A systematic study on the structural and optical properties of vertically aligned zinc oxide nanorods grown by high pressure assisted pulsed laser deposition technique

In this study, we synthesize high quality vertically aligned ZnO (VAZO) nanorods on silicon, sapphire, and indium tin oxide (ITO) substrates by using pulsed laser deposition (PLD) technique at high growth pressure (0.3 Torr). Systematic changes in structural and optical properties of VAZO nanorods are studied by varying the substrate temperature (500–600 °C) and number of pulsed laser shots during the deposition. ZnO nanoparticles deposited at high pressure act as nucleation sites, eliminating requirement of catalyst to fabricate VAZO nanorods. Two sharp ZnO peaks with high intensity correspond to the (0002) and (0004) planes in X-ray diffraction pattern confirm the growth of ZnO nanorods, oriented along the c-axis. Scanning Electron Microscopy (SEM) images indicate a regular arrangement of vertically aligned hexagonal closed pack nano-structures of ZnO. The vertical alignment of ZnO nanorods is also supported by the presence of E2 (high) and A1 (LO) modes in Raman spectra. We can tune the diameter of VAZO nanorods by changing growth temperature and annealing environments. Photoluminescence spectroscopy illustrates reduction in defect level peak intensities with increase in diameter of VAZO nanorods. This study signifies that high pressure PLD technique can be used more efficiently for controlled and efficient growth of VAZO nanorods on different substrates

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

A Study on Structural and Optical Properties of Vertically Aligned Zinc Oxide Nanorods

ZnO is an n-type semiconductor having a large band gap of 3.37eV. This study optimizes the fabrication process to grow high quality vertically aligned Zinc oxide (VAZO) nanorods on different substrates without catalyst by pulse laser deposition (PLD) technique at high chamber pressure of 0.3 Torr through varying substrate temperature and the number of laser pulses. The nanoparticles deposited at high pressure act as nucleation sites that help in the formation of nanostructures following Volmer Weber model and VS (Vapor-Solid) growth mechanism. X-ray diffraction (XRD), scanning electron microscopy (SEM), Raman spectroscopy, and photoluminescence (PL) spectroscopy techniques were used to characterize VAZO nanorods. Two sharp ZnO peaks (0002) and (0004) dominate the XRD pattern with high intensity consistent with the ZnO nanorods that are principally oriented along the c-axis. SEM images indicate a regular arrangement of the vertically aligned hexagonal closed pack nano structures of ZnO which is also supported by the presence of E2 (high) and A1 (LO) Raman active modes. A reduction in the defect level peak intensities can be analyzed from the PL spectra as the diameter of the VAZO nanorods has been increased, by changing the temperature and also been effected by annealing treatment. Molecular dynamics simulation studies were performed using LAMMPS software for better interpretation of the properties of VAZO nanorods annealed at different temperatures in oxygen and hydrogen atmosphere

Performance of Novel Antimicrobial Protein Bg_9562 and In Silico Predictions on Its Properties with Reference to Its Antimicrobial Efficiency against Rhizoctonia solani

Bg_9562 is a potential broad-spectrum antifungal effector protein derived from the bacteria Burkholderia gladioli strain NGJ1 and is effective against Rhizoctonia solani, the causal agent of sheath blight in rice. In the present study, in vitro antifungal assays showed that Bg_9562 was efficient at 35 °C and 45 °C and ineffective either at high acidic pH (3.0) or alkaline pH (9.5) conditions. Compatibility studies between the native bioagents Trichoderma asperellum TAIK1 and Bacillus subtilis BIK3 indicated that Bg_9562 was compatible with the bioagents. A field study using foliar spray of the Bg_9562 protein indicated the need of formulating the protein before its application. In silico analysis predicted that Bg_9562 possess 111 amino acid residues (46 hydrophobic residues, 12 positive and 8 negative residues) with the high aliphatic index of 89.92, attributing to its thermostability with a half-life of 30 h. Bg_9562 (C491H813N137O166S5) possessed a protein binding potential of 1.27 kcal/mol with a better possibility of interacting and perturbing the membrane, the main target for antimicrobial proteins. The secondary structure revealed the predominance of random coils in its structure, and the best 3D model of Bg_9562 was predicted using an ab initio method with Robetta and AlphaFold 2. The predicted binding ligands were nucleic acids and zinc with confidence scores of 0.07 and 0.05, respectively. The N-terminal region (1–14 residues) and C-terminal region (101 to 111) of Bg_9562 residues were predicted to be disordered regions. Stability and binding properties of the protein from the above studies would help to encapsulate Bg_9562 using a suitable carrier to maintain efficiency and improve delivery against Rhizoctonia solani in the most challenging rice ecosphere