Investigation of Photoluminescence and Optoelectronics Properties of Transition Metal-Doped ZnO Thin Films.

Thin films of zinc oxide (ZnO) doped with transition metals have recently gained significant attention due to their potential applications in a wide range of optoelectronic devices. This study focuses on ZnO thin films doped with the transition metals Co, Fe, and Zr, exploring various aspects of their structural, morphological, optical, electrical, and photoluminescence properties. The thin films were produced using RF and DC co-sputtering techniques. The X-ray diffraction (XRD) analysis revealed that all the doped ZnO thin films exhibited a stable wurtzite crystal structure, showcasing a higher structural stability compared to the undoped ZnO, while the atomic force microscopy (AFM) imaging highlighted a distinctive granular arrangement. Energy-dispersive X-ray spectroscopy was employed to confirm the presence of transition metals in the thin films, and Fourier-transform infrared spectroscopy (FTIR) was utilized to investigate the presence of chemical bonding. The optical characterizations indicated that doping induced changes in the optical properties of the thin films. Specifically, the doped ZnO thin film's bandgap experienced a significant reduction, decreasing from 3.34 to 3.30 eV. The photoluminescence (PL) analysis revealed distinguishable emission peaks within the optical spectrum, attributed to electronic transitions occurring between different bands or between a band and an impurity. Furthermore, the introduction of these transition metals resulted in decreased resistivity and increased conductivity, indicating their positive influence on the electrical conductivity of the thin films. This suggests potential applications in solar cells and light-emitting devices.

Synthesis and Characterization of Ferric Vanadate Nanorods for Efficient Electrochemical Detection of Ascorbic Acid.

This study reports the synthesis of ferric vanadate (FeVO4) via a facile hydrothermal method, focusing on demonstrating its exceptional electrochemical (EC) properties on detecting low-density ascorbic acid (AA). The phase purity, crystallinity, structure, morphology, and chemical compositional properties were characterized by employing X-ray diffraction, energy-dispersive X-ray spectroscopy, scanning electron microscopy, Raman spectroscopy, and X-ray photoelectron spectroscopy techniques. EC impedance spectroscopy and cyclic voltammetry techniques were also adopted in order to assess the EC response of a FeVO4-modified glassy carbon electrode for sensing AA at room temperature. The AA concentration range adopted in this experiment is 0.1-0.3 mM at a working electric potential of -0.13 V. The result showed functional excellence of this material for the EC determination of AA with good stability and reproducibility, promising its potentiality in connection with relevant sensing applications.

Advances of Blood Coagulation Factor XIII in Bone Healing.

The biologic process of bone healing is complicated, involving a variety of cells, cytokines, and growth factors. As a result of bone damage, the activation of a clotting cascade leads to hematoma with a high osteogenic potential in the initial stages of healing. A major factor involved in this course of events is clotting factor XIII (FXIII), which can regulate bone defect repair in different ways during various stages of healing. Autografts and allografts often have defects in clinical practice, making the development of advanced materials that support bone regeneration a critical requirement. Few studies, however, have examined the promotion of bone healing by FXIII in combination with biomaterials, in particular, its effect on blood coagulation and osteogenesis. Therefore, we mainly summarized the role of FXIII in promoting bone regeneration by regulating the extracellular matrix and type I collagen, bone-related cells, angiogenesis, and platelets, and described the research progress of FXIII = related biomaterials on osteogenesis. This review provides a reference for investigators to explore the mechanism by which FXIII promotes bone healing and the combination of FXIII with biomaterials to achieve targeted bone tissue repair.

Fabrication of Interleukin-4 Encapsulated Bioactive Microdroplets for Regulating Inflammation and Promoting Osteogenesis.

Background: Despite the inherent regenerative ability of bone, large bone defect regeneration remains a major clinical challenge for orthopedic surgery. Therapeutic strategies medicated by M2 phenotypic macrophages or M2 macrophage inducer have been widely used to promote tissue remodeling. In this study, ultrasound-responsive bioactive microdroplets (MDs) encapsulated with bioactive molecule interleukin-4 (IL4, hereafter designated MDs-IL4) were fabricated to regulate macrophage polarization and potentiate the osteogenic differentiation of human mesenchymal stem cells (hBMSCs). Materials and Methods: The MTT assay, live and dead staining, and phalloidin/DAPI dual staining were used to evaluate biocompatibility in vitro. H&E staining was used to evaluate biocompatibility in vivo. Inflammatory macrophages were further induced via lipopolysaccharide (LPS) stimulation to mimic the pro-inflammatory condition. The immunoregulatory role of the MDs-IL4 was tested via macrophage phenotypic marker gene expression, pro-inflammatory cytokine level, cell morphological analysis, and immunofluorescence staining, etc. The immune-osteogenic response of hBMSCs via macrophages and hBMSCs interactions was further investigated in vitro. Results: The bioactive MDs-IL4 scaffold showed good cytocompatibility in RAW 264.7 macrophages and hBMSCs. The results confirmed that the bioactive MDs-IL4 scaffold could reduce inflammatory phenotypic macrophages, as evidenced by changing in morphological features, reduction in pro-inflammatory marker gene expression, increase of M2 phenotypic marker genes, and inhibition of pro-inflammatory cytokine secretion. Additionally, our results indicate that the bioactive MDs-IL4 could significantly enhance the osteogenic differentiation of hBMSCs via its potential immunomodulatory properties. Conclusion: Our results demonstrate that the bioactive MDs-IL4 scaffold could be used as novel carrier system for other pro-osteogenic molecules, thus having potential applications in bone tissue regeneration.

Effects of the Hubbard potential on the NMR shielding and optoelectronic properties of BiMnVO5 compound.

This study explores the nuclear magnetic shielding, chemical shifts, and the optoelectronic properties of the BiMnVO5 compound using the full-potential linearized augmented plane wave method within the generalized gradient approximation by employing the Hubbard model (GGA + U). The 209Bi and 51V chemical shifts and bandgap values of the BiMnVO5 compound in a triclinic crystal structure are found to be directly related to Hubbard potential. The relationship between the isotropic nuclear magnetic shielding σiso and chemical shift δiso is obtained with a slope of 1.0231 and - 0.00188 for 209Bi and 51V atoms, respectively. It is also observed that the bandgap, isotropic nuclear magnetic shielding, and chemical shifts increase with the change in Hubbard potentials (U) of 3, 4, 5, 6, and 7.

The role of autophagy in bone metabolism and clinical significance.

The skeletal system is the basis of the vertebral body composition, which affords stabilization sites for muscle attachment, protects vital organs, stores mineral ions, supplies places to the hematopoietic system, and participates in complex endocrine and immune system. Not surprisingly, bones are constantly reabsorbed, formed, and remodeled under physiological conditions. Once bone metabolic homeostasis is interrupted (including inflammation, tumors, fractures, and bone metabolic diseases), the body rapidly initiates bone regeneration to maintain bone tissue structure and quality. Macroautophagy/autophagy is an essential metabolic process in eukaryotic cells, which maintains metabolic energy homeostasis and plays a vital role in bone regeneration by controlling molecular degradation and organelle renewal. One relatively new observation is that mesenchymal cells, osteoblasts, osteoclasts, osteocytes, chondrocytes, and vascularization process exhibit autophagy, and the molecular mechanisms and targets involved are being explored and updated. The role of autophagy is also emerging in degenerative diseases (intervertebral disc degeneration [IVDD], osteoarthritis [OA], etc.) and bone metabolic diseases (osteoporosis [OP], osteitis deformans, osteosclerosis). The use of autophagy regulators to modulate autophagy has benefited bone regeneration, including MTOR (mechanistic target of rapamycin kinase) inhibitors, AMPK activators, and emerging phytochemicals. The application of biomaterials (especially nanomaterials) to trigger autophagy is also an attractive research direction, which can exert superior therapeutic properties from the material-loaded molecules/drugs or the material's properties such as shape, roughness, surface chemistry, etc. All of these have essential clinical significance with the discovery of autophagy associated signals, pathways, mechanisms, and treatments in bone diseases in the future.Abbreviations: Δψm: mitochondrial transmembrane potential AMPK: AMP-activated protein kinase ARO: autosomal recessive osteosclerosis ATF4: activating transcription factor 4 ATG: autophagy-related ß-ECD: ß-ecdysone BMSC: bone marrow mesenchymal stem cell ER: endoplasmic reticulum FOXO: forkhead box O GC: glucocorticoid HIF1A/HIF-1α: hypoxia inducible factor 1 subunit alpha HSC: hematopoietic stem cell HSP: heat shock protein IGF1: insulin like growth factor 1 IL1B/IL-1ß: interleukin 1 beta IVDD: intervertebral disc degradation LPS: lipopolysaccharide MAPK: mitogen-activated protein kinase MSC: mesenchymal stem cell MTOR: mechanistic target of rapamycin kinase NP: nucleus pulposus NPWT: negative pressure wound therapy OA: osteoarthritis OP: osteoporosis PTH: parathyroid hormone ROS: reactive oxygen species SIRT1: sirtuin 1 SIRT3: sirtuin 3 SQSTM1/p62: sequestosome 1 TNFRSF11B/OPG: TNF receptor superfamily member 11b TNFRSF11A/RANK: tumor necrosis factor receptor superfamily, member 11a TNFSF11/RANKL: tumor necrosis factor (ligand) superfamily, member 11 TSC1: tuberous sclerosis complex 1 ULK1: unc-51 like autophagy activating kinase 1.

Tailoring TiO2/Al2O3 heterolayers as optical filters for the visible region.

Optical filters operating in the visible region of the spectrum are highly desired for applications ranging from optical communication and sensing to fluorescence microscopy and skin therapy. However, complex fabrication procedures and/or inferior performance, limit the practical applications of previously reported thin-film-based optical filters. Herein, we describe the structual design concepts and facile fabrication of vertically stacked heterolayers of TiO2/Al2O3 to obtain a bandpass filter and a longwave pass edge filter operating in the spectral range 410-600 nm and 400-597 nm, respectively. The optical filters are designed according to MacLeod simulation and fabricated via magnetron sputtering, depositing alternative stacks of low (Al2O3) and high (TiO2) refractive index materials with different thicknesses, as confirmed by spectroscopic ellipsometry. Owing to a reasonable matching between the design and the fabrication, our developed TiO2/Al2O3 heterolayer optical filters exhibited 54.60% transmission for 7-layer longwave pass edge filter and 15% reflectance for 14-layer bandpass filter of a selective set of wavelengths (400-800 nm).

Combined effectiveness of extracorporeal radial shockwave therapy and ultrasound-guided trigger point injection of lidocaine in upper trapezius myofascial pain syndrome.

OBJECTIVE: Myofascial pain syndrome (MPS) is a major musculoskeletal problem and a leading cause of disability worldwide. Extracorporeal shockwave therapy (ESWT) and trigger point injection (TPI) have shown positive results for MPS but no previous study has investigated the combined effects of radial shockwave and trigger point injection of lidocaine for upper trapezius myofascial pain syndrome. METHOD: For this purpose, forty-five participants were randomly divided into shockwave (n = 15), shockwave with ultrasound-guided trigger point injection (combined; n = 15), and control (standard care; n = 15) groups. Participants were assessed at baseline, one week and four weeks by using the visual analog scale, neck disability index, electromyography, infrared thermography, and sonoelastography. RESULTS: Compared with control group, both shockwave and combined groups showed a statistically significant reduction in pain (P<0.01), functional disability (P<0.01), skin temperature (P<0.01), and elastic stiffness, with greater reduction in the combined group (P<0.01) than shockwave group (P<0.05) at four weeks. However, no significant difference was found in electrical activity between the groups (P>0.05). The combined group also showed significant differences in pain (P<0.05) and elastic stiffness (P<0.01) compared with shockwave group at four weeks. CONCLUSION: Our study revealed that extracorporeal radial shockwave therapy combined with trigger point injection of lidocaine was more effective for decreasing pain and elastic stiffness in upper trapezius myofascial pain syndrome at four weeks.

miR172 downregulates the translation of cleistogamy 1 in barley.

Background and Aims: Floret opening in barley is induced by the swelling of the lodicule, a trait under the control of the cleistogamy1 (cly1) gene. The product of cly1 is a member of the APETALA2 (AP2) transcription factor family, which inhibits lodicule development. A sequence polymorphism at the miR172 target site within cly1 has been associated with variation in lodicule development and hence with the cleistogamous phenotype. It was unclear whether miR172 actually functions in cly1 regulation and, if it does, which miR172 gene contributes to cleistogamy. It was also interesting to explore whether miR172-mediated cly1 regulation occurs at transcriptional level or at translational level. Methods: Deep sequencing of small RNA identified the miR172 sequences expressed in barley immature spikes. miR172 genes were confirmed by computational and expression analysis. miR172 and cly1 expression profiles were determined by in situ hybridization and quantitative expression analysis. Immunoblot analysis provided the CLY1 protein quantifications. Definitive evidence of the role of miR172 in cleistogamy was provided by a transposon Ds-induced mutant of Hv-miR172a. Key Results: A small RNA analysis of the immature barley spike revealed three isomers, miR172a, b and c, of which miR172a was the most abundant. In situ hybridization analysis showed that miR172 and cly1 co-localize in the lodicule primordium, suggesting that these two molecules potentially interact with one another. Immunoblot analysis showed that the sequence polymorphism at the miR172 target site within cly1 reduced the abundance of the CLY1 protein, but not that of its transcript. In a Ds-induced mutant of Hv-miR172a, which generates no mature miR172a, the lodicules fail to grow, resulting in a very small lodicule. Conclusions: Direct evidence is presented to show that miR172a acts to reduce the abundance of the CLY1 protein, which enables open flowering in barley.

A GDSL-motif esterase/acyltransferase/lipase is responsible for leaf water retention in barley.

The hydrophobic cuticle covers the surface of the most aerial organs of land plants. The barley mutant eceriferum-zv (cer-zv), which is hypersensitive to drought, is unable to accumulate a sufficient quantity of cutin in its leaf cuticle. The mutated locus has been mapped to a 0.02 cM segment in the pericentromeric region of chromosome 4H. As a map-based cloning approach to isolate the gene was therefore considered unlikely to be feasible, a comparison was instead made between the transcriptomes of the mutant and the wild type. In conjunction with extant genomic information, on the basis of predicted functionality, only two genes were considered likely to encode a product associated with cutin formation. When eight independent cer-zv mutant alleles were resequenced with respect to the two candidate genes, it was confirmed that the gene underlying the mutation in each allele encodes a Gly-Asp-Ser-Leu (GDSL)-motif esterase/acyltransferase/lipase. The gene was transcribed in the epidermis, and its product was exclusively deposited in cell wall at the boundary of the cuticle in the leaf elongation zone, coinciding with the major site of cutin deposition. CER-ZV is speculated to function in the deposition of cutin polymer. Its homologs were found in green algae, moss, and euphyllophytes, indicating that it is highly conserved in plant kingdom.

Six-rowed spike4 (Vrs4) controls spikelet determinacy and row-type in barley.

Inflorescence architecture of barley (Hordeum vulgare L.) is common among the Triticeae species, which bear one to three single-flowered spikelets at each rachis internode. Triple spikelet meristem is one of the unique features of barley spikes, in which three spikelets (one central and two lateral spikelets) are produced at each rachis internode. Fertility of the lateral spikelets at triple spikelet meristem gives row-type identity to barley spikes. Six-rowed spikes show fertile lateral spikelets and produce increased grain yield per spike, compared with two-rowed spikes with sterile lateral spikelets. Thus, far, two loci governing the row-type phenotype were isolated in barley that include Six-rowed spike1 (Vrs1) and Intermedium-C. In the present study, we isolated Six-rowed spike4 (Vrs4), a barley ortholog of the maize (Zea mays L.) inflorescence architecture gene RAMOSA2 (RA2). Eighteen coding mutations in barley RA2 (HvRA2) were specifically associated with lateral spikelet fertility and loss of spikelet determinacy. Expression analyses through mRNA in situ hybridization and microarray showed that Vrs4 (HvRA2) controls the row-type pathway through Vrs1 (HvHox1), a negative regulator of lateral spikelet fertility in barley. Moreover, Vrs4 may also regulate transcripts of barley SISTER OF RAMOSA3 (HvSRA), a putative trehalose-6-phosphate phosphatase involved in trehalose-6-phosphate homeostasis implicated to control spikelet determinacy. Our expression data illustrated that, although RA2 is conserved among different grass species, its down-stream target genes appear to be modified in barley and possibly other species of tribe Triticeae.

Meeting report from the first meetings of the Computational Modeling in Biology Network (COMBINE).

The Computational Modeling in Biology Network (COMBINE), is an initiative to coordinate the development of the various community standards and formats in computational systems biology and related fields. This report summarizes the activities pursued at the first annual COMBINE meeting held in Edinburgh on October 6-9 2010 and the first HARMONY hackathon, held in New York on April 18-22 2011. The first of those meetings hosted 81 attendees. Discussions covered both official COMBINE standards-(BioPAX, SBGN and SBML), as well as emerging efforts and interoperability between different formats. The second meeting, oriented towards software developers, welcomed 59 participants and witnessed many technical discussions, development of improved standards support in community software systems and conversion between the standards. Both meetings were resounding successes and showed that the field is now mature enough to develop representation formats and related standards in a coordinated manner.

Pathway Commons, a web resource for biological pathway data.

Pathway Commons (http://www.pathwaycommons.org) is a collection of publicly available pathway data from multiple organisms. Pathway Commons provides a web-based interface that enables biologists to browse and search a comprehensive collection of pathways from multiple sources represented in a common language, a download site that provides integrated bulk sets of pathway information in standard or convenient formats and a web service that software developers can use to conveniently query and access all data. Database providers can share their pathway data via a common repository. Pathways include biochemical reactions, complex assembly, transport and catalysis events and physical interactions involving proteins, DNA, RNA, small molecules and complexes. Pathway Commons aims to collect and integrate all public pathway data available in standard formats. Pathway Commons currently contains data from nine databases with over 1400 pathways and 687,000 interactions and will be continually expanded and updated.

The BioPAX community standard for pathway data sharing.

Biological Pathway Exchange (BioPAX) is a standard language to represent biological pathways at the molecular and cellular level and to facilitate the exchange of pathway data. The rapid growth of the volume of pathway data has spurred the development of databases and computational tools to aid interpretation; however, use of these data is hampered by the current fragmentation of pathway information across many databases with incompatible formats. BioPAX, which was created through a community process, solves this problem by making pathway data substantially easier to collect, index, interpret and share. BioPAX can represent metabolic and signaling pathways, molecular and genetic interactions and gene regulation networks. Using BioPAX, millions of interactions, organized into thousands of pathways, from many organisms are available from a growing number of databases. This large amount of pathway data in a computable form will support visualization, analysis and biological discovery.

Francisella tularensis novicida proteomic and transcriptomic data integration and annotation based on semantic web technologies.

BACKGROUND: This paper summarises the lessons and experiences gained from a case study of the application of semantic web technologies to the integration of data from the bacterial species Francisella tularensis novicida (Fn). Fn data sources are disparate and heterogeneous, as multiple laboratories across the world, using multiple technologies, perform experiments to understand the mechanism of virulence. It is hard to integrate these data sources in a flexible manner that allows new experimental data to be added and compared when required. RESULTS: Public domain data sources were combined in RDF. Using this connected graph of database cross references, we extended the annotations of an experimental data set by superimposing onto it the annotation graph. Identifiers used in the experimental data automatically resolved and the data acquired annotations in the rest of the RDF graph. This happened without the expensive manual annotation that would normally be required to produce these links. This graph of resolved identifiers was then used to combine two experimental data sets, a proteomics experiment and a transcriptomic experiment studying the mechanism of virulence through the comparison of wildtype Fn with an avirulent mutant strain. CONCLUSION: We produced a graph of Fn cross references which enabled the combination of two experimental datasets. Through combination of these data we are able to perform queries that compare the results of the two experiments. We found that data are easily combined in RDF and that experimental results are easily compared when the data are integrated. We conclude that semantic data integration offers a convenient, simple and flexible solution to the integration of published and unpublished experimental data.

Improved data retrieval from TreeBASE via taxonomic and linguistic data enrichment.

BACKGROUND: TreeBASE, the only data repository for phylogenetic studies, is not being used effectively since it does not meet the taxonomic data retrieval requirements of the systematics community. We show, through an examination of the queries performed on TreeBASE, that data retrieval using taxon names is unsatisfactory. RESULTS: We report on a new wrapper supporting taxon queries on TreeBASE by utilising a Taxonomy and Classification Database (TCl-Db) we created. TCl-Db holds merged and consolidated taxonomic names from multiple data sources and can be used to translate hierarchical, vernacular and synonym queries into specific query terms in TreeBASE. The query expansion supported by TCl-Db shows very significant information retrieval quality improvement. The wrapper can be accessed at the URL http://spira.zoology.gla.ac.uk/app/tbasewrapper.phpThe methodology we developed is scalable and can be applied to new data, as those become available in the future. CONCLUSION: Significantly improved data retrieval quality is shown for all queries, and additional flexibility is achieved via user-driven taxonomy selection.