vondozeb 42SC, a.i. mancozeb (0.2%)], two systemic [Bavistin 50 WP, a.i. carbendazim (0.2%), and Protaf 250EC, propiconazole (0.05%)], and three combination formulations [Acrobat MZ690, dimethomorph 9% + mancozeb 60%, (0.2%); Secure 600 WG, phenomadone + mancozeb (0.2%); and Companion, mancozeb 63% + carbendazim 12% (0.2%)]. The results showed superiority of combination formulations involving both protectant and systemic fungicides over the sole application of either fungicide separately. Among the combination fungicides, Companion was most effective, resulting in the lowest disease severity (3.33 score on 1-9 scale) and the highest increase (38%) of grain yield in chickpea. Therefore, this product could be preferred over the sole application of either solo protectant or systemic fungicides to reduce yield losses and avoid fungicide resistance.
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