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

Direct Synthesis and Practical Bandgap Estimation of Multilayer Arsenene Nanoribbons

Direct Synthesis and Practical Bandgap Estimation of Multilayer Arsenene Nanoribbon

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

Enhanced Conversion Efficiency of Cu(In,Ga)Se₂ Solar Cells via Electrochemical Passivation Treatment

Defect control in Cu­(In,Ga)­Se₂ (CIGS) materials, no matter what the defect type or density, is a significant issue, correlating directly to PV performance. These defects act as recombination centers and can be briefly categorized into interface recombination and Shockley–Read–Hall (SRH) recombination, both of which can lead to reduced PV performance. Here, we introduce an electrochemical passivation treatment for CIGS films that can lower the oxygen concentration at the CIGS surface as observed by X-ray photoelectron spectrometer analysis. Temperature-dependent <i>J–V</i> characteristics of CIGS solar cells reveal that interface recombination is suppressed and an improved rollover condition can be achieved following our electrochemical treatment. As a result, the surface defects are passivated, and the power conversion efficiency performance of the solar cell devices can be enhanced from 4.73 to 7.75%

The <i>DAO</i> Gene Is Associated with Schizophrenia and Interacts with Other Genes in the Taiwan Han Chinese Population

<div><p>Background</p><p>Schizophrenia is a highly heritable disease with a polygenic mode of inheritance. Many studies have contributed to our understanding of the genetic underpinnings of schizophrenia, but little is known about how interactions among genes affect the risk of schizophrenia. This study aimed to assess the associations and interactions among genes that confer vulnerability to schizophrenia and to examine the moderating effect of neuropsychological impairment.</p> <p>Methods</p><p>We analyzed 99 SNPs from 10 candidate genes in 1,512 subject samples. The permutation-based single-locus, multi-locus association tests, and a gene-based multifactorial dimension reduction procedure were used to examine genetic associations and interactions to schizophrenia.</p> <p>Results</p><p>We found that no single SNP was significantly associated with schizophrenia. However, a risk haplotype, namely <i>A</i>-<i>T</i>-<i>C</i> of the SNP triplet rsDAO7-rsDAO8-rsDAO13 of the <i>DAO</i> gene, was strongly associated with schizophrenia. Interaction analyses identified multiple between-gene and within-gene interactions. Between-gene interactions including <i>DAO</i>*<i>DISC1</i><b>,</b><i>DAO</i>*<i>NRG1</i> and <i>DAO</i>*<i>RASD2</i> and a within-gene interaction for <i>CACNG2</i> were found among schizophrenia subjects with severe sustained attention deficits, suggesting a modifying effect of impaired neuropsychological functioning. Other interactions such as the within-gene interaction of <i>DAO</i> and the between-gene interaction of <i>DAO</i> and <i>PTK2B</i> were consistently identified regardless of stratification by neuropsychological dysfunction. Importantly, except for the within-gene interaction of <i>CACNG2</i>, all of the identified risk haplotypes and interactions involved SNPs from <i>DAO</i>.</p> <p>Conclusions</p><p>These results suggest that <i>DAO</i>, which is involved in the N-methyl-d-aspartate receptor regulation, signaling and glutamate metabolism, is the master gene of the genetic associations and interactions underlying schizophrenia. Besides, the interaction between <i>DAO</i> and <i>RASD2</i> has provided an insight in integrating the glutamate and dopamine hypotheses of schizophrenia.</p> </div

A schematic diagram to show the relation among genes that involved in the observed gene-gene interactions.

<p>The top, bottom, and left side components represent the pre-synaptic neuron, post-synaptic neuron, and glial cells, respectively. Three types of receptors (NMDA receptor, ERBB4 receptor, and AMPA receptor) are drawn on the post-synaptic neuron. All the genes involved in the gene-gene interactions are shown in boldface. <i>NRG1</i> is the ligand for ERBB4 receptor, which may trigger the long term potentiation by way of the <i>PTK2B</i> protein activation. <i>DISC1</i> may stabilize serine racemase (SR), which will convert L-Serine to d-Serine (d-Ser). The black triangle on the side of NMDA receptor represents d-Ser, which is a co-agonist of this receptor. Both NMDA and AMPA receptors are calcium channels, which may increase calcium influx upon activation. Two molecules of <i>CACNG2</i> (shown by the grey oval) were found on each AMPA receptor. Even though <i>CACNG2</i> is a subunit of AMPA receptor, this protein is explicitly drawn in order to show its role in gene-gene interaction.</p

The LD structures of 84 SNPs in 10 candidate genes for vulnerability to schizophrenia.

<p>For each gene, the id of each SNP in the gene is listed, and the locations reflect the relative physical positions of the SNPs (in units of base pairs). The LD coefficient, D’, is provided unless D’ = 1. The color scheme for D’ presentation is as follows: white depicts the case of D’ <1 and LOD <2; blue depicts the case of D’ = 1 and LOD <2; pink or light red depicts the case of D’ <1 and LOD ≥2; bright red depicts the case of D’ = 1 and LOD ≥2. The LD block(s) within each gene is marked by an inverted triangle based on Gabriel’s method <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060099#pone.0060099-Gabriel1" target="_blank">[81]</a>.</p

Within-gene and between-gene interactions in schizophrenia for the unstratified and CPT-stratified interaction analyses.

<p>The unstratified interaction plot is at the center, and the CPT-stratified plots with the stratum name are located in the four corners. Stratum name and sample size of cases and controls are provided in the title for each panel. Gene name, the number of SNPs in the gene, and the located chromosome are provided around each circle. If an interaction was identified, the SNP id along with its location in the gene (in parentheses) are provided. Abbreviations for SNP locations are: 3′, 3′ untranslated region; 5′, 5′ untranslated region; I, intron; E, exon; s, synonymous SNP; n, near-gene SNP; m, missense SNP. Interaction candidates with a pFDR <0.05 and ≥0.05 are connected by a solid line and dashed line, respectively, and the level of testing accuracy is represented by the line color from light green (less accurate) to dark green (highly accurate).</p

Wafer-Scale Growth of WSe₂ Monolayers Toward Phase-Engineered Hybrid WO_<i>x</i>/WSe₂ Films with Sub-ppb NO_<i>x</i> Gas Sensing by a Low-Temperature Plasma-Assisted Selenization Process

An inductively coupled plasma (ICP) process was used to synthesize transition metal dichalcogenides (TMDs) through a plasma-assisted selenization process of metal oxide (MO_<i>x</i>) at a temperature as low as 250 °C. In comparison with other CVD processes, the use of ICP facilitates the decomposition of the precursors at low temperatures. Therefore, the temperature required for the formation of TMDs can be drastically reduced. WSe₂ was chosen as a model material system due to its technological importance as a p-type inorganic semiconductor with an excellent hole mobility. Large-area synthesis of WSe₂ on polyimide (30 × 40 cm²) flexible substrates and 8 in. silicon wafers with good uniformity was demonstrated at the formation temperature of 250 °C confirmed by Raman and X-ray photoelectron (XPS) spectroscopy. Furthermore, by controlling different H₂/N₂ ratios, hybrid WO_<i>x</i>/WSe₂ films can be formed at the formation temperature of 250 °C confirmed by TEM and XPS. Remarkably, hybrid films composed of partially reduced WO_<i>x</i> and small domains of WSe₂ with a thickness of ∼5 nm show a sensitivity of 20% at 25 ppb at room temperature, and an estimated detection limit of 0.3 ppb with a <i>S</i>/<i>N</i> > 10 for the potential development of a low-cost plastic/wearable sensor with high sensitivity