Data from: Comparative analysis of models in predicting the effects of SNPs on TF-DNA binding using large-scale in vitro and in vivo data

Noncoding variants associated with complex traits can alter the motifs of transcription factor (TF)-DNA binding. Although many computational models have been developed to predict the effects of noncoding variants on TF binding, their predictive power lacks systematic evaluation. Here we have evaluated 14 different models built on position weight matrices (PWMs), support vector machine (SVM), ordinary least squares (OLS) and deep neural networks (DNN), using large-scale in vitro (i. e. SNP-SELEX) and in vivo (i. e. allele-specific binding, ASB) TF binding data. The SNP-SELEX data used in this study were collected from the GVAT database (http://renlab.sdsc.edu/GVATdb/), and the ASB data were collected from the ADASTRA database (https://adastra.autosome.org/bill-cipher/downloads). This dataset contains following files.SNP-SELEX_firstbatch_evaldata_positive_data.txt.gz: SNP-SELEX, first batch, positive setSNP-SELEX_firstbatch_evaldata_negative_data.txt.gz: SNP-SELEX, first batch, negative setSNP-SELEX_novelbatch_evaldata_positive_data.txt.gz: SNP-SELEX, novel batch, positive setSNP-SELEX_novelbatch_evaldata_negative_data.txt.gz: SNP-SELEX, novel batch, negative setASB_evaldata_positive_data.txt.gz: ASB, positive setASB_evaldata_negative_data.txt.gz: ASB, negative setSNP-SELEX_AUROC_AUPRC.xlsx: AUROC and AUPRC of 14 models based on SNP-SELEXASB_AUROC_AUPRC.xlsx: AUROC and AUPRC of 14 models based on ASB</p

Manipulating the Defect Structure (<i>V</i>_O) of In₂O₃ Nanoparticles for Enhancement of Formaldehyde Detection

Because defects such as oxygen vacancies (<i>V</i>_O) can affect the properties of nanomaterials, investigating the defect structure–function relationship are attracting intense attention. However, it remains an enormous challenge to the synthesis of nanomaterials with high sensing performance by manipulating <i>V</i>_O because understanding the role of surface or bulk <i>V</i>_O on the sensing properties of metal oxides is still missing. Herein, In₂O₃ nanoparticles with different contents of surface and bulk <i>V</i>_O were obtained by hydrogen reduction treatment, and the role of surface or bulk <i>V</i>_O on the sensing properties of In₂O₃ was investigated. The X-ray diffraction, ultraviolet–visible spectrophotometer, electron paramagnetic resonance, photoluminescence, Raman, X-ray photoelectron spectroscopy, Hall analysis, and the sensing results indicate that bulk <i>V</i>_O can decrease the band gap and energy barrier and increase the carrier mobility, hence facilitating the formation of chemisorbed oxygen and enhancing the sensing response. Benefiting from bulk <i>V</i>_O, In₂O₃–H10 exhibits the highest response, good selectivity, and stability for formaldehyde detection. However, surface <i>V</i>_O does not contribute to the improvement of formaldehyde-sensing performance, and the black In₂O₃–H30 with the highest content of surface <i>V</i>_O exhibits the lowest response. Our work provides a novel strategy for the synthesis of nanomaterials with high sensing performance by manipulating <i>V</i>_O

Controllable Defect Redistribution of ZnO Nanopyramids with Exposed {101̅1} Facets for Enhanced Gas Sensing Performance

ZnO nanopyramids (NPys) with exposed crystal facets of {101̅1} were synthesized via a one-step solvothermal method, having a uniform size with a hexagonal edge length of ∼100 nm and a height of ∼200 nm. Technologies of XRD, TEM, HRTEM, Raman, PL, and XPS were used to characterize the morphological and structural properties of the products, while the corresponding gas sensing properties were determined by using ethanol as the target gas. For the overall goal of defect engineering, the effect of aging temperature on the gas sensing performance of the ZnO NPys was studied. The test results showed that, at the aging temperature of 300 °C, the gas sensing property has been improved to the best, with the fast response-recovery time and the excellent selectivity, because the ZnO₃₀₀ has the most electron donors for absorbing the largest content of O^2–. Model of defect redistribution was used to explicate the changing of the surface defects at different aging temperatures. The findings showed that, in addition to V_O, Zn_i was the dominant defect of the {101̅1} crystal facet. The gas sensing performance of the ZnO NPys was determined by the contents of V_O and Zn_i, with all of the defects redistributed on the surface. All of the results will be noticeable for the improvement of the sensing performance of materials with special crystal facet exposing

Highly Sensitive and Selective Ethanol Sensor Fabricated with In-Doped 3DOM ZnO

ZnO is an important n-type semiconductor sensing material. Currently, much attention has been attracted to finding an effective method to prepare ZnO nanomaterials with high sensing sensitivity and excellent selectivity. A three-dimensionally ordered macroporous (3DOM) ZnO nanostructure with a large surface area is beneficial to gas and electron transfer, which can enhance the gas sensitivity of ZnO. Indium (In) doping is an effective way to improve the sensing properties of ZnO. In this paper, In-doped 3DOM ZnO with enhanced sensitivity and selectivity has been synthesized by using a colloidal crystal templating method. The 3DOM ZnO with 5 at. % of In-doping exhibits the highest sensitivity (∼88) to 100 ppm ethanol at 250 °C, which is approximately 3 times higher than that of pure 3DOM ZnO. The huge improvement to the sensitivity to ethanol was attributed to the increase in the surface area and the electron carrier concentration. The doping by In introduces more electrons into the matrix, which is helpful for increasing the amount of adsorbed oxygen, leading to high sensitivity. The In-doped 3DOM ZnO is a promising material for a new type of ethanol sensor

One-Step Synthesis of Co-Doped In₂O₃ Nanorods for High Response of Formaldehyde Sensor at Low Temperature

Uniform and monodisperse Co-doped In₂O₃ nanorods were fabricated by a facile and environmentally friendly hydrothermal strategy that combined the subsequent annealing process, and their morphology, structure, and formaldehyde (HCHO) gas sensing performance were investigated systematically. Both pure and Co-doped In₂O₃ nanorods had a high specific surface area, which could offer abundant reaction sites to gas molecular diffusion and improve the response of the gas sensor. Results revealed that the In₂O₃/1%Co nanorods exhibited a higher response of 23.2 for 10 ppm of HCHO than that of the pure In₂O₃ nanorods by 4.5 times at 130 °C. More importantly, the In₂O₃/1%Co nanorods also presented outstanding selectivity and long-term stability. The superior gas sensing properties were mainly attributed to the incorporation of Co, which suggested the important role of the amount of oxygen vacancies and adsorbed oxygen in enhancing HCHO sensing performance of In₂O₃ sensors

Macrodiols Derived from CO₂‑Based Polycarbonate as an Environmentally Friendly and Sustainable PVC Plasticizer: Effect of Hydrogen-Bond Formation

A macrodiol was successfully synthesized by the alcoholysis of high-molecular-weight poly­(propylene carbonate) (PPC). The molecular weight can readily be controlled in a range from 600 to 1500 Da. The low-molecular weight macrodiols can be effectively used as an environmentally friendly and sustainable plasticizer for poly­(vinyl chloride) (PVC) to substitute the traditional phthalate plasticizers. For enhancing the plasticizing effect, the macrodiols were further end-capped to transfer its hydroxyl groups into aromatic esters. The experiment results showed that the synthesized PPC macrodiols can effectively plasticize PVC by comparing with commonly used bis­(2-ethylhexyl) phthalate (DOP). The PVC sample plasticized using 30 wt % PPC macrodiol exhibited a tensile strength of 14.73 MPa with an elongation at break up to 415%, together with a relevant high impact strength compared with the samples plasticized with DOP. Finally, the PVC/PPC macrodiol demonstrated a dramatically low migration rate due to the relatively high molecular weight of PPC macrodiols. The most interested concerning is the inherent biodegradable nature of PPC macrodiols that endows the as-plasticized PVC biodegradability. This technology provides a brand new plasticizer for PVC and extends its application in various fields

A Novel Single-Ion-Conducting Polymer Electrolyte Derived from CO₂‑Based Multifunctional Polycarbonate

This work demonstrates the facile and efficient synthesis of a novel environmentally friendly CO₂-based multifunctional polycarbonate single-ion-conducting polymer electrolyte with good electrochemistry performance. The terpolymerizations of CO₂, propylene epoxide (PO), and allyl glycidyl ether (AGE) catalyzed by zinc glutarate (ZnGA) were performed to generate poly­(propylene carbonate allyl glycidyl ether) (PPCAGE) with various alkene groups contents which can undergo clickable reaction. The obtained terpolymers exhibit an alternating polycarbonate structure confirmed by ¹H NMR spectra and an amorphous microstructure with glass transition temperatures (<i>T</i>_g) lower than 11.0 °C evidenced by differential scanning calorimetry analysis. The terpolymers were further functionalized with 3-mercapto­pro­pionic acid via efficient thiol–ene click reaction, followed by reacting with lithium hydroxide, to afford single-ion-conducting polymer electrolytes with different lithium contents. The all-solid-state polymer electrolyte with the 41.0 mol % lithium containing moiety shows a high ionic conductivity of 1.61 × 10^–4 S/cm at 80 °C and a high lithium ion transference number of 0.86. It also exhibits electrochemical stability up to 4.3 V vs Li⁺/Li. This work provides an interesting design way to synthesize an all-solid-state electrolyte used for different lithium batteries

Additional file 3 of Genome-wide identification of the longan R2R3-MYB gene family and its role in primary and lateral root

Additional file 3

Additional file 2 of Genome-wide identification of the longan R2R3-MYB gene family and its role in primary and lateral root

Additional file 2: Supplemental Table 1. Primers used in this study

TiO₂‑Doped CeO₂ Nanorod Catalyst for Direct Conversion of CO₂ and CH₃OH to Dimethyl Carbonate: Catalytic Performance and Kinetic Study

A new class of TiO₂-doped CeO₂ nanorods was synthesized via a modified hydrothermal method, and these nanorods were first used as catalysts for the direct synthesis of dimethyl carbonate (DMC) from CO₂ and CH₃OH in a fixed-bed reactor. The micromorphologies and physical–chemical properties of nanorods were characterized by transmission electron microscopy, X-ray diffraction, N₂ adsorption, inductively coupled plasma atomic emission spectrometry, X-ray photoelectron spectroscopy, and temperature-programmed desorption of ammonia and carbon dioxide (NH₃-TPD and CO₂-TPD). The effects of the TiO₂ doping ratio on the catalytic performances were fully investigated. By doping TiO₂, the surface acid–base sites of CeO₂ nanorods can be obviously promoted and the catalytic activity can be raised evidently. Ti_0.04Ce_0.96O₂ nanorod catalysts exhibited remarkably high activity with a methanol conversion of 5.38% with DMC selectivity of 83.1%. Furthermore, kinetic and mechanistic investigations based on the initial rate method were conducted. Over the Ti_0.04Ce_0.96O₂ nanorod catalyst, the apparent activation energy of the reaction was 46.3 kJ/mol. The reaction rate law was determined to be of positive first-order to the CO₂ concentration and the catalyst loading amount. These results were practically identical with the prediction of the Langmuir–Hinshelwood mechanism in which the steps of CO₂ adsorption and activation are considered as rate-determining steps