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  1. Akbar N, Siddiqui R, Iqbal M, Sagathevan K, Khan NA
    Lett Appl Microbiol, 2018 May;66(5):416-426.
    PMID: 29457249 DOI: 10.1111/lam.12867
    Here, we hypothesized that the microbial gut flora of animals/pests living in polluted environments, produce substances to thwart bacterial infections. The overall aim of this study was to source microbes inhabiting unusual environmental niches for potential antimicrobial activity. Two cockroach species, Gromphadorhina portentosa (Madagascar) and Blaptica dubia (Dubia) were selected. The gut bacteria from these species were isolated and grown in RPMI 1640 and conditioned media were prepared. Conditioned media were tested against a panel of Gram-positive (Methicillin-resistant Staphylococcus aureus, Streptococcus pyogenes, Bacillus cereus) and Gram-negative (Escherichia coli K1, Salmonella enterica, Serratia marcescens, Pseudomonas aeruginosa, Klebsiella pneumoniae) bacteria, as well as the protist pathogen, Acanthamoeba castellanii. The results revealed that the gut bacteria of cockroaches produce active molecule(s) with potent antibacterial properties, as well as exhibit antiamoebic effects. However, heat-inactivation at 95°C for 10 min had no effect on conditioned media-mediated antibacterial and antiamoebic properties. These results suggest that bacteria from novel sources i.e. from the cockroach's gut produce molecules with bactericidal as well as amoebicidal properties that can ultimately lead to the development of therapeutic drugs.

    SIGNIFICANCE AND IMPACT OF THE STUDY: The bacteria isolated from unusual dwellings such as the cockroaches' gut are a useful source of antibacterial and antiamoebal molecules. These are remarkable findings that will open several avenues in our search for novel antimicrobials from unique sources. Furthermore studies will lead to the identification of molecules to develop future antibacterials from insects.

  2. Akbar N, Siddiqui R, Sagathevan K, Khan NA
    Int Microbiol, 2020 Nov;23(4):511-526.
    PMID: 32124096 DOI: 10.1007/s10123-020-00123-3
    Infectious diseases, in particular bacterial infections, are the leading cause of morbidity and mortality posing a global threat to human health. The emergence of antibiotic resistance has exacerbated the problem further. Hence, there is a need to search for novel sources of antibacterials. Herein, we explored gut bacteria of a variety of animals living in polluted environments for their antibacterial properties against multi-drug resistant pathogenic bacteria. A variety of species were procured including invertebrate species, Blaptica dubia (cockroach), Gromphadorhina portentosa (cockroach), Scylla serrata (crab), Grammostola rosea (tarantula), Scolopendra subspinipes (centipede) and vertebrate species including Varanus salvator (water monitor lizard), Malayopython reticulatus (python), Cuora amboinensis (tortoise), Oreochromis mossambicus (tilapia fish), Rattus rattus (rat), Gallus gallus domesticus (chicken) and Lithobates catesbeianus (frog). Gut bacteria of these animals were isolated and identified using microbiological, biochemical, analytical profiling index (API) and through molecluar identification using 16S rRNA sequencing. Bacterial conditioned media (CM) were prepared and tested against selected Gram-positive and Gram-negative pathogenic bacteria as well as human cells (HaCaT). The results revealed that CM exhibited significant broad-spectrum antibacterial activities. Upon heat inactivation, CM retained their antibacterial properties suggesting that this effect may be due to secondary metabolites or small peptides. CM showed minimal cytotoxicity against human cells. These findings suggest that gut bacteria of animals living in polluted environments produce broad-spectrum antibacterial molecule(s). The molecular identity of the active molecule(s) together with their mode of action is the subject of future studies which could lead to the rational development of novel antibacterial(s).
  3. Akbar N, Siddiqui R, Sagathevan KA, Khan NA
    Appl Microbiol Biotechnol, 2019 May;103(10):3955-3964.
    PMID: 30941460 DOI: 10.1007/s00253-019-09783-2
    The morbidity and mortality associated with bacterial infections have remained significant despite chemotherapeutic advances. With the emergence of drug-resistant bacterial strains, the situation has become a serious threat to the public health. Thus, there is an urgent need to identify novel antibacterials. The majority of antibiotics available in the market are produced by bacteria isolated from soil. However, the low-hanging fruit has been picked; hence, there is a need to mine bacteria from unusual sources. With this in mind, it is important to note that animals and pests such as cockroaches, snake, crocodiles, and water monitor lizard come across pathogenic bacteria regularly, yet flourish in contaminated environments. These species must have developed methods to defend themselves to counter pathogens. Although the immune system is known to possess antiinfective properties, gut bacteria of animals/pests may also offer a potential source of novel antibacterial agents, and it is the subject of this study. This paper discusses our current knowledge of bacteria isolated from land and marine animals with antibacterial properties and to propose untapped sources for the isolation of bacteria to mine potentially novel antibiotic molecules.
  4. Akbar N, Siddiqui R, Sagathevan K, Iqbal M, Khan NA
    Antibiotics (Basel), 2019 Sep 24;8(4).
    PMID: 31554316 DOI: 10.3390/antibiotics8040164
    For the past few decades, there has been limited progress in the development of novel antibacterials. Previously, we postulated that the gut microbiota of animals residing in polluted environments are a forthcoming supply of antibacterials. Among various species, the water monitor lizard is an interesting species that feeds on organic waste and the carcass of wild animals. Gut microbiota of the water monitor lizard were sequestered, identified and cultivated in RPMI-1640 to produce conditioned medium (CM). Next, the antimicrobial properties of CM were evaluated versus a selection of Gram-negative (Escherichia coli K1, Serratia marcescens,Pseudomonas aeruginosa, Salmonella enterica and Klebsiella pneumoniae) and Gram-positive bacteria (Streptococcus pyogenes, methicillin-resistant Staphylococcus aureus, and Bacillus cereus). CM were partially characterized by heat inactivation at 95°C for 10 min and tested against P. aeruginosa and S. pyogenes. CM were also tested against immortalized human keratinocytes (HaCaT) cells lines. The results demonstrated that gut microbiota isolated from water monitor lizard produced molecules with remarkable bactericidal activities. To determine the identity of the active molecules, CM were subjected to Liquid Chromatography-Mass Spectrometry. Several molecules were identified belonging to the classes of flavonoids, terpenoids, alkaloids, polyhydroxy alkaloids, polyacetylenes, bisphenols, amides, oxylipin and pyrazine derivatives with known broad-spectrum antimicrobial, anti-tumour, anti-oxidant, anti-inflammatory, and analgesic attributes. Furthermore, the detailed analysis of these molecules could lead us to develop effective therapeutic antibacterials.
  5. Mukheem A, Shahabuddin S, Akbar N, Anwar A, Sarih NM, Sudesh K, et al.
    Appl Microbiol Biotechnol, 2020 Apr;104(7):3121-3131.
    PMID: 32060693 DOI: 10.1007/s00253-020-10416-2
    Antibiotic resistance in pathogenic bacteria is a major health challenge, as Infectious Diseases Society of America (IDSA) has recognized that the past simply drugs susceptible pathogens are now the most dangerous pathogens due to their nonstop growing resistance towards conventional antibiotics. Therefore, due to the emergence of multi-drug resistance, the bacterial infections have become a serious global problem. Acute infections feasibly develop into chronic infections because of many factors; one of them is the failure of effectiveness of antibiotics against superbugs. Modern research of two-dimensional nanoparticles and biopolymers are of great interest to attain the intricate bactericidal activity. In this study, we fabricated an antibacterial nanocomposite consisting of representative two-dimensional molybdenum disulfide (2D MoS2) nanoparticles. Polyhydroxyalkanoate (PHA) and chitosan (Ch) are used to encapsulate MoS2 nanoparticles into their matrix. This study reports the in vitro antibacterial activity and host cytotoxicity of novel PHA-Ch/MoS2 nanocomposites. PHA-Ch/MoS2 nanocomposites were subjected to time-dependent antibacterial assays at various doses to examine their antibacterial activity against multi-drug-resistant Escherichia coli K1 (Malaysian Type Culture Collection 710859) and methicillin-resistant Staphylococcus aureus (MRSA) (Malaysian Type Culture Collection 381123). Furthermore, the cytotoxicity of nanocomposites was examined against spontaneously immortalized human keratinocyte (HaCaT) cell lines. The results indicated significant antibacterial activity (p value
  6. Akbar N, Khan NA, Sagathevan K, Iqbal M, Tawab A, Siddiqui R
    Sci Rep, 2019 11 18;9(1):17012.
    PMID: 31740685 DOI: 10.1038/s41598-019-52738-w
    Antimicrobial resistance is a major threat to human health, hence there is an urgent need to discover antibacterial molecule(s). Previously, we hypothesized that microbial gut flora of animals are a potential source of antibacterial molecules. Among various animals, Cuora amboinensis (turtle) represents an important reptile species living in diverse ecological environments and feed on organic waste and terrestrial organisms and have been used in folk medicine. The purpose of this study was to mine turtle's gut bacteria for potential antibacterial molecule(s). Several bacteria were isolated from the turtle gut and their conditioned media were prepared. Conditioned media showed potent antibacterial activity against several Gram-positive (Bacillus cereus, Streptococcus pyogenes and methicillin-resistant Staphylococcus aureus) and Gram-negative (neuropathogenic Escherichia coli K1, Serratia marcescens, Pseudomonas aeruginosa, Salmonella enterica and Klebsiella pneumoniae) pathogenic bacteria. Conditioned media-mediated bactericidal activity was heat-resistant when treated at 95°C for 10 min. By measuring Lactate dehydrogenase release, the results showed that conditioned media had no effect on human cell viability. Tandem Mass Spectrometric analysis revealed the presence of various secondary metabolites, i.e., a series of known as well as novel N-acyl-homoserine lactones, several homologues of 4-hydroxy-2-alkylquinolines, and rhamnolipids, which are the signature metabolites of Pseudomonas species. These findings are significant and provide the basis for rational development of therapeutic interventions against bacterial infections.
  7. Akbar N, Siddiqui R, Iqbal M, Sagathevan K, Kim KS, Habib F, et al.
    ACS Omega, 2021 May 11;6(18):12261-12273.
    PMID: 34056379 DOI: 10.1021/acsomega.1c01137
    Among several animals, Rattus rattus (rat) lives in polluted environments and feeds on organic waste/small invertebrates, suggesting the presence of inherent mechanisms to thwart infections. In this study, we isolated gut bacteria of rats for their antibacterial activities. Using antibacterial assays, the findings showed that the conditioned media from selected bacteria exhibited bactericidal activities against Gram-negative (Escherichia coli K1, Klebsiella pneumoniae, Pseudomonas aeruginosa, Serratia marcescens, and Salmonella enterica) and Gram-positive (Bacillus cereus, methicillin-resistant Staphylococcus aureus, and Streptococcus pyogenes) pathogenic bacteria. The conditioned media retained their antibacterial properties upon heat treatment at boiling temperature for 10 min. Using MTT assays, the conditioned media showed minimal cytotoxic effects against human keratinocyte cells. Active conditioned media were subjected to tandem mass spectrometry, and the results showed that conditioned media from Bacillus subtilis produced a large repertoire of surfactin and iturin A (lipopeptides) molecules. To our knowledge, this is the first report of isolation of lipopeptides from bacteria isolated from the rat gut. In short, these findings are important and provide a platform to develop effective antibacterial drugs.
  8. Mukheem A, Muthoosamy K, Manickam S, Sudesh K, Shahabuddin S, Saidur R, et al.
    Materials (Basel), 2018 Sep 10;11(9).
    PMID: 30201852 DOI: 10.3390/ma11091673
    Many wounds are unresponsive to currently available treatment techniques and therefore there is an immense need to explore suitable materials, including biomaterials, which could be considered as the crucial factor to accelerate the healing cascade. In this study, we fabricated polyhydroxyalkanoate-based antibacterial mats via an electrospinning technique. One-pot green synthesized graphene-decorated silver nanoparticles (GAg) were incorporated into the fibres of poly-3 hydroxybutarate-co-12 mol.% hydroxyhexanoate (P3HB-co-12 mol.% HHx), a co-polymer of the polyhydroxyalkanoate (PHA) family which is highly biocompatible, biodegradable, and flexible in nature. The synthesized PHA/GAg biomaterial has been characterized by field emission scanning electron microscopy (FESEM), elemental mapping, thermogravimetric analysis (TGA), UV-visible spectroscopy (UV-vis), and Fourier transform infrared spectroscopy (FTIR). An in vitro antibacterial analysis was performed to investigate the efficacy of PHA/GAg against gram-positive Staphylococcus aureus (S. aureus) strain 12,600 ATCC and gram-negative Escherichia coli (E. coli) strain 8739 ATCC. The results indicated that the PHA/GAg demonstrated significant reduction of S. aureus and E. coli as compared to bare PHA or PHA- reduced graphene oxide (rGO) in 2 h of time. The p value (p < 0.05) was obtained by using a two-sample t-test distribution.
  9. Nawar A, Khoja AH, Akbar N, Ansari AA, Qayyum M, Ali E
    BMC Res Notes, 2017 Dec 02;10(1):666.
    PMID: 29197425 DOI: 10.1186/s13104-017-2995-9
    OBJECTIVE: A major factor in practical application of photobioreactors (PBR) is the adhesion of algal cells onto their inner walls. Optimized algal growth requires an adequate sunlight for the photosynthesis and cell growth. Limitation in light exposure adversely affects the algal biomass yield. The removal of the biofilm from PBR is a challenging and expansive task. This study was designed to develop an inexpensive technique to prevent adhesion of algal biofilm on tubular PBR to ensure high efficiency of light utilization. Rubber balls with surface projections were introduced into the reactor, to remove the adherent biofilm by physical abrasion technique.

    RESULTS: The floatation of spike balls created a turbulent flow, thereby inhibiting further biofilm formation. The parameters such as, specific growth rate and doubling time of the algae before introducing the balls were 0.451 day-1 and 1.5 days respectively. Visible biofilm impeding light transmission was formed by 15-20 days. The removal of the biofilm commenced immediately after the introduction of the spike balls with visibly reduced deposits in 3 days. This was also validated by enhance cell count (6.95 × 106 cells mL-1) in the medium. The employment of spike balls in PBR is an environmental friendly and economical method for the removal of biofilm.

  10. Muneer A, Fati SM, Arifin Akbar N, Agustriawan D, Tri Wahyudi S
    J King Saud Univ Comput Inf Sci, 2022 Oct;34(9):7419-7432.
    PMID: 38620874 DOI: 10.1016/j.jksuci.2021.10.001
    Messenger RNA (mRNA) has emerged as a critical global technology that requires global joint efforts from different entities to develop a COVID-19 vaccine. However, the chemical properties of RNA pose a challenge in utilizing mRNA as a vaccine candidate. For instance, the molecules are prone to degradation, which has a negative impact on the distribution of mRNA among patients. In addition, little is known of the degradation properties of individual RNA bases in a molecule. Therefore, this study aims to investigate whether a hybrid deep learning can predict RNA degradation from RNA sequences. Two deep hybrid neural network models were proposed, namely GCN_GRU and GCN_CNN. The first model is based on graph convolutional neural networks (GCNs) and gated recurrent unit (GRU). The second model is based on GCN and convolutional neural networks (CNNs). Both models were computed over the structural graph of the mRNA molecule. The experimental results showed that GCN_GRU hybrid model outperform GCN_CNN model by a large margin during the test time. Validation of proposed hybrid models is performed by well-known evaluation measures. Among different deep neural networks, GCN_GRU based model achieved best scores on both public and private MCRMSE test scores with 0.22614 and 0.34152, respectively. Finally, GCN_GRU pre-trained model has achieved the highest AuC score of 0.938. Such proven outperformance of GCNs indicates that modeling RNA molecules using graphs is critical in understanding molecule degradation mechanisms, which helps in minimizing the aforementioned issues. To show the importance of the proposed GCN_GRU hybrid model, in silico experiments has been contacted. The in-silico results showed that our model pays local attention when predicting a given position's reactivity and exhibits interesting behavior on neighboring bases in the sequence.
  11. Khan MU, Ahmad A, Aqeel T, Akbar N, Salman S, Idress J
    PLoS One, 2015;10(11):e0142485.
    PMID: 26559184 DOI: 10.1371/journal.pone.0142485
    INTRODUCTION: Pakistan accounts for 85.2% of the total polio cases reported worldwide. Healthcare workers (HCWs) are an integral part of immunization campaigns and source of education for the general public. This study aimed to assess the knowledge and attitudes towards polio vaccination among HCWs providing immunisation and education to general public in Quetta and Peshawar divisions of Pakistan.

    METHODS: A cross-sectional survey of 490 HCWs was conducted in two major referral public teaching hospitals of Quetta and Peshawar divisions. During February to April, 2015, a random sample of 490 HCWs was invited to participate in this study. Knowledge and attitudes were assessed by using self-administered, anonymous and pretested questionnaire. Descriptive and logistic regression analyses were used to express the results.

    RESULTS: A total of 468 participants responded to the questionnaire, giving a response rate of 95.5%. Overall, participants demonstrated good knowledge and positive attitudes towards polio vaccination. The mean knowledge score of HCWs about polio was 13.42 ± 2.39 (based on 18 knowledge questions) while the mean attitude score was 28.75 ± 5.5 (based on 9 attitudes statements). Knowledge gaps were identified about the incubation period of poliovirus (19.5%), management issues (31.9%), use of polio vaccine in mild illnesses (34.7%) and the consequences of the polio virus (36.9%). The majority of participants agreed that all children should be vaccinated for polio (95.1%), while reservations were noted about the need of a booster (38.9%), and sterility issues associated with polio vaccines (43.6%). Internet (n = 167, 37%) and Posters (n = 158, 35%) were the main sources used by HCWs to educate themselves about polio.

    CONCLUSION: Participants in this study had good knowledge and positive attitudes towards polio vaccination. Although the data are indicative of gaps in the knowledge of HCWs, the findings may not be generalized to other hospitals in Pakistan.

  12. Baig AM, Khan NA, Katyara P, Lalani S, Baig R, Nadeem M, et al.
    Chem Biol Drug Des, 2021 01;97(1):18-27.
    PMID: 32602961 DOI: 10.1111/cbdd.13755
    Acanthamoeba spp. cause a corneal infection, Acanthamoeba keratitis (AK), and a cerebral infection, granulomatous amoebic encephalitis (GAE). Though aggressive chemotherapy has been able to kill the active trophozoite form of Acanthamoeba, the encysted form of this parasite has remained problematic to resist physiological concentrations of drugs. The emergence of encysted amoeba into active trophozoite form poses a challenge to eradicate this parasite. Acanthamoeba trophozoites have active metabolic machinery that furnishes energy in the form of ATPs by subjecting carbohydrates and lipids to undergo pathways including glycolysis and beta-oxidation of free fatty acids, respectively. However, very little is known about the metabolic preferences and dependencies of an encysted trophozoite on minerals or potential nutrients that it consumes to live in an encysted state. Here, we investigate the metabolic and nutrient preferences of the encysted trophozoite of Acanthamoeba castellanii and the possibility to target them by drugs that act on calcium ion dependencies of the encysted amoeba. The experimental assays, immunostaining coupled with bioinformatics tools show that the encysted Acanthamoeba uses diverse nutrient pathways to obtain energy in the quiescent encysted state. These findings highlight potential pathways that can be targeted in eradicating amoebae cysts successfully.
  13. Mukheem A, Shahabuddin S, Akbar N, Miskon A, Muhamad Sarih N, Sudesh K, et al.
    Nanomaterials (Basel), 2019 Apr 21;9(4).
    PMID: 31010071 DOI: 10.3390/nano9040645
    The present research focused on the fabrication of biocompatible polyhydroxyalkanoate, chitosan, and hexagonal boron nitride incorporated (PHA/Ch-hBN) nanocomposites through a simple solvent casting technique. The fabricated nanocomposites were comprehensively characterized by Fourier transform infrared spectroscope (FT-IR), field emission scanning electroscope (FESEM), and elemental mapping and thermogravimetric analysis (TGA). The antibacterial activity of nanocomposites were investigated through time-kill method against multi drug resistant (MDR) microbes such as methicillin-resistant Staphylococcus aureus (MRSA) and Escherichia coli (E. coli) K1 strains. In addition, nanocomposites have examined for their host cytotoxicity abilities using a Lactate dehydrogenase (LDH) assay against spontaneously immortalized human keratinocytes (HaCaT) cell lines. The results demonstrated highly significant antibacterial activity against MDR organisms and also significant cell viability as compared to the positive control. The fabricated PHA/Ch-hBN nanocomposite demonstrated effective antimicrobial and biocompatibility properties that would feasibly suit antibacterial and biomedical applications.
  14. Akbar N, Javed M, Arif Khan A, Masood A, Ahmed N, Mehmood RY, et al.
    ACS Omega, 2023 Aug 22;8(33):30095-30108.
    PMID: 37636959 DOI: 10.1021/acsomega.3c02457
    The degradation of organic dye pollutants is a critical environmental issue that has garnered significant attention in recent years. To address this problem, we investigated the potential of CaCrO4 chromite (CCO) as a photocatalyst for the degradation of cationic and anionic dye solutions under sunlight irradiation. CaCrO4 was synthesized via a sol-gel auto-combustion route and sintered at 900 °C. The Rietveld refined XRD profile confirmed the zircon-type structure of CaCrO4 crystallized in the tetragonal unit cell with I41/amd space group symmetry. The surface morphology of the sample was investigated by field emission scanning electron microscopy (FESEM), which revealed the polyhedral texture of the grains. Energy-dispersive X-ray spectroscopy (EDX) and X-ray photoelectron spectroscopy (XPS) studies were carried out to analyze the elemental composition and chemical states of the ions present in the compound. Fourier transform infrared (FT-IR) spectroscopy analysis revealed the vibrational modes corresponding to the tetrahedral and dodecahedral metal oxide bonds. The optical band gap was approximated to be in the range of 1.928 eV by using the Tauc relation. The CaCrO4 catalyst with different contents (5, 20, 35, and 50 mg) was investigated for its photocatalytic performance for the degradation of RhB dye solution under sunlight irradiation using a UV-Vis spectrometer over the experimental wavelength range of 450-600 nm. The degradation efficacy increased from 70.630 to 93.550% for 5-35 mg and then decreased to 68.720% for 50 mg in 140 min under visible light illumination. The comparative study demonstrates that a higher degradation rate was achieved for cationic than anionic dyes in the order RhB > MB > MO. The highest deterioration (93.80%) was achieved for the RhB dye in 140 min. Equilibrium and kinetic studies showed that the adsorption process followed the Langmuir isotherm and pseudo-second-order models, respectively. The maximum adsorption capacity of 21.125 mg/g was observed for the catalyst concentration of 35 mg. From the cyclic test, it has been observed that the synthesized photocatalyst is structurally and morphologically stable and reusable. The radical trapping experiment demonstrated that superoxide and hydroxyl radicals were the primary species engaged in the photodegradation process. A possible mechanism for the degradation of RhB has been proposed. Hence, we conclude that CaCrO4 can be used as an efficient photocatalyst for the remediation of organic dye pollutants from the environment.
  15. Javed M, Akbar N, Khan AA, Masood A, Ahmed N, Khan MJ, et al.
    Environ Sci Pollut Res Int, 2024 Aug;31(40):53532-53551.
    PMID: 39192152 DOI: 10.1007/s11356-024-34753-1
    Worldwide environmental challenges pose critical problems with the growth of the global economy. Addressing these issues requires the development of an eco-friendly and sustainable catalyst for degrading organic dye pollutants. In this study, copper-doped magnesium aluminates (CuxMg1-xAl2O4) with x = 0.0-0.8 were synthesized using a citrate-based combustion route. The inclusion of Cu(II) significantly impacted the structural, microstructural, optical, and photocatalytic activity of the catalyst. Rietveld analysis of X-ray diffraction powder profiles revealed single-phase spinels crystallized in the face-centered cubic unit cell with Fd 3 ¯ m space group. Chemical states of the ions, surface morphology, and elemental investigation were analyzed by X-ray photoelectron spectroscopy, field-emission scanning electron microscopy, and energy-dispersive X-ray spectroscopy, respectively. UV-visible and diffuse reflectance spectroscopies confirmed the reduction of the band gap due to Cu(II) doping, validated by first-principle investigations using the WIEN2k code. The catalyst with x = 0.8 showed higher photocatalytic efficacy (90% and 93%) for removing two azo organic dye pollutants, rhodamine B and methyl orange, respectively, within 120 min. Degradation kinetics followed a pseudo-first-order mechanism. The doped (0.8) sample was structurally and morphologically stable and reusable under visible irradiation, retaining performance after three runs. Scavenger studies confirmed hydroxyl and superoxide radicals' involvement in the degradation. This work presents an effective approach to enhancing CuxMg1-xAl2O4 catalysts' photodegradation performance, with potential applications in pharmaceuticals and wastewater remediation.
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