Abstract
Differential abundance (DA) analysis of microbiome data continues to be a challenging problem due to the complexity of the data. In this article we define the notion of “sampling fraction” ...and demonstrate a major hurdle in performing DA analysis of microbiome data is the bias introduced by differences in the sampling fractions across samples. We introduce a methodology called Analysis of Compositions of Microbiomes with Bias Correction (
ANCOM-BC
), which estimates the unknown sampling fractions and corrects the bias induced by their differences among samples. The absolute abundance data are modeled using a linear regression framework. This formulation makes a fundamental advancement in the field because, unlike the existing methods, it (a) provides statistically valid test with appropriate p-values, (b) provides confidence intervals for differential abundance of each taxon, (c) controls the False Discovery Rate (FDR), (d) maintains adequate power, and (e) is computationally simple to implement.
The aim of this study is to investigate the effect of green tea extract on patients with type 2 diabetes mellitus and lipid abnormalities on glycemic and lipid profiles, and hormone peptides by a ...double-blinded, randomized and placebo-controlled clinical trial. This trial enrolled 92 subjects with type 2 diabetes mellitus and lipid abnormalities randomized into 2 arms, each arm comprising 46 participants. Of the participants, 39 in therapeutic arm took 500 mg green tea extract, three times a day, while 38 in control arm took cellulose with the same dose and frequency to complete the 16-week study. Anthropometrics measurements, glycemic and lipid profiles, safety parameters, and obesity-related hormone peptides were analyzed at screening and after 16-week course. Within-group comparisons showed that green tea extract caused a significant decrease in triglyceride and homeostasis model assessment of insulin resistance index after 16 weeks. Green tea extract also increased significantly high density lipoprotein cholesterol. The HOMA-IR index decreased from 5.4±3.9 to 3.5±2.0 in therapeutic arm only. Adiponectin, apolipoprotein A1, and apolipoprotein B100 increased significantly in both arms, but only glucagon-like peptide 1 increased in the therapeutic arm. However, only decreasing trend in triglyceride was found in between-group comparison. Our study suggested that green tea extract significantly improved insulin resistance and increased glucagon-like peptide 1 only in within-group comparison. The potential effects of green tea extract on insulin resistance and glucagon-like peptide 1 warrant further investigation.
ClinicalTrials.gov NCT01360567.
The soaring demand for intercultural competence (IC) in the globalized world has made it a key concern in foreign language education. Most existing training on IC has often focused on providing ...immersive intercultural experiences, equipping learners with cultural knowledge, and simulating intercultural situations. However, some of these approaches may not be feasible in English as a foreign language (EFL) classrooms, nor are they effective to prepare learners to cope with the complexities and uncertainties in novel intercultural situations unless there specifically involves higher-order thinking. Thus, this study took a perspective of cultural metacognition and examined whether and how could an instructional design that highlighted cultural metacognition facilitate learners' IC development in an EFL classroom at the tertiary level in Chinese mainland. Fifty-eight undergraduate students enrolled in an English Listening, Viewing, and Speaking course were involved in the instruction, and questionnaires and focus groups were employed for the data collection. A paired sample
-test revealed that there was a significant enhancement in students' intercultural competence in terms of affective, metacognitive, and behavioral dimensions, but not in the knowledge dimension. Thematic analysis indicated that the instructional design was effective in supporting students' intentional knowledge acquiring, developing positive intercultural attitudes, and promoting the translation of cognition into actions. The findings thus confirmed that the instructional design featuring cultural metacognition can be used in domestic EFL contexts, such as College English classrooms at the tertiary level in Chinese mainland, as an effective way of enhancing learners' IC. This study also offered additional evidence of how students' IC development was achieved through a range of metacognitive processes, which may provide implications for teachers to design their IC instructions in similar EFL educational settings.
Palladium diselenide (PdSe2), a thus far scarcely studied group‐10 transition metal dichalcogenide has exhibited promising potential in future optoelectronic and electronic devices due to unique ...structures and electrical properties. Here, the controllable synthesis of wafer‐scale and homogeneous 2D PdSe2 film is reported by a simple selenization approach. By choosing different thickness of precursor Pd layer, 2D PdSe2 with thickness of 1.2–20 nm can be readily synthesized. Interestingly, with the increase in thickness, obvious redshift in wavenumber is revealed by Raman spectroscopy. Moreover, in accordance with density functional theory (DFT) calculation, optical absorption and ultraviolet photoemission spectroscopy (UPS) analyses confirm that the PdSe2 exhibits an evolution from a semiconductor (monolayer) to semimetal (bulk). Further combination of the PdSe2 layer with Si leads to a highly sensitive, fast, and broadband photodetector with a high responsivity (300.2 mA W−1) and specific detectivity (≈1013 Jones). By decorating the device with black phosphorus quantum dots, the device performance can be further optimized. These results suggest the as‐selenized PdSe2 is a promising material for optoelectronic application.
This study reports on the wafer‐area synthesis of a high‐quality 2D palladium diselenide (PdSe2) layer through a simple selenization method. Both experimental analysis and theoretical simulation reveal that the PdSe2 film exhibits a gradual transition from a semiconductor (monolayer) to semimetal (bulk). Further combination of PdSe2 with Si leads to a fast and sensitive broadband photodiode, with a high responsivity and specific detectivity.
Group‐10 layered transitional metal dichalcogenides including PtS2, PtSe2, and PtTe2 are excellent potential candidates for optoelectronic devices due to their unique properties such as high carrier ...mobility, tunable bandgap, stability, and flexibility. Large‐area platinum diselenide (PtSe2) with semiconducting characteristics is far scarcely investigated. Here, the development of a high‐performance photodetector based on vertically aligned PtSe2‐GaAs heterojunction which exhibits a broadband sensitivity from deep ultraviolet to near‐infrared light, with peak sensitivity from 650 to 810 nm, is reported. The Ilight/Idark ratio and responsivity of photodetector are 3 × 104 and 262 mA W−1 measured at 808 nm under zero bias voltage. The response speed of τr/τf is 5.5/6.5 µs, which represents the best result achieved for Group‐10 TMDs based optoelectronic device thus far. According to first‐principle density functional theory, the broad photoresponse ranging from visible to near‐infrared region is associated with the semiconducting characteristics of PtSe2 which has interstitial Se atoms within the PtSe2 layers. It is also revealed that the PtSe2/GaAs photodetector does not exhibit performance degradation after six weeks in air. The generality of the above good results suggests that the vertically aligned PtSe2 is an ideal material for high‐performance optoelectronic systems in the future.
This work shows the large‐area growth of high‐quality vertically aligned PtSe2, and its application to photodetectors based on PtSe2‐GaAs heterojunctions which exhibit a broadband sensitivity to illumination ranging from deep ultraviolet to near‐infrared light, with a peak sensitivity in the region from 650 to 810 nm. The high‐performance broadband photodetector will develop the next‐generation 2D Group‐10 materials based optoelectronic devices.
Since the outbreak of severe acute respiratory syndrome (SARS) 18 years ago, a large number of SARS-related coronaviruses (SARSr-CoVs) have been discovered in their natural reservoir host, bats
. ...Previous studies have shown that some bat SARSr-CoVs have the potential to infect humans
. Here we report the identification and characterization of a new coronavirus (2019-nCoV), which caused an epidemic of acute respiratory syndrome in humans in Wuhan, China. The epidemic, which started on 12 December 2019, had caused 2,794 laboratory-confirmed infections including 80 deaths by 26 January 2020. Full-length genome sequences were obtained from five patients at an early stage of the outbreak. The sequences are almost identical and share 79.6% sequence identity to SARS-CoV. Furthermore, we show that 2019-nCoV is 96% identical at the whole-genome level to a bat coronavirus. Pairwise protein sequence analysis of seven conserved non-structural proteins domains show that this virus belongs to the species of SARSr-CoV. In addition, 2019-nCoV virus isolated from the bronchoalveolar lavage fluid of a critically ill patient could be neutralized by sera from several patients. Notably, we confirmed that 2019-nCoV uses the same cell entry receptor-angiotensin converting enzyme II (ACE2)-as SARS-CoV.
Abstract
Increasingly, researchers are discovering associations between microbiome and a wide range of human diseases such as obesity, inflammatory bowel diseases, HIV, and so on. The first step ...towards microbiome wide association studies is the characterization of the composition of human microbiome under different conditions. Determination of differentially abundant microbes between two or more environments, known as differential abundance (DA) analysis, is a challenging and an important problem that has received considerable interest during the past decade. It is well documented in the literature that the observed microbiome data (OTU/SV table) are relative abundances with an excess of zeros. Since relative abundances sum to a constant, these data are necessarily compositional. In this article we review some recent methods for DA analysis and describe their strengths and weaknesses.
While immunotherapy holds great promise for combating cancer, the limited efficacy due to an immunosuppressive tumor microenvironment and systemic toxicity hinder the broader application of cancer ...immunotherapy. Here, we report a combinatorial immunotherapy approach that uses a highly efficient and tumor-selective gene carrier to improve anticancer efficacy and circumvent the systemic toxicity. In this study, we engineered tumor-targeted lipid-dendrimer-calcium-phosphate (TT-LDCP) nanoparticles (NPs) with thymine-functionalized dendrimers that exhibit not only enhanced gene delivery capacity but also immune adjuvant properties by activating the stimulator of interferon genes (STING)-cGAS pathway. TT-LDCP NPs delivered siRNA against immune checkpoint ligand PD-L1 and immunostimulatory IL-2-encoding plasmid DNA to hepatocellular carcinoma (HCC), increased tumoral infiltration and activation of CD8
T cells, augmented the efficacy of cancer vaccine immunotherapy, and suppressed HCC progression. Our work presents nanotechnology-enabled dual delivery of siRNA and plasmid DNA that selectively targets and reprograms the immunosuppressive tumor microenvironment to improve cancer immunotherapy.
Magnetic biochar was prepared by one-step pyrolysis using sewage sludge and nano-zero-valent iron particles as raw materials, and applied to remove Cr(VI) in simulated wastewater. When the initial pH ...of the solution was 2, the initial concentration of Cr(Ⅵ) was 50 mg L−1, the dosage of biochar was 4 g L−1, the reaction time was 24 h, and the reaction temperature was 298 K, the removal capacities of Cr(Ⅵ) and CrTotal were 11.56 mg g−1 and 9.840 mg g−1. Moreover, the removals of Cr(VI) were always greater than CrTotal under all controlled conditions, indicating that Cr(VI) may be preferentially reduced into Cr(III), and then removed by adsorption. The removals of Cr(VI) and CrTotal had the best correlation with the Langmuir model and Freundlich model, and they were followed the pseudo second-order dynamics model much better. The Cr(VI) and CrTotal removals were spontaneous, endothermic, and chemisorption-based processes. The characterization of biochar before and after adsorption and component analysis of the solution after adsorption showed the electron donors for Cr(VI) reduction should be Fe0, Fe2+ and organics in biochar, and Cr(III) was very likely removed by the generation of CrOOH. The rate-controlling steps for Cr(VI) and CrTotal removals may individually be liquid-film/intra-particle diffusion and liquid-film diffusion/chemical reaction.
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