SMART: Statistical Metabolomics AnalysisAn R Tool

Metabolomics data provide unprecedented opportunities to decipher metabolic mechanisms by analyzing hundreds to thousands of metabolites. Data quality concerns and complex batch effects in metabolomics must be appropriately addressed through statistical analysis. This study developed an integrated analysis tool for metabolomics studies to streamline the complete analysis flow from initial data preprocessing to downstream association analysis. We developed Statistical Metabolomics AnalysisAn R Tool (SMART), which can analyze input files with different formats, visually represent various types of data features, implement peak alignment and annotation, conduct quality control for samples and peaks, explore batch effects, and perform association analysis. A pharmacometabolomics study of antihypertensive medication was conducted and data were analyzed using SMART. Neuromedin N was identified as a metabolite significantly associated with angiotensin-converting-enzyme inhibitors in our metabolome-wide association analysis (<i>p</i> = 1.56 × 10^–4 in an analysis of covariance (ANCOVA) with an adjustment for unknown latent groups and <i>p</i> = 1.02 × 10^–4 in an ANCOVA with an adjustment for hidden substructures). This endogenous neuropeptide is highly related to neurotensin and neuromedin U, which are involved in blood pressure regulation and smooth muscle contraction. The SMART software, a user guide, and example data can be downloaded from http://www.stat.sinica.edu.tw/hsinchou/metabolomics/SMART.htm

Low-Temperature Chemical Synthesis of Three-Dimensional Hierarchical Ni(OH)₂‑Coated Ni Microflowers for High-Performance Enzyme-Free Glucose Sensor

Since prevention methods of type-II diabetes and knowledge of prediabetes are lacking, the development of sensitive and accurate glucose sensors with an ultralow detection limit is imperative. In this work, the enzyme-free glucose sensor based on three-dimensional (3D) hierarchical Ni microflowers with a Ni­(OH)2 coating layer has been demonstrated in a simple one-step chemical reaction at a low temperature of 80 °C. The as-synthesized materials were characterized by several analytical and spectroscopic techniques. In addition, the thin Ni­(OH)2 layer formed at the surface of the Ni microflower was evidenced by Raman, HRTEM, and XPS, which is the key factor to achieve highly sensitive enzyme-free glucose sensors based on low-cost materials such as copper, nickel, and their oxide and hydroxide. Moreover, our modified electrode exhibits an outstanding detection limit as low as 2.4 nM with an ultrahigh sensitivity of 2392 μA mM–1 cm–2, which is attributed to not only the increased surface area due to the controlled formation of spikes but also the contribution of the Ni­(OH)2 coating layer

Transfer-Free Growth of Atomically Thin Transition Metal Disulfides Using a Solution Precursor by a Laser Irradiation Process and Their Application in Low-Power Photodetectors

Although chemical vapor deposition is the most common method to synthesize transition metal dichalcogenides (TMDs), several obstacles, such as the high annealing temperature restricting the substrates used in the process and the required transfer causing the formation of wrinkles and defects, must be resolved. Here, we present a novel method to grow patternable two-dimensional (2D) transition metal disulfides (MS₂) directly underneath a protective coating layer by spin-coating a liquid chalcogen precursor onto the transition metal oxide layer, followed by a laser irradiation annealing process. Two metal sulfides, molybdenum disulfide (MoS₂) and tungsten disulfide (WS₂), are investigated in this work. Material characterization reveals the diffusion of sulfur into the oxide layer prior to the formation of the MS₂. By controlling the sulfur diffusion, we are able to synthesize continuous MS₂ layers beneath the top oxide layer, creating a protective coating layer for the newly formed TMD. Air-stable and low-power photosensing devices fabricated on the synthesized 2D WS₂ without the need for a further transfer process demonstrate the potential applicability of TMDs generated via a laser irradiation process

Additional file 1: of Integrated omics-based pathway analyses uncover CYP epoxygenase-associated networks as theranostic targets for metastatic triple negative breast cancer

Table S1. Publicly available resources utilized to download and process relevant data for multi-omics network and pathway analysis. Table S2. Clinico-pathological characteristics of patient-derived breast tissue specimen included in the study. Table S3. Oxylipin metabolites identified in patient-derived mammary tumor or adjacent normal tissues. Table S4. Discovery and validation cohorts used for multi-omics network and pathway analysis. Table S5. List of pathways upregulated in histologically classified ER−/PR−/HER2+ mammary tumor samples with mRNA expression of CYP2J2 z-score ≥ 2.0. Table S6. List of pathways upregulated in histologically classified ER+/PR+/HER2- and TPBC tumor samples with gene expression of CYP2J2 z-score ≥ 2.0. Table S7. List of pathways upregulated in histologically classified TNBC tumor samples with gene expression of CYP2J2 z-score ≥ 2.0. (DOCX 98 kb

Direct Synthesis and Practical Bandgap Estimation of Multilayer Arsenene Nanoribbons

Direct Synthesis and Practical Bandgap Estimation of Multilayer Arsenene Nanoribbon

Additional file 3: of Integrated omics-based pathway analyses uncover CYP epoxygenase-associated networks as theranostic targets for metastatic triple negative breast cancer

Gene enrichment associations for the tumor specimens in the discovery set with mRNA expression z score of ≥2.0 for CYP2J2 and CYP2C9. (XLS 7282 kb

Additional file 2: of Integrated omics-based pathway analyses uncover CYP epoxygenase-associated networks as theranostic targets for metastatic triple negative breast cancer

Supporting information for delineation of CYP epoxygenase-associated networks as theranostic targets for metastatic triple negative breast cancer (Figures S1-S8). (PDF 28634 kb

Synthesis and Evaluation of a New Fluorescent Transglycosylase Substrate: Lipid II-Based Molecule Possessing a Dansyl-C20 Polyprenyl Moiety

The preparation of a novel fluorescent lipid II-based substrate for transglycosylases (TGases) is described. This substrate has characteristic structural features including a shorter lipid chain, a fluorophore tag at the end of the lipid chain rather than on the peptide chain, and no labeling with a radioactive atom. This fluorescent substrate is readily utilized in TGase activity assays to characterize TGases and also to evaluate the activities of TGase inhibitors

Additional file 5: of Integrated omics-based pathway analyses uncover CYP epoxygenase-associated networks as theranostic targets for metastatic triple negative breast cancer

Quantitative proteomic data of eight paired TNBC tumors and adjacent normal tissues using iTRAQ. (XLS 3510 kb

Environmentally and Mechanically Stable Selenium 1D/2D Hybrid Structures for Broad-Range Photoresponse from Ultraviolet to Infrared Wavelengths

Selenium (Se) is one of the potential candidates as photodetector because of its outstanding properties such as high photoconductivity (∼8 × 104 S cm–1), piezoelectricity, thermoelectricity, and nonlinear optical responses. Solution phase synthesis becomes an efficient way to produce Se, but a contamination issue that could deteriorate the electric characteristic of Se should be taken into account. In this work, a facile, controllable approach of synthesizing Se nanowires (NWs)/films via a plasma-assisted growth process was demonstrated at the low substrate temperature of 100 °C. The detailed formation mechanisms of nanowires arrays to thin films at different plasma powers were investigated. Moreover, indium (In) layer was used to enhance the adhesive strength with 50% improvement on a SiO2/Si substrate by mechanical interlocking and surface alloying between Se and In layers, indicating great tolerance for mechanical stress for future wearable devices applications. Furthermore, the direct growth of Se NWs/films on a poly­(ethylene terephthalate) substrate was demonstrated, exhibiting a visible to broad infrared detection ranges from 405 to 1555 nm with a high on/off ratio of ∼700 as well as the fast response time less than 25 ms. In addition, the devices exhibited fascinating stability in the atmosphere over one month