Previous in vivo and in vitro studies have linked perfluorinated compound (PFC) exposure with metabolic interruption, but the inter-species difference and high treatment doses usually make the ...results difficult to be extrapolated to humans directly. The best strategy for identifying the metabolic interruption may be to establish the direct correlations between monitored PFCs data and metabolic data on human samples. In this study, serum metabolome data and PFC concentrations were acquired for a Chinese adult male cohort. The most abundant PFCs are PFOA and PFOS with concentration medians 7.56 and 12.78 nM, respectively; in together they count around 81.6% of the total PFCs. PFC concentration-related serum metabolic profile changes and the related metabolic biomarkers were explored by using partial least squares-discriminant analysis (PLS-DA). Respectively taking PFOS, PFOA and total PFC as the classifiers, serum metabolome can be differentiated between the lowest dose group (1st quartile PFCs) and the highest PFC dose group (4th quartile PFCs). Ten potential PFC biomarkers were identified, mainly involving in pollutant detoxification, antioxidation and nitric oxide (NO) signal pathways. These suggested that low-level environmental PFC exposure has significantly adverse impacts on glutathione (GSH) cycle, Krebs cycle, nitric oxide (NO) generation and purine oxidation in humans. To the best of our knowledge, this is the first report investigating the association of environmental PFC exposure with human serum metabolome alteration. Given the important biological functions of the identified biomarkers, we suggest that PFC could increase the metabolism syndromes risk including diabetes and cardiovascular diseases.
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•We investigated serum metabolome alteration associated with PFC exposure in humans.•Metabolic profiles could be differentiated according to the internal exposure levels of PFC.•PFC exposure was associated with the disturbance in GSH cycle, TCA cycle, NO generation and purine oxidations.•Combinational biomarker pattern provided good discrimination for PFC exposure in humans.
De novo transcriptome sequencing is a robust method of predicting miRNA target genes, especially for organisms without reference genomes. Differentially expressed miRNAs had been identified ...previously in kidney samples collected from susceptible and resistant grass carp (Ctenopharyngodon idella) affected by Aeromonas hydrophila. Target identification for these differentially expressed miRNAs poses a major challenge in this non-model organism.
Two cDNA libraries constructed from mRNAs of susceptible and resistant C. idella were sequenced by Illumina Hiseq 2000 technology. A total of more than 100 million reads were generated and de novo assembled into 199,593 transcripts which were further extensively annotated by comparing their sequences to different protein databases. Biochemical pathways were predicted from these transcript sequences. A BLASTx analysis against a non-redundant protein database revealed that 61,373 unigenes coded for 28,311 annotated proteins. Two cDNA libraries from susceptible and resistant samples showed that 721 unigenes were expressed at significantly different levels; 475 were significantly up-regulated and 246 were significantly down-regulated in the SG samples compared to the RG samples. The computational prediction of miRNA targets from these differentially expressed genes identified 188 unigenes as the targets of 5 conserved and 4 putative novel miRNA families.
This study demonstrates the feasibility of identifying miRNA targets by transcriptome analysis. The transcriptome assembly data represent a substantial increase in the genomic resources available for C. idella and will provide insights into the gene expression profile analysis and the miRNA function annotations in further studies.
Reconstruction of the acoustic relaxation absorption curve is a powerful approach to ultrasonic gas sensing, but it requires knowledge of a series of ultrasonic absorptions at various frequencies ...around the effective relaxation frequency. An ultrasonic transducer is the most widely deployed sensor for ultrasonic wave propagation measurement and works only at a fixed frequency or in a specific environment like water, so a large number of ultrasonic transducers operating at various frequencies are required to recover an acoustic absorption curve with a relative large bandwidth, which cannot suit large-scale practical applications. This paper proposes a wideband ultrasonic sensor using a distributed Bragg reflector (DBR) fiber laser for gas concentration detection through acoustic relaxation absorption curve reconstruction. With a relative wide and flat frequency response, the DBR fiber laser sensor measures and restores a full acoustic relaxation absorption spectrum of COsub.2 using a decompression gas chamber between 0.1 and 1 atm to accommodate the main molecular relaxation processes, and interrogates with a non-equilibrium Mach-Zehnder interferometer (NE-MZI) to gain a sound pressure sensitivity of −45.4 dB. The measurement error of the acoustic relaxation absorption spectrum is less than 1.32%.
•miR-29b was suppressed in calcified radial arteries from patients with ESRD.•miR-29b was a negative regulator of IS induced HASMCs calcification.•miR-29b attenuated IS induced vascular calcification ...through repressing Wnt7b/β-catenin expression.
Vascular calcification (VC) is a very common phenomenon in patients with chronic kidney disease(CKD) and it increases the incidence of cardiovascular disease and leads to high mortality in CKD patients. It has been reported that some microRNAs (miRs) play roles in vascular calcification as an epigenetic regulator. Indoxyl sulfate (IS) is a protein-bound uremic toxin which has been proven as one of the major risk factors of cardiovascular disease in CKD. Here we investigated whether microRNA-29b (miR-29b) is involved in IS-induced vascular calcification. We found that vascular miR-29b was down-regulated in radial arteries of patients with end-stage renal disease. Consistently, IS also decreased miR-29b expression in human aortic smooth muscle cells (HASMCs) and potentiated their calcification. MiR-29b mimics significantly suppressed, while miR-29b anti-miR markedly enhanced, IS-induced runt-related transcription factor 2 and osteopontin expression. The expression of Wnt7b/β-catenin in radial arteries was higher in end stage renal disease than in control group, and IS increased Wnt7b/β-catenin expression in HASMCs as early as 3days after stimulation. Furthermore, miR-29b mimics potently repressed Wnt7b/β-catenin protein expression in HASMCs, whereas miR-29b anti-miR increased their expression, indicating miR-29b indeed negatively regulates Wnt7b/β-catenin signaling. Dickkopf-1 protein, the Wnt/β-catenin signaling inhibitor, suppressed anti-miR-29b-enhanced HASMCs calcification. Our data thus indicate that miR-29b downregulation and Wnt/β-catenin signaling activation may be the key mechanism of IS induced vascular calcification in chronic kidney disease.
COVIDSum (COVID-19 scientific paper Summarization) consists of four major modules: (1) Dataset Preprocessing, (2) Heuristic Sentence Extraction, (3) Word Cooccurrence Graph Construction, and (4) ...Linguistically Enriched Abstractive Summarization. The Data Preprocessing module retrieves abstract and textual content of each paper and removes papers which have missed abstracts or are not written in English language. Sentence Extraction module applies three heuristic methods to extract sentences of each paper. Word Co-occurrence Relationship Graph Construction module extracts word co-occurrence relationship to construct an un-weighted directed word co-occurrence graph. Linguistically Enriched Abstractive Summarization module proposes a hybrid summarization approach, which utilizes SciBERT and a GATbased graph encoder to encode the word sequences and word co-occurrence graphs respectively, adopts highway networks to fuse the above two encodings for obtaining context vectors of sentences, and applies Transformer decoder to generate summaries. Display omitted
•Heuristic sentence extraction methods based on prior knowledge are developed.•Word co-occurrence graph is constructed to capture linguistic features of sentences.•A novel linguistically enhanced SciBERT-based summarization model is proposed.
The coronavirus disease (COVID-19) has claimed the lives of over 350,000 people and infected more than 173 million people worldwide, it triggers researchers from diverse fields are accelerating their research to help diagnostics, therapies, and vaccines. Researchers also publish their recent research progress through scientific papers. However, manually writing the abstract of a paper is time-consuming, and it increases the writing burden of the researchers. Abstractive summarization technique which automatically provides researchers reliable draft abstracts, can alleviate this problem. In this work, we propose a linguistically enriched SciBERT-based summarization model for COVID-19 scientific papers, named COVIDSum. Specifically, we first extract salient sentences from source papers and construct word co-occurrence graphs. Then, we adopt a SciBERT-based sequence encoder and a Graph Attention Networks-based graph encoder to encode sentences and word co-occurrence graphs, respectively. Finally, we fuse the above two encodings and generate an abstractive summary of each scientific paper. When evaluated on the publicly available COVID-19 open research dataset, the performance of our proposed model achieves significant improvement compared with other document summarization models.
Shear-wave elastography (SWE) can improve the diagnostic specificity of the B-model ultrasonography (US) in breast cancer. However, whether deep learning-based radiomics signatures based on the ...B-mode US (B-US-RS) or SWE (SWE-RS) could further improve the diagnostic performance remains to be investigated. We aimed to develop the B-US-RS and SWE-RS and determine their performances in classifying breast masses.
This retrospective study included 291 women (mean age ± standard deviation, 40.9 ± 12.3 years) from two centers who had US-visible solid breast masses and underwent biopsy and/or surgical resection between June 2015 and July 2017. B-mode US and SWE images of the 198 masses in 198 patients (training cohort) from center 1 were segmented, respectively, to construct B-US-RS and SWE-RS using the least absolute shrinkage and selection operator regression and tested in an independent validation cohort of 65 masses in 65 patients from center 1 and in an external validation cohort of 28 masses in 28 patients from center 2. The performances of B-US-RS and SWE-RS were assessed using receiver operating characteristic (ROC) analysis and compared with that of radiologist assessment Breast Imaging Reporting and Data System (BI-RADS) and quantitative SWE parameters maximum elasticity (
), mean elasticity (
), elasticity ratio (
), and elastic modulus standard deviation (
) by using the McNemar test.
The single best-performing quantitative SWE parameter,
, had a higher specificity than BI-RADS assessment in the training and independent validation cohorts (
< 0.001 for both). The areas under the ROC curves (AUCs) of B-US-RS and SWE-RS both were 0.99 (95% CI = 0.99-1.00) in the training cohort, 1.00 (95% CI = 1.00-1.00) in the independent validation cohort, and 1.00 (95% CI = 1.00-1.00) in the external validation cohort. The specificities of B-US-RS and SWE-RS were higher than that of
in the training (
< 0.001 for both) and independent validation cohorts (
= 0.02 for both).
The B-US-RS and SWE-RS outperformed the quantitative SWE parameters and BI-RADS assessment for classifying breast masses. The integration of the deep learning-based radiomics approach would help improve the classification ability of B-mode US and SWE for breast masses.
Few bacteria are resistant to tetracycline and can even biodegrade tetracycline in the environment. In this study, we isolated a bacterium
sp. XY-2, which could biodegrade 74% tetracycline at pH 7.0 ...and 30°C within 6 days. Thereafter, we determined the whole genome sequence of
sp. XY-2 genome is a single circular chromosome of 5.06 Mb in size. Genomic annotation showed that two AA6 family members-encoding genes and nine glutathione S-transferase (GSTs)-encoding genes could be relevant to tetracycline biodegradation. In addition, the average nucleotide identities (ANI) analysis between the genomes of
sp. XY-2 and other
spp. revealed that
sp. XY-2 belongs to a new species. Moreover, comparative genome analysis of 36
strains identified the pan and specific genes, numerous single nucleotide polymorphisms (SNPs), insertions, and deletion variations (InDels) and different syntenial relationships in the genome of
sp. XY-2. Finally, the evolution and the origin analysis of genes related to tetracycline resistance revealed that the six
(48) genes and two specificgenes
and
in
sp. XY-2 were acquired by horizontal gene transfer (HGT) events from sources related to
, and some unidentified sources. As a new species,
sp. XY-2 will be an excellent resource for the bioremediation of tetracycline-contaminated environment.
Ansamitocins isolated from Actinosynnema pretiosum, potent antitumor compounds, belong to the family of maytansinoids, and the antibody-maytansinoid conjugates are currently under different phases of ...clinical trials. The clinical applications of ansamitocins have stimulated extensive studies to improve their production yields. In this study, we investigated the function of a pathway-specific S treptomyces antibiotic regulatory protein (SARP) family regulator, Asm18, and observed that ectopic overexpression of the asm18 gene increased the production of N-demethyl-4,5-desepoxy-maytansinol (2) to 50 mg/L in the HGF052 + pJTU824-asm18 strain, an increase by 4.7-fold compared to that of the control strain HGF052 + pJTU824. Real-time PCR analysis showed that the overexpression of the asm18 gene selectively increased the transcription levels of the genes involved in the biosynthesis of the starter unit (asm43), polyketide assembly (asmA), post-PKS modification (asm21), as well as the transcription levels of the regulatory gene (asm8), which is a specific LAL-type activator in ansamitocin biosynthesis. With the increase of fermentation titre, seven ansamitocin analogs (1–7) including three new ones (1, 5, and 6) and maytansinol (7) were isolated from the HGF052 + pJTU824-asm18 strain. Our results not only pave the way for further improving the production of ansamitocin analogs but also indicate that the post-PKS modifications of ansamitocin biosynthesis are flexible, which brings a potential of producing maytansinol, the most fascinating intermediate for the synthesis of antibody-maytansinoid conjugates, by optimizing the HGF052 and/or HGF052 + pJTU824-asm18 strains.
Chinese classrooms, whether on school grounds or online, have long suffered from a lack of interactivity. Many online classes simply provide recorded instructor lectures, which only reinforces the ...negative effects of passive nonparticipatory learning. At Shanghai Jiaotong University, researchers and developers actively seek technologic interventions that can greatly increase interactivity in large blended classes. They developed a cutting‐edge mobile learning system that can deliver live broadcasts of real‐time classroom teaching to students with mobile devices. Their system allows students to customise means of content‐reception based on when and where they tune into the broadcast. The system also supports short text messaging and instant polls. Through these venues, students can ask questions and make suggestions in real time, and the instructor can address them immediately. This article describes this system in detail, and also reports results from a formal implementation of the system in a blended English classroom of 1000 students (with about 800 being online). As the data reveal, m‐learning activities can much better engage students in the learning process. Students in this class changed from passive learners to truly engaged learners who are behaviourally, intellectually and emotionally involved in their learning tasks.
To improve the performance of intermediate-temperature solid oxide electrolysis cells (IT-SOECs) based on the Ce0.85Sm0.15O2-δ (SDC) interlayer, a transition metal oxide (CuO) was added to the ...interlayer to enhance its oxygen ion conduction, and thereby, reduce the oxygen electrode polarization resistance of the SOEC. The performance of SOECs based on the SDC–CuO interlayers was studied. The experimental results showed that SDC–CuO interlayers sintered for 10 h at 1050 °C, 1075 °C, and 1100 °C (referred to as SDC–CuO-1050, SDC–CuO-1075, and SDC–CuO-1100, respectively) are highly dense. This indicates that the preparation temperature of a dense SDC interlayer can be reduced by compositing it with CuO. The performances of SOECs based on the SDC–CuO-1050, SDC–CuO-1075, and SDC–CuO-1100 interlayers were higher than that of the SOEC based on the SDC interlayer. This indicates that oxygen ions can move faster from the SDC–CuO-1050, SDC–CuO-1075, and SDC–CuO-1100 interlayers to the oxygen electrode to participate in the electrochemical reaction. This reduces the polarization resistance of oxygen electrodes and improves the performance of the SOECs. The performance of the SOEC based on the SDC–CuO-1050 interlayer is the highest, indicating that sintering at 1050 °C for 10 h is the best condition to prepare high-performance SDC–CuO interlayers. Thus, this study provides an effective method for improving the performance of IT-SOEC based on SDC interlayer.
•CuO is added into SDC interlayer of SOEC to enhance its oxygen ion conduction.•SDC-CuO interlayer can reduce the oxygen electrode polarization resistance of SOEC.•1050 °C for 10 h is the best condition to prepare high performance SDC-CuO interlayer of SOEC.
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