cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.17033038
title: Classification Trees for Imbalanced Data: Surface-to-Volume Regularization

description: Classification algorithms face difficulties when one or more classes have limited training data. We are particularly interested in classification trees, due to their interpretability and flexibility. When data are limited in one or more of the classes, the estimated decision boundaries are often irregularly shaped due to the limited sample size, leading to poor generalization error. We propose a novel approach that penalizes the Surface-to-Volume Ratio (SVR) of the decision set, obtaining a new class of SVR-Tree algorithms. We develop a simple and computationally efficient implementation while proving estimation consistency for SVR-Tree and rate of convergence for an idealized empirical risk minimizer of SVR-Tree. SVR-Tree is compared with multiple algorithms that are designed to deal with imbalance through real data applications. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.7579883
title: Manhattan plots of the differential alternative splicing events and differentially expressed genes by splicing factors

description: The data show circular Manhattan overview of genome-wide alternative splicing and gene expression changes regulated by each SF.
DOI: 10.25402/fon.19114490.v1
title: PRISMA Checklist – Efficacy of adjuvant EGFR inhibitors and impact of clinical factors in resected EGFR-mutated NSCLC：A meta-analysis

description: <b>Supplementary data</b>. Efficacy of adjuvant EGFR inhibitors and
 impact of clinical factors in resected EGFR-mutated NSCLC：A
 meta-analysis
 <i>PRISMA checklist.</i>
DOI: 10.6084/m9.figshare.9677123.v1
title: Experimental data from Peg–hole disassembly using active compliance

description: When considered in two-dimensional space, a cylindrical peg being withdrawn from a clearance-fit hole can exhibit one of four contact states: no contact, one-point contact, two-point contact and line contact. Jamming and wedging can occur during the two-point contact. Effective control of the two-point contact region can significantly reduce resistance in peg–hole disassembly. In this paper, we explore generic peg–hole disassembly processes with compliance and identify the effects of key parameters including the degree of compliance, the location of the compliance centre and initial position errors. A quasi-static analysis of peg–hole disassembly has been performed to obtain the boundary conditions of the two-point contact region. The effects of key variables on the two-point contact region have been simulated. Finally, peg–hole disassemblies with different locations of compliance centre achieved using active compliance have been experimentally investigated. The proposed theoretical model can be implemented to predict the range and position of the two-point contact region from the perspective of peg–hole disassembly.
DOI: 10.6084/m9.figshare.6007250
title: Dietary exposure to cadmium of Shenzhen adult residents from a total diet study

description: Cadmium (Cd) contamination has become a public health concern in recent decades. The aim of the present study was to assess the contribution of dietary Cd exposure and its health risk among Shenzhen adult residents using the Total Diet Study (TDS) approach. Cd was determined in 13 food groups using 276 individual samples by ICP-MS. The major food contributors to Cd exposure of Shenzhen adult residents were ‘Vegetables’ (32.6% of the total exposure), ‘Rice and its products’ (19.2% of the total exposure) and ‘Fish, seafood and shellfish’ (18.5% of the total exposure). The mean and the 95th percentile dietary exposure to Cd of Shenzhen adults were 9.9 and 13 μg kg<sup>−1</sup> bw month<sup>−1</sup>, respectively. The dietary exposures of all individual age-gender population subgroups were below the provisional tolerable monthly intake (PTMI = 25 μg kg<sup>−1</sup> bw month<sup>−1</sup>), so the health risk of Cd dietary exposure of Shenzhen adults is considered to be low, but still, cadmium pollution should be strictly controlled and monitored continuously due to an exceptionally long biological half-life of cadmium.
DOI: 10.6084/m9.figshare.6007250.v1
title: Dietary exposure to cadmium of Shenzhen adult residents from a total diet study

description: Cadmium (Cd) contamination has become a public health concern in recent decades. The aim of the present study was to assess the contribution of dietary Cd exposure and its health risk among Shenzhen adult residents using the Total Diet Study (TDS) approach. Cd was determined in 13 food groups using 276 individual samples by ICP-MS. The major food contributors to Cd exposure of Shenzhen adult residents were ‘Vegetables’ (32.6% of the total exposure), ‘Rice and its products’ (19.2% of the total exposure) and ‘Fish, seafood and shellfish’ (18.5% of the total exposure). The mean and the 95th percentile dietary exposure to Cd of Shenzhen adults were 9.9 and 13 μg kg<sup>−1</sup> bw month<sup>−1</sup>, respectively. The dietary exposures of all individual age-gender population subgroups were below the provisional tolerable monthly intake (PTMI = 25 μg kg<sup>−1</sup> bw month<sup>−1</sup>), so the health risk of Cd dietary exposure of Shenzhen adults is considered to be low, but still, cadmium pollution should be strictly controlled and monitored continuously due to an exceptionally long biological half-life of cadmium.
DOI: 10.6084/m9.figshare.7580174.v1
title: Computer vision technology-based face mirroring system providing mirror therapy for Bell’s palsy patients

description: <b>Purpose:</b> Mirror therapy (MT) is an effective adjunct treatment for Bell’s palsy (BP); however, a bifold mirror-based apparatus hindered the effectiveness. Besides, few studies have reported the related factors of facial embodiment. The aim of this study was to evaluate the feasibility of a novel face mirroring System (FMS) and the effects on facial embodiment in BP patients, comparing with conventional mirror book (MB) therapy. <b>Method:</b> This was a within-subject design trial. Thirty-six BP patients were recruited and received investigations on user experience and perception of facial embodiment after each facial task (reset, facial expression, and enunciation) when using both FMS and MB separately and randomly. <b>Results:</b> Data of questionnaires showed FMS had a better user experience and perception of facial embodiment comparing with MB. Patients agreed more strongly on the statements of facial embodiment for facial expression and enunciation tasks when using both apparatuses, comparing with rest. <b>Conclusions:</b> The FMS is a feasible and optimal setup to provide MT for BP patients. Moreover, speech paired motor training is a superior strategy for facilitating facial embodiment.Implications for RehabilitationThe Face Mirroring System is a feasible and optimal apparatus for mirror therapy in Bell’s palsy patients.Perception of facial embodiment can be increased via combining multiple sensory feedbacks.Speech paired motor tasks have considerable potential to facilitate facial embodiment. The Face Mirroring System is a feasible and optimal apparatus for mirror therapy in Bell’s palsy patients. Perception of facial embodiment can be increased via combining multiple sensory feedbacks. Speech paired motor tasks have considerable potential to facilitate facial embodiment.
DOI: 10.6084/m9.figshare.21200783
title: Additional file 6 of Analysis of controlling genes for tiller growth of Psathyrostachys juncea based on transcriptome sequencing technology

description: Additional file 6.
DOI: 10.6084/m9.figshare.5483284.v1
title: Genome-wide analysis of antioxidant enzyme gene families involved in drought and low-temperature responses in Apple (<i>Malus domestica</i>)

description: Antioxidant enzymes were well-known for reactive oxygen scavenging and protecting cells from oxidative damage in multiple biotic and abiotic stresses. Aimed to overview of antioxidant enzyme gene families and screen for drought and low-temperature response members, the whole apple antioxidant enzyme genes in apple genome were studied. Out of 73candidates in seven antioxidant enzyme gene families among the entire apple genome, a total of 49 genes were identified, showed more antioxidant enzyme gene members than those in other plant species. A phylogenetic tree based on predicted functional domains and motifs of apple and Arabidopsis antioxidant enzymes revealed 19 putative drought or low-temperature response genes, and 9 out 19 genes belong to five families responded to both drought and low-temperature stresses. Subsequently, cis-elements in those nine antioxidant enzyme gene promoters were examined and abundant elements involved in multiple hormone regulation and abiotic stresses response, including drought and low-temperature were found. The tissue expression specificity for those nine members in eight kinds of tissues was also examined. Screening and identifying both drought and low-temperature response genes provide useful information to understand gene functions and promote application of antioxidant enzyme genes in apple abiotic resistance breeding.
DOI: 10.6084/m9.figshare.5483296
title: Petrogenesis and metallogenic implications of Late Mesozoic intrusive rocks in the Tongling region, eastern China: a case study and perspective review

description: Large-scale Cu–Au mineralization is associated with Late Mesozoic intrusive rocks in the Tongling region of eastern China, which mainly comprise pyroxene monzodiorite, quartz monzodiorite, and granodiorite. To constrain the petrogenesis of the intrusive rocks and Cu–Au mineralization, detailed analyses of the geochronology, apatite <i>in situ</i> geochemistry, whole-rock geochemistry, and zircon Hf isotopic compositions were performed. Magmatic zircons from pyroxene monzodiorites, quartz monzodiorites, and granodiorites yield U–Pb ages of 136–149 Ma, 136–146 Ma, and 138–152 Ma, respectively, indicating that their formation ages are contemporaneous. Quartz monzodiorites and granodiorites (SiO<sub>2</sub> = 57.9–69.5 wt.%) are highly potassic calc-alkaline rocks with adakitic affinity and have low MgO and Y contents, low zircon ε<sub>Hf</sub>(<i>t</i>) values (−11.7 to −39.0), high apatite Cl contents (&gt;0.2 wt.%), and log fO<sub>2</sub> values (−23.2 to −8.23), indicating that they may have formed when metasomatized mantle-derived magmas mixed with slab-derived magmas before undergoing crustal assimilation and fractional crystallization. Pyroxene monzodiorites (SiO<sub>2</sub> = 48.4–53.0 wt.%) are shoshonitic and record high MgO, P<sub>2</sub>O<sub>5</sub>, and Y contents, high zircon ε<sub>Hf</sub>(<i>t</i>) values (1.55 to −7.87), high oxygen fugacity, low Nb and Ta contents, and low apatite Cl contents (mainly &lt;0.2 wt.%), suggesting that they were primarily derived from a metasomatized lithospheric mantle-derived magma that experienced the assimilation of lower crustal materials. The results indicate that the intrusive rocks and associated large-scale Cu–Au mineralization of the Tongling region resulted from the partial melting of the subducted oceanic slab in an oxidizing environment.
DOI: 10.6084/m9.figshare.13363067
title: Set 3,7,8_70Cq.csvAptamarker prediction of brain amyloid-β status in cognitively normal individuals at risk for Alzheimer’s disease

description: The data comprises Cq values for individual Aptamarkers (columns) against individual samples (rows) that vary for brain amyloid deposition.This data comprises Cq values from qPCR analysis of Aptamarkers that was used to build a model to predict brain amyloid deposition. <br>
DOI: 10.34740/kaggle/dsv/7302121
title: BdSLW60
DOI: 10.6084/m9.figshare.7580639.v1
title: Additional file 10: of Identification and analysis of long non-coding RNAs in response to H5N1 influenza viruses in duck (Anas platyrhynchos)

description: Table S8. KEGG analysis of DEGs co-expressed with DElncRNAs. (XLSX 83 kb)
DOI: 10.21251/d8387316-cd6b-4ebc-be81-2bb06cc97b9b
title: Non-equilibrium defect chemistry in oxygen-rich zinc oxide nano-tetrapods synthesized by atmospheric pressure microplasma dataset.

description: Coaliated dataset of the article titled "Non-equilibrium defect chemistry in oxygen-rich zinc oxide nano-tetrapods synthesized by atmospheric pressure microplasma"

The dataset that corresponds to the results reported in the paper are included within this record as an Excel file and with tabs corresponding to each figure. Additional results and raw data underlying this work (theoretical calculations) are available on request following instructions provided here.
DOI: 10.6084/m9.figshare.21200824
title: Additional file 3 of Repeated turnovers keep sex chromosomes young in willows

description: Additional file 3:Dataset S1. Multifasta file of all intact and partial RR duplicates of the Salicaceae species used for the phylogenetic analysis shown in Fig. 4B.
DOI: 10.6084/m9.figshare.9693056.v1
title: Emergence of mobile tigecycline resistance mechanism in <i>Escherichia coli</i> strains from migratory birds in China

description: Plasmid-mediated antimicrobial resistance has emerged as one of the principal global issues, posing significant threats to public health. Herein, we reported a mobile tigecycline resistance mechanism Tet(X4) on both plasmid and chromosome in <i>Escherichia coli</i> strains from migratory birds in China. Besides tigecycline, these <i>tet</i>(X4)-positive strains also exhibited elevated MICs to the FDA newly approved tetracycline antibiotics, eravacycline (4 µg/ml) and omadacycline (8 µg/ml). Worrisomely, the <i>tet</i>(X4)-carrying plasmids and chromosome also shared high homology with the plasmids from human. Taken together, Tet(X4) represents another emerging antimicrobial threat and collective efforts from different sectors are needed to control its further spread.
DOI: 10.6084/m9.figshare.21200821.v1
title: Additional file 2 of Repeated turnovers keep sex chromosomes young in willows

description: Additional file 2:Table S1-S13. Supplementary Tables.
DOI: 10.6084/m9.figshare.21200824.v1
title: Additional file 3 of Repeated turnovers keep sex chromosomes young in willows

description: Additional file 3:Dataset S1. Multifasta file of all intact and partial RR duplicates of the Salicaceae species used for the phylogenetic analysis shown in Fig. 4B.
DOI: 10.6084/m9.figshare.11265941
title: The perturbed expression of m6A in parthenogenetic mouse embryos

description: Abstract Parthenogenetically activated oocytes cannot develop to term in mammals owing to abnormal epigenetic modifications. Methylation of the N6 position of adenosine (m6A) is a post-transcriptional epigenetic modification of RNA. To investigate the role of m6A methylation in parthenogenetic (PA) embryonic development, we analyzed METTL3, METTL14, FTO, ALKBH5, YTHDF2, IGF2BP1, and IGF2BP2 expression by quantitative real-time PCR. These genes were found dynamically expressed during the 2-cell, 4-cell, 8-cell, and blastocyst stages of the embryo. Compared to normally fertilized embryos, the expression of these genes was perturbed in PA embryos, especially at the 8-cell stage. Furthermore, immunofluorescence was used to detect m6A expression. The results demonstrated that m6A expression decreased in the 2-cell stage, whereas it increased in the 8-cell stage of PA embryos. Taken together, these results suggest that the expression of RNA methylation-related genes was perturbed, leading to abnormal m6A modification during early development in PA embryos.
DOI: 10.6084/m9.figshare.11265941.v1
title: The perturbed expression of m6A in parthenogenetic mouse embryos

description: Abstract Parthenogenetically activated oocytes cannot develop to term in mammals owing to abnormal epigenetic modifications. Methylation of the N6 position of adenosine (m6A) is a post-transcriptional epigenetic modification of RNA. To investigate the role of m6A methylation in parthenogenetic (PA) embryonic development, we analyzed METTL3, METTL14, FTO, ALKBH5, YTHDF2, IGF2BP1, and IGF2BP2 expression by quantitative real-time PCR. These genes were found dynamically expressed during the 2-cell, 4-cell, 8-cell, and blastocyst stages of the embryo. Compared to normally fertilized embryos, the expression of these genes was perturbed in PA embryos, especially at the 8-cell stage. Furthermore, immunofluorescence was used to detect m6A expression. The results demonstrated that m6A expression decreased in the 2-cell stage, whereas it increased in the 8-cell stage of PA embryos. Taken together, these results suggest that the expression of RNA methylation-related genes was perturbed, leading to abnormal m6A modification during early development in PA embryos.
DOI: 10.6084/m9.figshare.14935983
title: Predator kairomone triggers sexual reproduction of Daphnia population via increasing population density

description: Original data of the paper.
DOI: 10.6084/m9.figshare.19130295
title: A novel prognostic model for predicting the mortality risk of patients with sepsis-related acute respiratory failure: a cohort study using the MIMIC-IV database

description: Acute respiratory failure increases short-term mortality in sepsis patients. Hence, in this study, we aimed to develop a novel model for predicting the risk of hospital mortality in sepsis patients with acute respiratory failure. From the Medical Information Mart for Intensive Care (MIMIC)-IV database, we developed a matched cohort of adult sepsis patients with acute respiratory failure. After applying a multivariate COX regression analysis, we developed a nomogram based on the identified risk factors of mortality. Further, we evaluated the ability of the nomogram in predicting individual hospital death by the area under a receiver operating characteristic (ROC) curve. A total of 663 sepsis patients with acute respiratory failure were included in this study. Systolic blood pressure, neutrophil percentage, white blood cells count, mechanical ventilation, partial pressure of oxygen &lt; 60 mmHg, abdominal cavity infection, <i>Klebsiella pneumoniae</i> and <i>Acinetobacter baumannii</i> infection, and immunosuppressive diseases were the independent risk factors of mortality in sepsis patients with acute respiratory failure. The area under the ROC curve of the nomogram was 0.880 (95% CI: 0.851–0.908), which provided significantly higher discrimination compared to that of the simplified acute physiology score II [0.656 (95% CI: 0.612–0.701)]. The model shows a good performance in predicting the mortality risk of patients with sepsis-related acute respiratory failure. Hence, this model can be used to evaluate the short-term prognosis of critically ill patients with sepsis and acute respiratory failure.
DOI: 10.6084/m9.figshare.19130295.v1
title: A novel prognostic model for predicting the mortality risk of patients with sepsis-related acute respiratory failure: a cohort study using the MIMIC-IV database

description: Acute respiratory failure increases short-term mortality in sepsis patients. Hence, in this study, we aimed to develop a novel model for predicting the risk of hospital mortality in sepsis patients with acute respiratory failure. From the Medical Information Mart for Intensive Care (MIMIC)-IV database, we developed a matched cohort of adult sepsis patients with acute respiratory failure. After applying a multivariate COX regression analysis, we developed a nomogram based on the identified risk factors of mortality. Further, we evaluated the ability of the nomogram in predicting individual hospital death by the area under a receiver operating characteristic (ROC) curve. A total of 663 sepsis patients with acute respiratory failure were included in this study. Systolic blood pressure, neutrophil percentage, white blood cells count, mechanical ventilation, partial pressure of oxygen &lt; 60 mmHg, abdominal cavity infection, <i>Klebsiella pneumoniae</i> and <i>Acinetobacter baumannii</i> infection, and immunosuppressive diseases were the independent risk factors of mortality in sepsis patients with acute respiratory failure. The area under the ROC curve of the nomogram was 0.880 (95% CI: 0.851–0.908), which provided significantly higher discrimination compared to that of the simplified acute physiology score II [0.656 (95% CI: 0.612–0.701)]. The model shows a good performance in predicting the mortality risk of patients with sepsis-related acute respiratory failure. Hence, this model can be used to evaluate the short-term prognosis of critically ill patients with sepsis and acute respiratory failure.
DOI: 10.25402/fon.19114490
title: PRISMA Checklist – Efficacy of adjuvant EGFR inhibitors and impact of clinical factors in resected EGFR-mutated NSCLC：A meta-analysis

description: <b>Supplementary data</b>. Efficacy of adjuvant EGFR inhibitors and
 impact of clinical factors in resected EGFR-mutated NSCLC：A
 meta-analysis
 <i>PRISMA checklist.</i>
DOI: 10.6084/m9.figshare.7580678
title: Additional file 5: of Identification and analysis of long non-coding RNAs in response to H5N1 influenza viruses in duck (Anas platyrhynchos)

description: Table S3. Protein-coding genes located within 10/100â kb upstream and downstream of duck lncRNAs. (XLSX 642 kb)
DOI: 10.6084/m9.figshare.14385265.v1
title: Additional file 1 of Overexpression of DSCR1 prevents proliferation and predicts favorable prognosis in colorectal cancer patients

description: Additional file 1: Fig 1. Overexpression of DSCR1-1 showed no effect on proliferation and colony formation in CRC cells. (A). Western blot showed overexpression of DSCR1-1 in LoVo cells. (B). CCK8 assays showed that overexpression of DSCR1-1 had no effect on cell proliferation of CRC cells. Data are mean ±SEM of 5 replicates. (C). Overexpression of DSCR1-1 had no effect on cell colony formation of CRC cells. Data are mean ±SEM of 4 replicates.
DOI: 10.25402/fon.19114499
title: Supplementary Tables – Efficacy of adjuvant EGFR inhibitors and impact of clinical factors in resected EGFR-mutated NSCLC：A meta-analysis

description: <b>Supplementary
 Table 1</b>. Efficacy of adjuvant EGFR
 inhibitors and impact of clinical factors in resected EGFR-mutated NSCLC：A
 meta-analysis
 <i>The data available
 status for subgroup-analyses among the included trials.</i>
 
 <b>Supplementary
 Table 2</b>. Efficacy of adjuvant EGFR
 inhibitors and impact of clinical factors in resected EGFR-mutated NSCLC：A
 meta-analysis
 <i>Sensitivity
 analysis after removing the trials using the third-generation EGFR TKI.</i>
 
 <b>Supplementary
 Table 3</b>. Efficacy of adjuvant EGFR
 inhibitors and impact of clinical factors in resected EGFR-mutated NSCLC：A
 meta-analysis
 <i>Sensitivity
 analysis after removing the trials unselecting EGFR mutation status.</i>
 
 <b>Supplementary
 Table 4</b>. Efficacy of adjuvant EGFR
 inhibitors and impact of clinical factors in resected EGFR-mutated NSCLC：A
 meta-analysis
 <i>Sensitivity
 analysis using both fixed-effects and random-effects models.</i>
DOI: 10.25402/fon.19114499.v1
title: Supplementary Tables – Efficacy of adjuvant EGFR inhibitors and impact of clinical factors in resected EGFR-mutated NSCLC：A meta-analysis

description: <b>Supplementary
 Table 1</b>. Efficacy of adjuvant EGFR
 inhibitors and impact of clinical factors in resected EGFR-mutated NSCLC：A
 meta-analysis
 <i>The data available
 status for subgroup-analyses among the included trials.</i>
 
 <b>Supplementary
 Table 2</b>. Efficacy of adjuvant EGFR
 inhibitors and impact of clinical factors in resected EGFR-mutated NSCLC：A
 meta-analysis
 <i>Sensitivity
 analysis after removing the trials using the third-generation EGFR TKI.</i>
 
 <b>Supplementary
 Table 3</b>. Efficacy of adjuvant EGFR
 inhibitors and impact of clinical factors in resected EGFR-mutated NSCLC：A
 meta-analysis
 <i>Sensitivity
 analysis after removing the trials unselecting EGFR mutation status.</i>
 
 <b>Supplementary
 Table 4</b>. Efficacy of adjuvant EGFR
 inhibitors and impact of clinical factors in resected EGFR-mutated NSCLC：A
 meta-analysis
 <i>Sensitivity
 analysis using both fixed-effects and random-effects models.</i>