cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7639859.v1
title: Spatial Variable Selection and An Application to Virginia Lyme Disease Emergence

description: Lyme disease is an infectious disease, that is, caused by a bacterium called <i>Borrelia burgdorferi</i> sensu stricto. In the United States, Lyme disease is one of the most common infectious diseases. The major endemic areas of the disease are New England, Mid-Atlantic, East-North Central, South Atlantic, and West North-Central. Virginia is on the front-line of the disease’s diffusion from the northeast to the south. One of the research objectives for the infectious disease community is to identify environmental and economic variables that are associated with the emergence of Lyme disease. In this article, we use a spatial Poisson regression model to link the spatial disease counts and environmental and economic variables, and develop a spatial variable selection procedure to effectively identify important factors by using an adaptive elastic net penalty. The proposed methods can automatically select important covariates, while adjusting for possible spatial correlations of disease counts. The performance of the proposed method is studied and compared with existing methods via a comprehensive simulation study. We apply the developed variable selection methods to the Virginia Lyme disease data and identify important variables that are new to the literature. Supplementary materials for this article, including a standardized description of the materials available for reproducing the work, are available as an online supplement.
DOI: 10.6084/m9.figshare.8164154.v1
title: Additional file 8: of lncRNA profile of Apis mellifera and its possible role in behavioural transition from nurses to foragers

description: The top 20 enriched KEGG pathways in the TC_F vs. TC_N, SCC_YF vs. SCC_YN and SCC_OF vs. SCC_ ON comparisons (trans). (XLS 30 kb)
DOI: 10.6084/m9.figshare.8163878
title: Additional file 5: of Tracing the history of LINE and SINE extinction in sigmodontine rodents

description: Alignment of L1 subfamily sequences used in the tables and figures. CpG sites with evidence of methylation-induced mutations were removed from the alignment. (FA 15 kb)
DOI: 10.6084/m9.figshare.7639889
title: Estimation of Conditional Prevalence From Group Testing Data With Missing Covariates

description: We consider estimating the conditional prevalence of a disease from data pooled according to the group testing mechanism. Consistent estimators have been proposed in the literature, but they rely on the data being available for all individuals. In infectious disease studies where group testing is frequently applied, the covariate is often missing for some individuals. There, unless the missing mechanism occurs completely at random, applying the existing techniques to the complete cases without adjusting for missingness does not generally provide consistent estimators, and finding appropriate modifications is challenging. We develop a consistent spline estimator, derive its theoretical properties, and show how to adapt local polynomial and likelihood estimators to the missing data problem. We illustrate the numerical performance of our methods on simulated and real examples. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.7639889.v2
title: Estimation of Conditional Prevalence From Group Testing Data With Missing Covariates

description: We consider estimating the conditional prevalence of a disease from data pooled according to the group testing mechanism. Consistent estimators have been proposed in the literature, but they rely on the data being available for all individuals. In infectious disease studies where group testing is frequently applied, the covariate is often missing for some individuals. There, unless the missing mechanism occurs completely at random, applying the existing techniques to the complete cases without adjusting for missingness does not generally provide consistent estimators, and finding appropriate modifications is challenging. We develop a consistent spline estimator, derive its theoretical properties, and show how to adapt local polynomial and likelihood estimators to the missing data problem. We illustrate the numerical performance of our methods on simulated and real examples. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.8164205.v1
title: MOESM3 of Effect of intestinal tapeworms on the gut microbiota of the common carp, Cyprinus carpio

description: Additional file 3: Table S1. Maturity of the two tapeworms Khawia japonensis and Atractolytocestus tenuicollis in the intestine of common carp (Cyprinus carpio) from China.
DOI: 10.6084/m9.figshare.8164217
title: Additional file 2: of Iso-Seq analysis of the Taxus cuspidata transcriptome reveals the complexity of Taxol biosynthesis

description: Table S2. Primers used in this study. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.8163686
title: MOESM2 of Genomic characterization of Escherichia coli LCT-EC001, an extremely multidrug-resistant strain with an amazing number of resistance genes

description: Additional file 2. Repeat sequences of LCT-EC001.
DOI: 10.6084/m9.figshare.8163884
title: Additional file 6: of Tracing the history of LINE and SINE extinction in sigmodontine rodents

description: Alignment of B1 subfamily sequences used in the tables and figures. CpG sites with evidence of methylation-induced mutations were removed from the alignment. (FA 7 kb)
DOI: 10.6084/m9.figshare.8164034.v1
title: Additional file 4: of Genome-wide characterization of a SRO gene family involved in response to biotic and abiotic stresses in banana (Musa spp.)

description: Protein sequences used for the construction of phylogenetic trees. (TXT 39 kb)
DOI: 10.6084/m9.figshare.8163851.v1
title: Additional file 6: of Physiological responses and proteomic changes reveal insights into Stylosanthes response to manganese toxicity

description: Table S5. List of primers used in the study for gene expression analysis. (XLSX 9â kb)
DOI: 10.6084/m9.figshare.8164373
title: Additional file 5: of Integrated microRNA and transcriptome profiling reveals a miRNA-mediated regulatory network of embryo abortion under calcium deficiency in peanut (Arachis hypogaea L.)

description: Table S1. Summary of data from the sequencing of peanut sRNA libraries. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.8164379.v1
title: Additional file 6: of Integrated microRNA and transcriptome profiling reveals a miRNA-mediated regulatory network of embryo abortion under calcium deficiency in peanut (Arachis hypogaea L.)

description: Table S2. Mapping results of sRNA sequences and the peanut genome. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.8164403.v1
title: Additional file 4: of Both chronic HBV infection and naturally acquired HBV immunity confer increased risks of B-cell non-Hodgkin lymphoma

description: Table S2. Main characteristics of the case-control studies evaluating the association between HBV infection and NHL. Abbreviations: ICD-O3 = International Classification of Disease for Oncology 3rd edition; SEER = Surveillance, Epidemiology, and Results; ICD-10 = International Classification of Diseases-10th revision. (XLS 41 kb)
DOI: 10.6084/m9.figshare.20222020
title: Additional file 4 of OsPP65 Negatively Regulates Osmotic and Salt Stress Responses Through Regulating Phytohormone and Raffinose Family Oligosaccharide Metabolic Pathways in Rice

description: Additional file 4: Table S3. 120 metabolites identified by GC-MS in WT and the OsPP65 knockout plants. Number after the metabolite represents the isomer.
DOI: 10.6084/m9.figshare.20222014
title: Additional file 2 of OsPP65 Negatively Regulates Osmotic and Salt Stress Responses Through Regulating Phytohormone and Raffinose Family Oligosaccharide Metabolic Pathways in Rice

description: Additional file 2: Table S1. Differentially expressed genes in ko6 plants by RNA-seq analysis before (0 h) and after (4 h) osmotic stress treatment. |log2 Ratio| ≥1 and FDR ≤ 0.05.
DOI: 10.6084/m9.figshare.20222017
title: Additional file 3 of OsPP65 Negatively Regulates Osmotic and Salt Stress Responses Through Regulating Phytohormone and Raffinose Family Oligosaccharide Metabolic Pathways in Rice

description: Additional file 3: Table S2. Cis-elements analysis of the OsPP65 promoter.
DOI: 10.6084/m9.figshare.8163884.v1
title: Additional file 6: of Tracing the history of LINE and SINE extinction in sigmodontine rodents

description: Alignment of B1 subfamily sequences used in the tables and figures. CpG sites with evidence of methylation-induced mutations were removed from the alignment. (FA 7 kb)
DOI: 10.6084/m9.figshare.20222017.v1
title: Additional file 3 of OsPP65 Negatively Regulates Osmotic and Salt Stress Responses Through Regulating Phytohormone and Raffinose Family Oligosaccharide Metabolic Pathways in Rice

description: Additional file 3: Table S2. Cis-elements analysis of the OsPP65 promoter.
DOI: 10.6084/m9.figshare.8163890
title: Additional file 7: of Tracing the history of LINE and SINE extinction in sigmodontine rodents

description: Alignment of L1 subfamily sequences based on RepeatScout-generated seeds and S. hispidus genome. CpG sites with evidence of methylation-induced mutations were removed from the alignment. (FA 21 kb)
DOI: 10.6084/m9.figshare.20222023
title: Additional file 5 of OsPP65 Negatively Regulates Osmotic and Salt Stress Responses Through Regulating Phytohormone and Raffinose Family Oligosaccharide Metabolic Pathways in Rice

description: Additional file 5: Table S4. Primers used for vector construction and quantitative RT-PCR analysis.
DOI: 10.6084/m9.figshare.20222023.v1
title: Additional file 5 of OsPP65 Negatively Regulates Osmotic and Salt Stress Responses Through Regulating Phytohormone and Raffinose Family Oligosaccharide Metabolic Pathways in Rice

description: Additional file 5: Table S4. Primers used for vector construction and quantitative RT-PCR analysis.
DOI: 10.6084/m9.figshare.8164010
title: Additional file 1: of Genome-wide characterization of a SRO gene family involved in response to biotic and abiotic stresses in banana (Musa spp.)

description: The components of amino acids in the conserved motifs. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.8164040
title: Additional file 5: of Genome-wide characterization of a SRO gene family involved in response to biotic and abiotic stresses in banana (Musa spp.)

description: A newick file of the phylogenetic tree. (TXT 2 kb)
DOI: 10.6084/m9.figshare.20222551
title: Additional file 2 of Sequence, structure, and function of the Dps DNA-binding protein from Deinococcus wulumuqiensis R12

description: Additional file 2. GO_terms_Level2_Classify.
DOI: 10.6084/m9.figshare.20222548
title: Additional file 1 of Sequence, structure, and function of the Dps DNA-binding protein from Deinococcus wulumuqiensis R12

description: Additional file 1. GO_enrichment.
DOI: 10.6084/m9.figshare.20222548.v1
title: Additional file 1 of Sequence, structure, and function of the Dps DNA-binding protein from Deinococcus wulumuqiensis R12

description: Additional file 1. GO_enrichment.
DOI: 10.6084/m9.figshare.21443223
title: The chromosome-scale assembly of the Salvia rosmarinus genome reveals key genes in carnosic acid biosynthesis

description: The chromosomal-level genome sequence and gene annotation of <i>Salvia rosmarinus.</i>
DOI: 10.6084/m9.figshare.20222551.v1
title: Additional file 2 of Sequence, structure, and function of the Dps DNA-binding protein from Deinococcus wulumuqiensis R12

description: Additional file 2. GO_terms_Level2_Classify.
DOI: 10.6084/m9.figshare.16553291
title: Supplementary Dataset Table 2: Zircon LA–ICP–MS U–Pb results. Exhumation of the crustal-scale Gaoligong strike-slip shear belt in Southeast Asia

description: Supplementary Dataset: Results of zircon LA–ICP–MS U–Pb results for the granitoid from the Gaoligong metamorphic belt
DOI: 10.6084/m9.figshare.16553291.v1
title: Supplementary Dataset Table 2: Zircon LA–ICP–MS U–Pb results. Exhumation of the crustal-scale Gaoligong strike-slip shear belt in Southeast Asia

description: Supplementary Dataset: Results of zircon LA–ICP–MS U–Pb results for the granitoid from the Gaoligong metamorphic belt
DOI: 10.6084/m9.figshare.16553294
title: Supplementary Dataset Table 1: EPMA test results. Exhumation of the crustal-scale Gaoligong strike-slip shear belt in Southeast Asia

description: Supplementary Dataset Table 1: EPMA test results.
DOI: 10.6084/m9.figshare.16553294.v1
title: Supplementary Dataset Table 1: EPMA test results. Exhumation of the crustal-scale Gaoligong strike-slip shear belt in Southeast Asia

description: Supplementary Dataset Table 1: EPMA test results.
DOI: 10.6084/m9.figshare.22320495
title: Frame-shifting instead of incongruity is necessary for pun comprehension: evidence from an ERP study on Chinese homophone puns

description: Recent psycholinguistic research has made significant progress in understanding the meaning-access process during pun comprehension. However, to date, little research has directly investigated how the two retrieved meanings are integrated into the pun context afterwards. In the current ERP study, we examined this process by comparing homophone puns with two control conditions. Different from previous ERP studies on jokes, we did not observe significantly enhanced N400 amplitudes (300-500 ms) in the pun condition, indicating no apparent detection of incongruity. However, we observed a sustained positivity around the left anterior regions (500-900 ms) and enhanced LPC amplitudes around the central-parietal regions (600-900 ms). These two components could index the sudden access to the second meaning and the additional integration operations to establish a new cognitive model respectively. These findings were compatible with the Space Structure Model, which emphasises the frame-shifting process as a crucial element for understanding verbal humour.
DOI: 10.6084/m9.figshare.22320495.v1
title: Frame-shifting instead of incongruity is necessary for pun comprehension: evidence from an ERP study on Chinese homophone puns

description: Recent psycholinguistic research has made significant progress in understanding the meaning-access process during pun comprehension. However, to date, little research has directly investigated how the two retrieved meanings are integrated into the pun context afterwards. In the current ERP study, we examined this process by comparing homophone puns with two control conditions. Different from previous ERP studies on jokes, we did not observe significantly enhanced N400 amplitudes (300-500 ms) in the pun condition, indicating no apparent detection of incongruity. However, we observed a sustained positivity around the left anterior regions (500-900 ms) and enhanced LPC amplitudes around the central-parietal regions (600-900 ms). These two components could index the sudden access to the second meaning and the additional integration operations to establish a new cognitive model respectively. These findings were compatible with the Space Structure Model, which emphasises the frame-shifting process as a crucial element for understanding verbal humour.
DOI: 10.6084/m9.figshare.20222573
title: Additional file 3 of Circular RNA EIF4G3 suppresses gastric cancer progression through inhibition of β-catenin by promoting δ-catenin ubiquitin degradation and upregulating SIK1

description: Additional file 3:
DOI: 10.6084/m9.figshare.7116233
title: Additional file 1: of Genome-wide analysis of long non-coding RNAs in Catalpa bungei and their potential function in floral transition using high-throughput sequencing

description: Table S1. List of the floral transition genes in C. bungei. (XLSX 1035 kb)
DOI: 10.6084/m9.figshare.8164001.v1
title: Additional file 10: of Genome-wide characterization of a SRO gene family involved in response to biotic and abiotic stresses in banana (Musa spp.)

description: The primer sequences were used in the present study. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.20222621.v1
title: Additional file 6 of APEX1 regulates alternative splicing of key tumorigenesis genes in non-small-cell lung cancer

description: Additional file 6: Table S6. Ras KEGG pathway identify.
DOI: 10.6084/m9.figshare.20222612.v1
title: Additional file 4 of APEX1 regulates alternative splicing of key tumorigenesis genes in non-small-cell lung cancer

description: Additional file 4: Table S4. All known AS events detected by type.
DOI: 10.6084/m9.figshare.20222606.v1
title: Additional file 2 of APEX1 regulates alternative splicing of key tumorigenesis genes in non-small-cell lung cancer

description: Additional file 2: Table S2. HiSeqV2 APEX1 expression box.
DOI: 10.6084/m9.figshare.20222618
title: Additional file 5 of APEX1 regulates alternative splicing of key tumorigenesis genes in non-small-cell lung cancer

description: Additional file 5: Table S5. Classification of all RASE events between sample groups.
DOI: 10.6084/m9.figshare.20222618.v1
title: Additional file 5 of APEX1 regulates alternative splicing of key tumorigenesis genes in non-small-cell lung cancer

description: Additional file 5: Table S5. Classification of all RASE events between sample groups.
DOI: 10.6084/m9.figshare.8164010.v1
title: Additional file 1: of Genome-wide characterization of a SRO gene family involved in response to biotic and abiotic stresses in banana (Musa spp.)

description: The components of amino acids in the conserved motifs. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.20222624
title: Additional file 7 of APEX1 regulates alternative splicing of key tumorigenesis genes in non-small-cell lung cancer

description: Additional file 7: Table S7. Mapping of clean reads on the reference genome.
DOI: 10.6084/m9.figshare.20222609.v1
title: Additional file 3 of APEX1 regulates alternative splicing of key tumorigenesis genes in non-small-cell lung cancer

description: Additional file 3: Table S3. Mapping of clean reads on the reference genome.
DOI: 10.6084/m9.figshare.20222612
title: Additional file 4 of APEX1 regulates alternative splicing of key tumorigenesis genes in non-small-cell lung cancer

description: Additional file 4: Table S4. All known AS events detected by type.
DOI: 10.6084/m9.figshare.20222624.v1
title: Additional file 7 of APEX1 regulates alternative splicing of key tumorigenesis genes in non-small-cell lung cancer

description: Additional file 7: Table S7. Mapping of clean reads on the reference genome.
DOI: 10.6084/m9.figshare.24942061
title: Spaceflight associated neuro-ocular syndrome (SANS): a systematic review, implications for the sans case definition

description: Astronauts undergoing long-duration space flights (LDSF) often experience a unique set of neuro-ocular findings known as Spaceflight Associated Neuro-ocular Syndrome (SANS). However, the exact mechanisms and the true incidence of SANS remain unclear. This paper aims to review the existing literature on SANS, focusing on its incidence and sequence of findings, and to provide a comprehensive understanding of this condition. Studies reporting SANS and optic disc edema in astronauts from PubMed, Scopus, and WOS have been collected. Eligible studies were selected based on stringent inclusion criteria. Statistical analysis utilized R software with random effect models for them, and heterogeneity was assessed using I2 and chi-squared tests. Our study includes 19 studies that met the inclusion criteria, which encompassed 294 participants. Included studies revealed that optic disc edema and choroidal folds were highly prevalent, with proportions of 75% and 71%, respectively. Hyperopic shifts (95%CI 0.51, 0.76, I2 = 0%) were also statistically significant, appearing gradually and persisting even after astronauts returned to Earth. This study provides a comprehensive assessment of SANS in astronauts. The study suggests that the current clinical definition of SANS may underestimate its true incidence and proposes the inclusion of quantitative metrics to enhance sensitivity and accuracy in diagnosis.
DOI: 10.6084/m9.figshare.20222621
title: Additional file 6 of APEX1 regulates alternative splicing of key tumorigenesis genes in non-small-cell lung cancer

description: Additional file 6: Table S6. Ras KEGG pathway identify.
DOI: 10.6084/m9.figshare.24942061.v1
title: Spaceflight associated neuro-ocular syndrome (SANS): a systematic review, implications for the sans case definition

description: Astronauts undergoing long-duration space flights (LDSF) often experience a unique set of neuro-ocular findings known as Spaceflight Associated Neuro-ocular Syndrome (SANS). However, the exact mechanisms and the true incidence of SANS remain unclear. This paper aims to review the existing literature on SANS, focusing on its incidence and sequence of findings, and to provide a comprehensive understanding of this condition. Studies reporting SANS and optic disc edema in astronauts from PubMed, Scopus, and WOS have been collected. Eligible studies were selected based on stringent inclusion criteria. Statistical analysis utilized R software with random effect models for them, and heterogeneity was assessed using I2 and chi-squared tests. Our study includes 19 studies that met the inclusion criteria, which encompassed 294 participants. Included studies revealed that optic disc edema and choroidal folds were highly prevalent, with proportions of 75% and 71%, respectively. Hyperopic shifts (95%CI 0.51, 0.76, I2 = 0%) were also statistically significant, appearing gradually and persisting even after astronauts returned to Earth. This study provides a comprehensive assessment of SANS in astronauts. The study suggests that the current clinical definition of SANS may underestimate its true incidence and proposes the inclusion of quantitative metrics to enhance sensitivity and accuracy in diagnosis.
DOI: 10.6084/m9.figshare.8164019
title: Additional file 2: of Genome-wide characterization of a SRO gene family involved in response to biotic and abiotic stresses in banana (Musa spp.)

description: Chromosomal location, subcellular localization and putatively physicochemical characters of banana MaSROs. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.8164028.v1
title: Additional file 3: of Genome-wide characterization of a SRO gene family involved in response to biotic and abiotic stresses in banana (Musa spp.)

description: Information of the SRO orthologs in representative sequenced 16 plant species. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.20222609
title: Additional file 3 of APEX1 regulates alternative splicing of key tumorigenesis genes in non-small-cell lung cancer

description: Additional file 3: Table S3. Mapping of clean reads on the reference genome.
DOI: 10.17188/1319497
title: Materials Data on Mg2CoN2 by Materials Project

description: Mg2CoN2 crystallizes in the monoclinic C2/m space group. The structure is three-dimensional. there are two inequivalent Mg2+ sites. In the first Mg2+ site, Mg2+ is bonded to five N3- atoms to form a mixture of edge and corner-sharing MgN5 square pyramids. There are a spread of Mg–N bond distances ranging from 2.14–2.40 Å. In the second Mg2+ site, Mg2+ is bonded in a rectangular see-saw-like geometry to four N3- atoms. There are a spread of Mg–N bond distances ranging from 2.09–2.20 Å. Co2+ is bonded in a distorted trigonal planar geometry to three N3- atoms. There are a spread of Co–N bond distances ranging from 1.82–1.88 Å. There are two inequivalent N3- sites. In the first N3- site, N3- is bonded to five Mg2+ and one Co2+ atom to form a mixture of edge and corner-sharing NMg5Co octahedra. The corner-sharing octahedra tilt angles range from 1–36°. In the second N3- site, N3- is bonded to four Mg2+ and two equivalent Co2+ atoms to form a mixture of distorted edge and corner-sharing NMg4Co2 octahedra. The corner-sharing octahedra tilt angles range from 1–36°.