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  • Article
    Nsengimana J, Laye J, Filia A, Walker C, Jewell R, Van den Oord JJ, Wolter P, Patel P, Sucker A, Schadendorf D, Jönsson GB, Bishop DT, Newton-Bishop J.
    Oncotarget. 2015 May 10;6(13):11683-93.
    Development and validation of robust molecular biomarkers has so far been limited in melanoma research. In this paper we used a large population-based cohort to replicate two published gene signatures for melanoma classification. We assessed the signatures prognostic value and explored their biological significance by correlating them with factors known to be associated with survival (vitamin D) or etiological routes (nevi, sun sensitivity and telomere length). Genomewide microarray gene expressions were profiled in 300 archived tumors (224 primaries, 76 secondaries). The two gene signatures classified up to 96% of our samples and showed strong correlation with melanoma specific survival (P=3 x 10(-4)), Breslow thickness (P=5 x 10(-10)), ulceration (P=9.x10-8) and mitotic rate (P=3 x 10(-7)), adding prognostic value over AJCC stage (adjusted hazard ratio 1.79, 95%CI 1.13-2.83), as previously reported. Furthermore, molecular subtypes were associated with season-adjusted serum vitamin D at diagnosis (P=0.04) and genetically predicted telomere length (P=0.03). Specifically, molecular high-grade tumors were more frequent in patients with lower vitamin D levels whereas high immune tumors came from patients with predicted shorter telomeres. Our data confirm the utility of molecular biomarkers in melanoma prognostic estimation using tiny archived specimens and shed light on biological mechanisms likely to impact on cancer initiation and progression.
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  • Article
    Hu Y, Xu R, Ma J, Yan Z, Ma J.
    Bioengineered. 2022 05;13(5):11668-11683.
    Cisplatin is a primary chemotherapeutic drug for gastric cancer (GC) patients, but the drug resistance remains the leading cause of treatment failure and high mortality. Curcumol is a bioactive sesquiterpenoid that has reportedly been linked to cisplatin sensitivity in GC. This study focuses on the exact functions of curcumol in the cisplatin sensitivity of GC cells and the molecules of action. The curcumol treatment reduced the viability and migration and enhanced cisplatin sensitivity of GC cells in a dose-dependent manner. Microarray analysis suggested that microRNA-7 (miR-7) was the most upregulated miRNA in GC cells after curcumol treatment. The Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis showed that the curcumol-affected genes, including the target genes of miR-7, were enriched in the nuclear factor-kappa B (NF-κB) pathway, whose activity was suppressed after curcumol treatment. miR-7 was found to target and suppress RELA proto-oncogene (RELA, also known as p65), a NF-κB subunit. Downregulation of miR-7 blocked the sensitizing effects of curcumol on cells to cisplatin and led to increased expression of NF-κB p65 and snail family transcriptional repressor 1 (SNAIL). Further downregulation of RELA enhanced, whereas upregulation of SNAIL suppressed the sensitivity again. In summary, this study suggests that curcumol sensitizes GC cells to cisplatin via miR-7 and the suppression of the NF-κB/SNAIL axis. The findings may offer new thoughts that curcumol in combination with cisplatin might be a useful strategy for GC management.
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  • Article
    Simón D, Borsani O, Filippi CV.
    PeerJ. 2022;10:e11683.
    Background: Plant innate immunity relies on a broad repertoire of receptor proteins that can detect pathogens and trigger an effective defense response. Bioinformatic tools based on conserved domain and sequence similarity are within the most popular strategies for protein identification and characterization. However, the multi-domain nature, high sequence diversity and complex evolutionary history of disease resistance (DR) proteins make their prediction a real challenge. Here we present RFPDR, which pioneers the application of Random Forest (RF) for Plant DR protein prediction.
    Methods: A recently published collection of experimentally validated DR proteins was used as a positive dataset, while 10x10 nested datasets, ranging from 400-4,000 non-DR proteins, were used as negative datasets. A total of 9,631 features were extracted from each protein sequence, and included in a full dimension (FD) RFPDR model. Sequence selection was performed, to generate a reduced-dimension (RD) RFPDR model. Model performances were evaluated using an 80/20 (training/testing) partition, with 10-cross fold validation, and compared to baseline, sequence-based and state-of-the-art strategies. To gain some insights into the underlying biology, the most discriminatory sequence-based features in the RF classifier were identified.
    Results and Discussion: RD-RFPDR showed to be sensitive (86.4 ± 4.0%) and specific (96.9 ± 1.5%) for identifying DR proteins, while robust to data imbalance. Its high performance and robustness, added to the fact that RD-RFPDR provides valuable information related to DR proteins underlying properties, make RD-RFPDR an interesting approach for DR protein prediction, complementing the state-of-the-art strategies.
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  • Article
    Nguyen TH, Edwards C, Goddard LL, Popescu G.
    Opt Express. 2016 May 30;24(11):11683-93.
    In this paper, we extend our recent work on partially coherent quantitative phase imaging (pcQPI) from two-dimensional (2D) to three-dimensional (3D) imaging of weakly scattering samples. Due to the mathematical complexity, most theoretical modeling of quantitative phase image formation under partial coherence has focused on thin, well-focused samples. It is unclear how these abberations are affected by defocusing. Also, as 3D QPI techniques continue to develop, a better model needs to be developed to understand and quantify these aberrations when imaging thicker samples. Here, using the first order Born's approximation, we derived a mathematical framework that provides an intuitive model of image formation under varying degrees of coherence. Our description provides a clear connection between the halo effect and phase underestimation, defocusing and the 3D structure of the sample under investigation. Our results agree very well with the experiments and show that the microscope objective defines the sectioning ability of the imaging system while the condenser lens is responsible for the halo effect.
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  • Article
    Chen X, Wang D, Wang Z, Zhou P, Wu Z, Jiang F.
    Chem Commun (Camb). 2014 Oct 11;50(79):11683-5.
    Molybdenum phosphide was adopted as a new electrocatalyst for the hydrogen evolution reaction for the first time, exhibiting an excellent electrocatalytic activity with a small Tafel slope of 60 mV dec(-1), which is amongst the most active, acid-stable, earth abundant HER electrocatalysts reported to date.
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  • Article
    Owen RE, O'Byrne JP, Mattia D, Plucinski P, Pascu SI, Jones MD.
    Chem Commun (Camb). 2013 Dec 25;49(99):11683-5.
    A series of cobalt heterogeneous catalysts have been developed that are effective for the conversion of CO2 to hydrocarbons. The effect of the promoter and loadings have been investigated.
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  • Article
    Hao N, Wang Z, Song Y, Ruan S, He C, Dong Z.
    Heliyon. 2022 Nov;8(11):e11683.
    Honeycomb plate (HP), which is a high-strength and lightweight structure, has good vibration characteristics, while beetle elytron plate (BEP) has better mechanical properties. To promote the engineering application of BEPs, the vibration and sound transmission characteristics of aluminium BEPs were investigated in this paper with HP as the comparison object. This paper investigated the effects of the number of trabeculae, the ratio of length and width, skin thickness, core height and core thickness on the first 4 frequencies using finite element method. The results show that (1) the vibration characteristic of BEP is optimal when the number of trabeculae is 6, and its 3rd and 4th modes show mixed mode, i.e., torsion-bending or bending-torsion mode. (2) The frequencies of BEPs are generally lower than those of HPs. Compared with HPs, the ratio of length and width and core thickness have a smaller influence on the mode shapes of BEPs, and the core height has a smaller influence on BEPs' frequencies. When the skin thickness is small, increasing the thickness can effectively change the natural frequencies of BEPs and HPs. (3) Considering the common frequencies of four applications (aircrafts, unmanned aerial vehicles, high-speed trains and automobiles) of sandwich plates, the effects of the abovementioned parameters including the ratio of length and width, skin thickness, core height and core thickness are analysed. (4) Combined with the theoretical calculation formula, the effect of the above structural parameters on the sound transmission characteristic is explored using the index of sound transmission loss, and targeted recommendations are given. This paper progresses the application in engineering.
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  • Article
    Cinčić D, Brekalo I, Kaitner B.
    Chem Commun (Camb). 2012 Dec 11;48(95):11683-5.
    The presence of water or organic solvent vapour accelerates the solid-state condensation of solid aromatic amines and aromatic aldehydes into Schiff bases; we show the important role of catalytic triethylamine in the vapour phase in such vapour digestion synthesis, as well as in the liquid phase in synthesis via liquid-assisted grinding.
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  • Article
    Goh XM, Lin L, Roberts A.
    Opt Express. 2010 May 24;18(11):11683-8.
    Resonances in subwavelength apertures are accompanied by wavelength-dependent phase shifts in the transmitted fields offering a potential for manipulation of wavefields. Here, we present Finite Element Method simulations and experiments investigating light passing through arrays of nanometric spatially varying near-resonant slits perforated in a silver film. We demonstrate that a one-dimensional focusing element can be obtained by tailoring the phase across the device through varying slit sizes around the resonant dimensions for a particular design wavelength.
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  • Article
    Motta C, Pellegrini A, Camaione S, Geoghegan J, Speziale P, Barbieri G, Pietrocola G.
    Sci Rep. 2023 07 19;13(1):11683.
    The secreted von Willebrand factor-binding protein (vWbp) from Staphylococcus aureus interacts with the coagulation factors prothrombin and fibrinogen (Fbg), leading to the non-proteolytic transglutaminase activation of Factor XIII (FXIII). In this study we found that vWbp-activated FXIII catalyses the incorporation of amino-donor dansylcadaverine into region A of fibronectin-binding protein A (FnBPA). Incubation of Fbg with recombinant region A of S. aureus Fbg-binding proteins FnBPA, FnBPB, ClfA or ClfB in presence of vWbp-activated FXIII resulted in the formation of high molecular heteropolymers with FnBPA only, suggesting a specificity of the cross-linking reaction between fibrin(ogen) and the staphylococcal surface. As previously observed, cross-linking sites were mapped to the α-chain and the N1 subdomain of fibrin(ogen) and region A of FnBPA, respectively. Comparable results were obtained when tissue tranglutaminase-2 (TG2) was tested for cross-linking of FnBPA and Fbg. Of note, FnBPA-mediated covalent cross-linking promoted by vWbp-activated FXIII was also observed when bacteria were allowed to attach to fibrin(ogen). Together these findings suggest a novel pathogenetic mechanism by which the transglutaminase action of FXIII and/or TG2 contributes to entrapment and persistence of S. aureus in blood and host tissues.
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  • Article
    Wolff M, Okrut A, Feldmann C.
    Inorg Chem. 2011 Nov 21;50(22):11683-94.
    The five polyhalides [(Ph)(3)PBr][Br(7)], [(Bz)(Ph)(3)P](2)[Br(8)], [(n-Bu)(3)MeN](2)[Br(20)], [C(4)MPyr](2)[Br(20)] ([C(4)MPyr] = N-butyl-N-methylpyrrolidinium), and [(Ph)(3)PCl](2)[Cl(2)I(14)] were prepared by the reaction of dibromine and iodine monochloride in ionic liquids. The compounds [(Ph)(3)PBr][Br(7)] and [(Bz)(Ph)(3)P](2)[Br(8)] contain discrete pyramidal [Br(7)](-) and Z-shaped [Br(8)](2-) polybromide anions. [(n-Bu)(3)MeN](2)[Br(20)] and [C(4)MPyr](2)[Br(20)] exhibit new infinite two- and three-dimensional polybromide networks and contain the highest percentage of dibromine ever observed in a compound. [(Ph)(3)PCl](2)[Cl(2)I(14)] also consists of a three-dimensional network and is the first example of an infinite polyiodine chloride. All compounds were obtained from ionic liquids as the solvent that, on the one hand, guarantees for a high stability against strongly oxidizing Br(2) and ICl and that, on the other hand, reduces the high volatility of the molecular halogens.
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  • Article
    Ren L, Lei T, Gong LZ.
    Chem Commun (Camb). 2011 Nov 14;47(42):11683-5.
    A highly enantioselective Friedländer condensation has been established by using chiral Brønsted acids in combination with achiral amines to give quinolines in high yields (up to 99%) and with excellent enantioselectivities (up to 95%).
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  • Article
    Atapour A, Vosough P, Jafari S, Sarab GA.
    Sci Rep. 2022 07 08;12(1):11683.
    Malaria is a complex disease caused by parasites of the genus Plasmodium and is the leading cause of morbidity and mortality worldwide. The most severe form of malaria disease is caused by Plasmodium falciparum. Thus, a combination of different approaches is needed to control malaria. Resistance to first-line drugs and insecticides, on the other hand, makes the need for an effective vaccination more urgent than ever. Because erythrocyte parasites cause the most clinical symptoms, developing a vaccination for this stage of infection might be highly beneficial. In this research, we employed various bioinformatics methods to create an efficient multi-epitope vaccine that induces antibodies against the blood stage of malaria infection. For this purpose, we selected the malaria PfGARP protein as the target here. The B, HTL epitopes, and epitope conservation were predicted. The predicted epitopes (including 5 B and 5 HTL epitopes) were connected using suitable linkers, and the flagellin molecule was used as an adjuvant to improve its immunogenicity. The final construct vaccine with 414 amino acids long was designed. The vaccine's allergenicity, antigenicity, solubility, physicochemical characteristics, 2D and 3D structure modeling, molecular docking, molecular dynamics simulation, in silico cloning, and immunological simulation were tested. In silico immune simulation results showed significantly elevated IgG1 and IgM and T helper cells, INF γ, IL 2, and B-cell populations after the injection of the designed vaccine. These significant computational analyses indicated that our proposed vaccine candidate might activate suitable immune responses against malaria. However, in vitro and in vivo studies are essential for further validation.
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  • Article
    deQuilettes DW, Zhang W, Burlakov VM, Graham DJ, Leijtens T, Osherov A, Bulović V, Snaith HJ, Ginger DS, Stranks SD.
    Nat Commun. 2016 05 24;7:11683.
    Organic-inorganic perovskites such as CH3NH3PbI3 are promising materials for a variety of optoelectronic applications, with certified power conversion efficiencies in solar cells already exceeding 21%. Nevertheless, state-of-the-art films still contain performance-limiting non-radiative recombination sites and exhibit a range of complex dynamic phenomena under illumination that remain poorly understood. Here we use a unique combination of confocal photoluminescence (PL) microscopy and chemical imaging to correlate the local changes in photophysics with composition in CH3NH3PbI3 films under illumination. We demonstrate that the photo-induced 'brightening' of the perovskite PL can be attributed to an order-of-magnitude reduction in trap state density. By imaging the same regions with time-of-flight secondary-ion-mass spectrometry, we correlate this photobrightening with a net migration of iodine. Our work provides visual evidence for photo-induced halide migration in triiodide perovskites and reveals the complex interplay between charge carrier populations, electronic traps and mobile halides that collectively impact optoelectronic performance.
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  • Article
    Morais JE, Forte P, Nevill AM, Barbosa TM, Marinho DA.
    Sci Rep. 2020 07 15;10(1):11683.
    Short-distance swimmers may exhibit imbalances in their upper-limbs' thrust (differences between the thrust produced by each upper-limb). At maximal speed, higher imbalances are related to poorer performances. Additionally, little is known about the relationship between thrust and swim speed, and whether hypothetical imbalances exist in the speed achieved while performing each upper-limb arm-pull. This could be a major issue at least while swimming at maximal speed. This study aimed to: (1) verify a hypothetical inter-upper limb difference in the determinants related to front-crawl at maximal swim speed, and; (2) identify the main predictors responsible for the swim speed achieved during each upper-limb arm-pull. Twenty-two male swimmers of a national junior swim team (15.92 ± 0.75 years) were recruited. A set of anthropometric, dry-land strength, thrust and speed variables were assessed. Anthropometrics identified a significant difference between dominant and non-dominant upper-limbs (except for the hand surface area). Dry-land strength presented non-significant difference (p < 0.05) between the dominant and non-dominant upper-limbs. Overall, thrust and speed variables revealed a significant difference (p < 0.05) between dominant and non-dominant upper-limbs over a 25 m time-trial in a short-course pool. Swimmers were not prone to maintaining the thrust and speed along the trial where a significant variation was noted (p < 0.05). Using multilevel regression, the speed achieved by each upper-limb identified a set of variables, with the peak speed being the strongest predictor (dominant: estimate = 0.522, p < 0.001; non-dominant: estimate = 0.756, p < 0.001). Overall, swimmers exhibit significant differences between upper-limbs determinants. The upper-limb noting a higher dry-land strength also presented a higher thrust, and consequently higher speed. Coaches should be aware that sprint swimmers produce significant differences in the speed achieved by each one of their upper-limbs arm-pull.
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  • Article
    Peña-Alvarez M, Qiu L, Taravillo M, Baonza VG, Delgado MC, Yamago S, Jasti R, Navarrete JT, Casado J, Kertesz M.
    Phys Chem Chem Phys. 2016 04 28;18(17):11683-92.
    Cyclic paraphenylenes, [n]CPPs, and linear paraphenylenes, [n]LPPs, formed by n benzenes, are investigated by Raman spectroscopy for n = 5 to 12 and density functional theory (DFT) for n = 4 to 20. The information on the experimental Raman frequencies and intensities, combined with DFT computations and reported X-ray diffraction structures, provides a consistent interpretation of the Raman spectra and allows establishing relevant structure-property trends. Structural and electronic effects such as benzene ring bending, inter-ring torsions, π-conjugation (aromaticity) and orbital energy gaps as a function of the linear elongation in [n]LPPs versus the macrocyclic curvature in [n]CPPs and of the molecular size (i.e., polymer limit) are systematically analyzed on the basis of the vibrational Raman properties. Changes in the BLA as an indicator of the degree of quinonoid character are analyzed and linked to the Effective Conjugation Coordinate (ECC) model. The BLA patterns involved in twisted and non-twisted conformations and in different species (bipolarons, quinonoid tautomers, and ECC active modes) are compared and their differences are discussed. This paper offers a unified interpretation of structural and electronic aspects in relation to the evolution from linear 1D π-systems to cyclic 2D structures.
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  • Article
    Chi P, Wang Z, Li B, Shi AC.
    Langmuir. 2011 Sep 20;27(18):11683-9.
    The self-assembly of diblock copolymers under soft confinement is studied systematically using a simulated annealing method applied to a lattice model of polymers. The soft confinement is realized by the formation of polymer droplets in a poor solvent environment. Multiple sequences of soft confinement-induced copolymer aggregates with different shapes and self-assembled internal morphologies are predicted as functions of solvent-polymer interaction and the monomer concentration. It is discovered that the self-assembled internal morphology of the aggregates is largely controlled by a competition between the bulk morphology of the copolymer and the solvent-polymer interaction, and the shape of the aggregates can be non-spherical when the internal morphology is anisotropic and the solvent-polymer interaction is weak. These results demonstrate that droplets of diblock copolymers formed in poor solvents can be used as a model system to study the self-assembly of copolymers under soft confinement.
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  • Article
    Bonomo S, Ferrante G, Palazzi E, Pelosi N, Lirer F, Viegi G, La Grutta S.
    Sci Rep. 2019 08 12;9(1):11683.
    An association between climatic conditions and asthma mortality has been widely assumed. However, it is unclear whether climatic variations have a fingerprint on asthma dynamics over long time intervals. The aim of this study is to detect a possible correlation between climatic indices, namely the Atlantic Multidecadal Oscillation and Pacific Decadal Oscillation, and asthma mortality rates over the period from 1950 to 2015 in the contiguous US. To this aim, an analysis of non-stationary and non-linear signals was performed on time series of US annual asthma mortality rates, AMO and PDO indices to search for characteristic periodicities. Results revealed that asthma death rates evaluated for four different age groups (5-14 yr; 15-24 yr; 25-34 yr; 35-44 yr) share the same pattern of fluctuation throughout the 1950-2015 time interval, but different trends, i.e. a positive (negative) trend for the two youngest (oldest) categories. Annual asthma death rates turned out to be correlated with the dynamics of the AMO, and also modulated by the PDO, sharing the same averaged ∼44 year-periodicity. The results of the current study suggest that, since climate patterns have proved to influence asthma mortality rates, they could be advisable in future studies aimed at elucidating the complex relationships between climate and asthma mortality.
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  • Article
    Ghabban SJ, Althobaiti B, Farouk IM, Al Hablany M, Ghabban A, Alghbban R, Harbi S, Albalawi AE.
    Cureus. 2020 Nov 24;12(11):e11683.
    Background Diabetes mellitus (DM) is one of the most common diseases worldwide and affects many patients all over the globe. Diabetic complications vary between microvascular and macrovascular, affecting a wide range of organs and systems in the body. Understanding, determining, and in return, preventing such factors is essential to alleviate the quality of life of diabetic patients. Therefore, we aim to determine the poor glycemic control and the factors associated with it in our diabetes population. Methods This is a retrospective study where data was reviewed for all patients with Type II DM (T2DM) who attended the chronic illness clinic at King Khaled Hospital in Tabuk. We included patients aged ≥ 18 years, of Saudi nationality, and residents of the Tabuk region. Any patient not satisfying all the inclusion criteria was excluded from the current study. Diagnosis with diabetes was made according to the American Diabetes Association guidelines, 2020. Patients' demographic data, medical history, and social and lifestyle history were extracted from records. In addition, age, body mass index (BMI), drugs (insulin vs. oral hypoglycemic agents), duration of the disease, lipid profile, and other comorbidities were also extracted from the files. A p-value of <0.05 was selected as the statistically significant level in all tests. Results A total of 697 patients were included in the current study, with a mean age of 58.2±11.6 years. The mean glycosylated hemoglobin (HbA1c) of the study participants was 8.4±1.7%, and their fasting blood sugar (FBS) level was 9.9±3.9 mmol/l. With HbA1c cut-off at 7%, the overall prevalence of poor glycemic control was 81.5% (565/693). A higher prevalence of poor glycemic control was reported among study participants with higher DM duration (p=0.002). Diabetes complications were found in 208 (29.8%) of the study participants, where microvascular complications were present in 140 patients, and microvascular ones were found in 102. In the logistic regression model, older patients were less prone to poor glycemic control (OR=0.98; 95% CI=0.96-0.99; p=0.010). In addition, longer disease duration was a predictive factor of poor glycemic control (OR=1.05; 95% CI=1.02-1.08; p=0.003). Furthermore, the usage of combined insulin and tablet treatments were associated with a higher risk of poor glycemic control when compared to insulin only treatments (OR=4.65; 95% CI=1.55-13.94; p=0.006). Conclusion The results of this study indicate a high prevalence rate of poor glycemic control among Saudi patients, which is higher than previous reports have shown. More interest should be given to awareness programs with regard to promoting self-control protocols for the disease.
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  • Article
    Xie C, Xu L, Gang R, Zhang L, Ye Q, Xu Z.
    Langmuir. 2022 09 27;38(38):11683-11690.
    Defect engineering is a promising method for improving the performance of MoS2 in various fields. In this study, sulfur-defect-enriched MoS2 (SD-MoS2) nanosheets were fabricated via a facile microwave-hydrothermal strategy in 10 min for tetracycline (TC) adsorption applications. The introduction of sulfur defects in MoS2 induced more exposed unsaturated sulfur atoms at the edge, enhancing the interaction between the adsorbent and antibiotic and improving the adsorption activity of the antibiotic. Density functional theory calculations further revealed that sulfur defects in MoS2 could alter the electronic structure and exhibited low TC adsorption energy of -2.09 eV. This work provides a new method for fabricating MoS2 nanosheets and other transition metal dichalcogenide-based adsorbents with enhanced antibiotic removal performance and a comprehensive understanding of antibiotic removal mechanisms in SD-MoS2.
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