cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8015588.v1
title: Seed coat removal in pear accelerates embryo germination by down-regulating key genes in ABA biosynthesis

description: Seed coat-induced dormancy protects embryos from environmental conditions, and delays seed germination. In this study, we developed a simple method to accelerate embryo germination. That is, pear seeds were peeled the coats and then put on the humid gauze under 16 h day-light (75 μmol m<sup>−2</sup> s<sup>−1</sup>), the embryo was germinated at 36 h after treatment. This germination results from the reduction of ABA concentration and unrelated to IAA, GA3, and ZR concentrations. Key genes for ABA biosynthesis were isolated and phylogenetically classified for pear. Only <i>PbZEP2, PbZEP3</i>, and <i>PbNECD.C1</i> were found to be down-regulated in the germinated embryos, while the other genes, such as <i>SDR</i> and <i>AO</i> genes, are not correlated with ABA biosynthesis. Thus, the reduction of ABA concentration in the germinated embryos resulted from the down-regulations of <i>PbZEP2, PbZEP3</i>, and <i>PbNECD.C1</i> genes. We speculate that the embryo in the pear cultivar Cuiguang is stressed by the seed coat, which leads to an accumulation of ABA in the embryo. We suggest that when abiotic stress of the seed coat is removed, signal transduction of the stresses is terminated and key genes for ABA biosynthesis are down-regulated. <b>Abbreviations:</b> ABA: Abscisic acid; GA: Gibberellic; ZR: Ribosylzeatin; IAA: auxin; ZEP: Zeaxanthin epoxidase; NCED: 9-cis-epoxycarotenoid dioxygenase; SDR: Short-chain dehydrogenase/reductase; AO: Aldehyde oxidase; MS: Mass spectrometer; ESI: Electrospray ionization; HPLC: High-performance liquid chromatography; qRT-PCR: Quantitative real-time PCR.
DOI: 10.6084/m9.figshare.14304101
title: An Electrochemiluminescence Biosensor for the Determination of Mercury Ion via Dual-Amplification Strategy

description: A novel dual-signal amplificatory electrochemiluminescence (ECL) deoxyribonucleic acid (DNA) biosensor was designed for the determination of Hg2+. One amplification unit was gold nanoparticles (AuNPs) modified on a glassy carbon electrode, and the other was single-stranded DNA (ssDNA) (with amino at the 3’ terminal and thiol at the 5’ terminal) labeled with a carboxyl-functionalized Ru@SiO2 nanoparticles (Ru1@SiO2) as a nanoprobe. The ECL biosensor was obtained through a strong gold-sulfur bond between Au on AuNPs modified electrode and thiol in the nanoprobe. In the presence of Hg2+, the ECL signal reduced because the T-Hg2+-T existed between the ECL nanoprobe and the complementary DNA (c-DNA), which exhibited a sensing platform for the detection of Hg2+. The results revealed that the reduced ECL intensity was linearly proportional to the logarithm of the Hg2+ concentration in the range of 1.0 pmol L-1-100 nmol L-1 with limit of detection 0.02 pmol L-1. The proposed method was applied for the analysis of Hg2+ in the river water and the results were in good agreement with that obtained by atomic fluorescence spectroscopy.
DOI: 10.6084/m9.figshare.12731617.v1
title: Additional file 1 of Comprehensive analysis and establishment of a prediction model of alternative splicing events reveal the prognostic predictor and immune microenvironment signatures in triple negative breast cancer

description: Additional file 1: The optimal OS-related AS events was selected by LASSO regression for constructing the prediction models.
DOI: 10.6084/m9.figshare.12731620
title: Additional file 2 of Comprehensive analysis and establishment of a prediction model of alternative splicing events reveal the prognostic predictor and immune microenvironment signatures in triple negative breast cancer

description: Additional file 2: The optimal PFS-related AS events was selected by LASSO regression for constructing the prediction models.
DOI: 10.6084/m9.figshare.20071677.v1
title: Efficacy comparison of immune treating strategies for NSCLC patients with negative PD-L1 expression

description: We intended to compare and grade the proposed immune treating strategies for non-small cell lung cancer (NSCLC) with negative Programmed Cell Death Ligand 1(PD-L1). We compared the efficacy of single immune checkpoint inhibitor (ICI), single ICI plus chemotherapy, and doublet ICIs with chemotherapy alone, as well as single ICI plus radiotherapy with single ICI for negative PD-L1 (&lt;1%) NSCLC patients. Hazard Ratio (HR) and 95% confidence interval (CI) of progression-free survival (PFS) and overall survival (OS) were used as outcomes. We included 23 randomized control trials with 4665 patients. Compared with chemotherapy alone, single ICI, single ICI plus chemotherapy and doublet ICIs all showed a better OS (0.84 [0.71, 0.99] ; 0.77 [0.69, 0.85] ; 0.64 [0.53, 0.77])), while single ICI plus chemotherapy and doublet ICIs showed a better PFS (0.68 [0.61, 0.75] ; 0.69 [0.56, 0.85]). Additionally, single ICI plus radiotherapy obtained a greater pooled PFS (0.49 [0.28–0.87]) than single ICI. Both single ICI plus chemotherapy and doublet ICIs were probably better treatment decisions than chemotherapy alone for negative PD-L1 NSCLC patients. Also, single ICI plus radiotherapy carved out a new strategy.
DOI: 10.6084/m9.figshare.12731412.v1
title: Additional file 1 of Evaluating metagenomics tools for genome binning with real metagenomic datasets and CAMI datasets

description: Additional file 1: Table S1. Binning results for CAMI-high datasets.
DOI: 10.6084/m9.figshare.14304101.v1
title: An Electrochemiluminescence Biosensor for the Determination of Mercury Ion via Dual-Amplification Strategy

description: A novel dual-signal amplificatory electrochemiluminescence (ECL) deoxyribonucleic acid (DNA) biosensor was designed for the determination of Hg2+. One amplification unit was gold nanoparticles (AuNPs) modified on a glassy carbon electrode, and the other was single-stranded DNA (ssDNA) (with amino at the 3’ terminal and thiol at the 5’ terminal) labeled with a carboxyl-functionalized Ru@SiO2 nanoparticles (Ru1@SiO2) as a nanoprobe. The ECL biosensor was obtained through a strong gold-sulfur bond between Au on AuNPs modified electrode and thiol in the nanoprobe. In the presence of Hg2+, the ECL signal reduced because the T-Hg2+-T existed between the ECL nanoprobe and the complementary DNA (c-DNA), which exhibited a sensing platform for the detection of Hg2+. The results revealed that the reduced ECL intensity was linearly proportional to the logarithm of the Hg2+ concentration in the range of 1.0 pmol L-1-100 nmol L-1 with limit of detection 0.02 pmol L-1. The proposed method was applied for the analysis of Hg2+ in the river water and the results were in good agreement with that obtained by atomic fluorescence spectroscopy.
DOI: 10.6084/m9.figshare.12731620.v1
title: Additional file 2 of Comprehensive analysis and establishment of a prediction model of alternative splicing events reveal the prognostic predictor and immune microenvironment signatures in triple negative breast cancer

description: Additional file 2: The optimal PFS-related AS events was selected by LASSO regression for constructing the prediction models.
DOI: 10.6084/m9.figshare.20064874
title: Additional file 2 of Mendelian randomization analysis of 37 clinical factors and coronary artery disease in East Asian and European populations

description: Additional file 2: Table S5. Pairwise genetic correlation between the 37 selected clinical factors and CAD in East Asian and European populations.
DOI: 10.6084/m9.figshare.14304234
title: Single-Layered Paper-Based Microfluidic Devices Made by Paint-Spraying Technique with Great Barrier Resistance for Colorimetric Assays

description: The single-layered paint-spraying paper based microfluidic devices (sp-μPADs) have been for the first time integrated with the colorimetric assay. The polymethyl methacrylate (PMMA) board was applied as the mask instead of the iron mask, reducing the power requirement of the cutting machine. The paint was sprayed into the paper, which blocked the pores of the paper and constructed the hydrophobic barrier on the paper. The paint barrier was highly resistant to the various kind of chemicals and the minimum channel dimensions was 1.4 mm. By using the PMMA masks with different designs, the sp-μPADs with different designs have been fabricated and successfully applied to the single analyte assay of iron or bovine serum albumin (BSA) and the simultaneous assay of copper and nickel. Moreover, the feasibility of the multiplexed assay of eight analytes was also demonstrated. The analytical performances indicated that the fabricated sp-μPADs offered a promising platform in the colorimetric assays of either single or multiple analytes.
DOI: 10.6084/m9.figshare.20064902.v1
title: Additional file 1 of Differential weighting of temporal envelope cues from the low-frequency region for Mandarin sentence recognition in noise

description: Additional file 1: Table S1. The examples of MHINT materials and corresponding translations. Table S2. Percent-correct scores in SSN. Table S3. Percent-correct scores in SAM SSN. Table S4. Percent-correct scores in SAM white noise.
DOI: 10.6084/m9.figshare.23741632
title: Virtual screening strategy for anti-DPP-IV natural flavonoid derivatives based on machine learning

description: Flavonoids, especially their inhibitory effect on DPP-IV activity, have been widely recognized for their antidiabetic effects. However, the variety of natural flavonoid derivatives is very rich, and even subtle structural differences can lead to several orders of magnitude differences in their inhibitory activities against DPP-IV, which makes it challenging to find novel and potent anti-DPP-IV flavonoid derivatives experimentally. Therefore, there is an urgent need to develop an efficient screening pipeline that targets active natural products. Here, we propose a fusion strategy based on a QSAR model, and to simplify this process, it was applied to the discovery of flavonoid derivatives with potent anti-DPP-IV activity. First, the high-quality QSAR model (Rtest2 = 0.816, MAE<sub>test</sub> = 0.14, MSE<sub>test</sub> = 0.026) was composed of seven key molecular property parameters, which were constructed with the genetic algorithm (GA) and passed the leave-one-out cross-validation evaluation. A total of 1,668 flavonoid derivatives were obtained from the natural product enriched by NPCD based on molecular fingerprint similarity (&gt; 0.8). Further, the enriched flavonoid derivatives were further predicted and screened using the QED score combined with the QSAR model, and a total of 33 flavonoid derivatives (IC50<sub>pre</sub> &lt; 6.5 μM) were found. Subsequently, three flavonoid derivatives (5,7,3’,5’-tetrahydroxyflavone, 3,7-dihydroxy-5,3’,4’-trimethoxyflavone, and 5,7,2’,5’-tetrahydroxyflavone) with highly effective anti-DPP-IV activity were obtained by ADMET analysis. Finally, the DPP-IV inhibitory potential of these three flavonoid derivatives was verified by 100 ns MD simulation and MM/PB(GB)SA. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.20064680.v1
title: Additional file 13 of Lignocellulose degradation in Protaetia brevitarsis larvae digestive tract: refining on a tightly designed microbial fermentation production line

description: Additional file 13: Table S11. Counts of lignocellulose degradation-related modules in the PBL hindgut, cow and camel rumen microbiomes. The CAZyme profiles of PBL hindgut microbiome were compared with those present in cow and camel rumens, using same methods as in study of Gharechahi et al (2018). Contigs longer than 1000 nt were subjected to ORF prediction and a dbCAN database search.
DOI: 10.6084/m9.figshare.12731427.v1
title: Additional file 6 of Evaluating metagenomics tools for genome binning with real metagenomic datasets and CAMI datasets

description: Additional file 6: Table S6. Evaluation results on chicken gut metagenomic datasets.
DOI: 10.6084/m9.figshare.14304132.v1
title: An Efficient and Recyclable Sn-Based Phosphotungstic Acid with Tunable Brønsted/Lewis Acidity for Selective Oxidation of Benzyl Alcohol

description: A series of metal ion (M = Sn2+, Fe3+, Ni2+, Co2+, Ag+, Cu2+) exchanged tungstophosphoric acid (H3PW12O40; TPA) catalysts with tunable Brønsted/Lewis acidity were synthesized and exploited for the oxidation of benzyl alcohol (BzOH) to benzaldehyde (BzH) using hydrogen peroxide (H2O2) as oxidant. The structure of these M-TPA composite salts was also characterized by Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), thermogravimetric analyses (TGA) and solid-state 31P nuclear magnetic resonance (NMR) probe molecule method. Among these M-TPAs, the Sn1/2H2PW12O40 catalyst, which presented strong Brønsted acidity, the synergistic effect of Brønsted/Lewis and pseudo-liquid characteristic property, exhibited excellent catalytic activity and durability with 98.2% of BzH selectivity and 95.1% of BzH yield. The optimal conditions for the oxidation of BzOH optimized by response surface methodology (RSM) were as follows: n(BzOH)/n(H2O2) = 1:1.25, catalyst amount of 5.5 wt.% to BzOH, water amount of 17 mL, 3.3 h of reaction time, and temperature 393 K. Moreover, further kinetic study confirmed that the reaction order was 2.64 and the activation energy was 21.75 kJ mol-1.
DOI: 10.6084/m9.figshare.23744264
title: Morphological and molecular analysis of <i>Ephydatia fluviatilis</i> (Porifera: Spongillida: Spongillidae) from Nanjing, China

description: We present a comprehensive morphological description of <i>Ephydatia fluviatilis</i> collected in Nanjing for the first time in studies of freshwater sponges in China, based on scanning electron micrography of the sponge meshwork, the megascleres, the gemmules, and the delicate gemmuloscleres, in comparison with relevant data reported worldwide. The morphotype revealed in this study shows a peculiar spicular complement of the skeleton composed of two types of megascleres (the normal oxeas and occasional styles) with abundant tiny, centrally distributed microspinoses, gemmules (ca. 440 μm in diameter) bearing two types of spinose decoration on the shaft (i.e., erect long spines and microspinoses). We report the first complete ITS sequences of the morphotype of <i>E. fluviatilis</i> from China, which, combined with homologous sequences of related taxa from GenBank, are used in a phylogenetic analysis in order to understand the species relationship within <i>Ephydatia</i> and neighbouring taxa. Combining the ITS phylogeny and the gemmulosclere morphotypes, we identify three clades in the paraphyletic genus <i>Ephydatia</i> that are distinguished by different birotule gemmulosclere morphotypes for gemmule-bearing species. Multiple losses of gemmules within endemic taxa, as previously proposed, are confirmed in this study in a phylogenetic context obtained herein. Additionally, genetic similarities are found in some morphologically diverse species, likely indicating recent endemism leading to morphological specialization. Considering the diverse fossil record of <i>Ephydatia</i> from Cenozoic sedimentary strata of wide geographic ranges, we hypothesize that <i>Ephydatia</i> might have a deep root in the Paleogene or earlier and experienced a rapid, Quaternary radiation with emergences of specialized endemic species that lost gemmules under glacial-interglacial paleoenvironment.
DOI: 10.6084/m9.figshare.23744264.v1
title: Morphological and molecular analysis of <i>Ephydatia fluviatilis</i> (Porifera: Spongillida: Spongillidae) from Nanjing, China

description: We present a comprehensive morphological description of <i>Ephydatia fluviatilis</i> collected in Nanjing for the first time in studies of freshwater sponges in China, based on scanning electron micrography of the sponge meshwork, the megascleres, the gemmules, and the delicate gemmuloscleres, in comparison with relevant data reported worldwide. The morphotype revealed in this study shows a peculiar spicular complement of the skeleton composed of two types of megascleres (the normal oxeas and occasional styles) with abundant tiny, centrally distributed microspinoses, gemmules (ca. 440 μm in diameter) bearing two types of spinose decoration on the shaft (i.e., erect long spines and microspinoses). We report the first complete ITS sequences of the morphotype of <i>E. fluviatilis</i> from China, which, combined with homologous sequences of related taxa from GenBank, are used in a phylogenetic analysis in order to understand the species relationship within <i>Ephydatia</i> and neighbouring taxa. Combining the ITS phylogeny and the gemmulosclere morphotypes, we identify three clades in the paraphyletic genus <i>Ephydatia</i> that are distinguished by different birotule gemmulosclere morphotypes for gemmule-bearing species. Multiple losses of gemmules within endemic taxa, as previously proposed, are confirmed in this study in a phylogenetic context obtained herein. Additionally, genetic similarities are found in some morphologically diverse species, likely indicating recent endemism leading to morphological specialization. Considering the diverse fossil record of <i>Ephydatia</i> from Cenozoic sedimentary strata of wide geographic ranges, we hypothesize that <i>Ephydatia</i> might have a deep root in the Paleogene or earlier and experienced a rapid, Quaternary radiation with emergences of specialized endemic species that lost gemmules under glacial-interglacial paleoenvironment.
DOI: 10.6084/m9.figshare.23744453
title: The association between SARS-CoV-2 infection with menstrual characteristics changes in China: a cross-sectional study

description: To evaluate the association between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection with menstrual changes, and analyze the possible related factors to menstrual changes. A cross-sectional study based on online survey was conducted. Women who had been infected with SARS-CoV-2 completed the questionnaires voluntarily and were enrolled in this study. Participants were divided into menstrual change group and no menstrual change group, based on the presence or absence of menstrual changes. A total of 1016 women were enrolled, including 530 in the menstrual change group and 486 in the no menstrual change group. The three most common abnormalities were changes of menstruation cycles, menstruation flow and menstruation duration. Compared with the no menstrual change group, participants in the menstrual change group were significantly younger (32.55 ± 7.00 vs. 33.67 ± 7.39, <i>p</i> = .013), reported more severe symptoms with score<i> ≥</i> 6 (32.1% vs. 21.1%), and had more severe mental health problems, showing nervous (22.6% vs. 17.3%, <i>p</i> = .009), anxiety (34.9% vs. 24.5%, <i>p</i> &lt; .001), depression (14.7% vs. 8.2%, <i>p</i> = .003) and fear (10.8% vs. 6.4%, <i>p</i> = .011). SARS-CoV-2 infection was associated with menstrual changes. The age, the severity of symptoms and mental health problems were related to menstrual changes.
DOI: 10.6084/m9.figshare.23744453.v1
title: The association between SARS-CoV-2 infection with menstrual characteristics changes in China: a cross-sectional study

description: To evaluate the association between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection with menstrual changes, and analyze the possible related factors to menstrual changes. A cross-sectional study based on online survey was conducted. Women who had been infected with SARS-CoV-2 completed the questionnaires voluntarily and were enrolled in this study. Participants were divided into menstrual change group and no menstrual change group, based on the presence or absence of menstrual changes. A total of 1016 women were enrolled, including 530 in the menstrual change group and 486 in the no menstrual change group. The three most common abnormalities were changes of menstruation cycles, menstruation flow and menstruation duration. Compared with the no menstrual change group, participants in the menstrual change group were significantly younger (32.55 ± 7.00 vs. 33.67 ± 7.39, <i>p</i> = .013), reported more severe symptoms with score<i> ≥</i> 6 (32.1% vs. 21.1%), and had more severe mental health problems, showing nervous (22.6% vs. 17.3%, <i>p</i> = .009), anxiety (34.9% vs. 24.5%, <i>p</i> &lt; .001), depression (14.7% vs. 8.2%, <i>p</i> = .003) and fear (10.8% vs. 6.4%, <i>p</i> = .011). SARS-CoV-2 infection was associated with menstrual changes. The age, the severity of symptoms and mental health problems were related to menstrual changes.
DOI: 10.6084/m9.figshare.14304254
title: Ventilator-associated tracheobronchitis: an update

description: ABSTRACT Ventilator-associated lower respiratory tract infection is one of the most frequent complications in mechanically ventilated patients. Ventilator-associated tracheobronchitis has been considered a disease that does not warrant antibiotic treatment by the medical community for many years. In the last decade, several studies have shown that tracheobronchitis could be considered an intermediate process that leads to ventilator-associated pneumonia. Furthermore, ventilator-associated tracheobronchitis has a limited impact on overall mortality but shows a significant association with increased patient costs, length of stay, antibiotic use, and duration of mechanical ventilation. Although we still need clear evidence, especially concerning treatment modalities, the present study on ventilator-associated tracheobronchitis highlights that there are important impacts of including this condition in clinical management and epidemiological and infection surveillance.
DOI: 10.6084/m9.figshare.14304254.v1
title: Ventilator-associated tracheobronchitis: an update

description: ABSTRACT Ventilator-associated lower respiratory tract infection is one of the most frequent complications in mechanically ventilated patients. Ventilator-associated tracheobronchitis has been considered a disease that does not warrant antibiotic treatment by the medical community for many years. In the last decade, several studies have shown that tracheobronchitis could be considered an intermediate process that leads to ventilator-associated pneumonia. Furthermore, ventilator-associated tracheobronchitis has a limited impact on overall mortality but shows a significant association with increased patient costs, length of stay, antibiotic use, and duration of mechanical ventilation. Although we still need clear evidence, especially concerning treatment modalities, the present study on ventilator-associated tracheobronchitis highlights that there are important impacts of including this condition in clinical management and epidemiological and infection surveillance.
DOI: 10.6084/m9.figshare.12731418
title: Additional file 3 of Evaluating metagenomics tools for genome binning with real metagenomic datasets and CAMI datasets

description: Additional file 3: Table S3. Binning results for CAMI-medium datasets.
DOI: 10.6084/m9.figshare.12731421.v1
title: Additional file 4 of Evaluating metagenomics tools for genome binning with real metagenomic datasets and CAMI datasets

description: Additional file 4: Table S4. Binning results for chicken gut metagenomic datasets.