cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14609248
title: Additional file 6 of Genome-wide detection of CNVs and their association with performance traits in broilers

description: Additional file 6. H3K27ac and CpG islands tracks alingment with significant CNV segments. H3K27ac ChIP-seq data of chicken skeletal muscle (blue and red tracks) overlap with the significant CNV segment on chr5:12059966–12062666 (green bar) near the KCNJ11 gene (black bar). The blue rows represent replicate A, while red rows represent replicate B. The overlap with the H3K27ac enriched region is indicated by the dashed box. No overlap was found between the significant CNV segments on chr3:64169030–64171297 or chr3:97801202–97809208 and H3K27ac regions. CpG islands were only located in promoter regions and TSSs (orange track)
DOI: 10.6084/m9.figshare.14609245
title: Additional file 5 of Genome-wide detection of CNVs and their association with performance traits in broilers

description: Additional file 5. Validation rates of 9 samples
DOI: 10.6084/m9.figshare.14609239
title: Additional file 4 of Genome-wide detection of CNVs and their association with performance traits in broilers

description: Additional file 4. Information of the CNV segments validated by qPCR and the primers used for qPCR
DOI: 10.6084/m9.figshare.14609236
title: Additional file 3 of Genome-wide detection of CNVs and their association with performance traits in broilers

description: Additional file 3 QQ-plots show the relation of normal theoretical quantiles of the probability distributions between expected (X-axis) and observed (Y-axis) p-values from (a) birth weight, (b) body weight at 35 days, (c) body weight at 41 days, (d) body weight at 42 days and (e) body weight gain
DOI: 10.6084/m9.figshare.14609230
title: Additional file 2 of Genome-wide detection of CNVs and their association with performance traits in broilers

description: Additional file 2 Manhattan plots for CNV segments across the 33 autosomal chromosomes associated with (a) birth weight, (b) body weight at 35 days, (c) body weight at 41 days and (d) body weight at 42 days and (e) body weight gain. The X-axis represents the somatic chromosomes, and Y-axis shows the corresponding -log10 p-value. Red and blue lines indicate p-values of 0.05 and 0.1, respectively
DOI: 10.6084/m9.figshare.14609224
title: Additional file 1 of Genome-wide detection of CNVs and their association with performance traits in broilers

description: Additional file 1. Information of identified CNVRs
DOI: 10.6084/m9.figshare.14609201
title: Additional file 2 of Single nucleotide polymorphisms reveal genetic diversity in New Mexican chile peppers (Capsicum spp.)

description: Additional file 2: Table S1. Fixation indices (Fst) across the different Capsicum species. Table S2. Inference on the best number of clusters K for the Capsicum population using Evanno criterion. Table S3. Distribution of the Capsicum genotypes based on hierarchical and Bayesian-based model clustering for number of clusters, K = 2. Inferred group designation for each entry is highlighted. Table S4. Distribution of the Capsicum genotypes based on hierarchical and Bayesian-based model clustering for number of clusters, K= 4. Inferred group designation for each entry is highlighted. Table S5. Overview of linkage disequilibrium for the intrachromosomal marker pairs in the Capsicum population. Table S6. Details of the 165 Capsicum genotypes used in this study.
DOI: 10.6084/m9.figshare.14609198
title: Additional file 1 of Single nucleotide polymorphisms reveal genetic diversity in New Mexican chile peppers (Capsicum spp.)

description: Additional file 1: Table S1. Flanking sequences for the 66,750 SNP markers identified in the Capsicum population.
DOI: 10.6084/m9.figshare.14609195
title: Additional file 2 of Career-computer simulation increases perceived importance of learning about rare diseases

description: Additional file 2.
DOI: 10.6084/m9.figshare.14609168
title: Additional file 1 of Effects of precarious work on symptomatology of anxiety and depression in Chilean workers, a cross sectional study

description: Additional file 1.
DOI: 10.6084/m9.figshare.14609147
title: Additional file 1 of Sports nutrition knowledge and perceptions among professional basketball athletes and coaches in Lebanon-a cross-sectional study

description: Additional file 1: Dataset. (data analyzed during the study).
DOI: 10.6084/m9.figshare.14609119
title: Additional file 1 of Design considerations of an IL13Rα2 antibody–drug conjugate for diffuse intrinsic pontine glioma

description: Additional file 3: Table 1. Table of information, properties, and clinical and genomic characteristics for cell lines used in this study.
DOI: 10.6084/m9.figshare.14609074
title: Additional file 2 of Rapid protein sequence evolution via compensatory frameshift is widespread in RNA virus genomes

description: Additional file 2: Supplementary Table S2.
DOI: 10.25345/c5q52h
title: MassIVE MSV000087451 - Plasma amyloid proteins IP LC-targeted MS1 analysis for early AD diagnosis
title: LC-targeted MS1 analysis of plasma beta amyloid proteins for early AD diagnosis
DOI: 10.6084/m9.figshare.14609071
title: Additional file 1 of Rapid protein sequence evolution via compensatory frameshift is widespread in RNA virus genomes

description: Additional file 1: Supplementary Table S1.
DOI: 10.6084/m9.figshare.14609051
title: Additional file 2 of Structural landscape of the complete genomes of dengue virus serotypes and other viral hemorrhagic fevers

description: Additional file 2.
DOI: 10.6084/m9.figshare.14609023
title: Additional file 6 of Macrophage mediated recognition and clearance of Borrelia burgdorferi elicits MyD88-dependent and -independent phagosomal signals that contribute to phagocytosis and inflammation

description: Additional file 6: Supplemental File 6. Identified master regulators.
DOI: 10.6084/m9.figshare.14609020
title: Additional file 5 of Macrophage mediated recognition and clearance of Borrelia burgdorferi elicits MyD88-dependent and -independent phagosomal signals that contribute to phagocytosis and inflammation

description: Additional file 5: Supplemental File 5. Identified transcription factors.
DOI: 10.6084/m9.figshare.14609017
title: Additional file 4 of Macrophage mediated recognition and clearance of Borrelia burgdorferi elicits MyD88-dependent and -independent phagosomal signals that contribute to phagocytosis and inflammation

description: Additional file 4: Supplemental File 4. Identified differentially expressed genes.
DOI: 10.6084/m9.figshare.14609014
title: Additional file 3 of Macrophage mediated recognition and clearance of Borrelia burgdorferi elicits MyD88-dependent and -independent phagosomal signals that contribute to phagocytosis and inflammation

description: Additional file 3: Supplemental File 3. Gene ontology analysis of identified master regulators.
DOI: 10.6084/m9.figshare.14609011
title: Additional file 2 of Macrophage mediated recognition and clearance of Borrelia burgdorferi elicits MyD88-dependent and -independent phagosomal signals that contribute to phagocytosis and inflammation

description: Additional file 2: Supplemental File 2. Gene ontology analysis of identified transcription factors.
DOI: 10.6084/m9.figshare.14609008
title: Additional file 1 of Macrophage mediated recognition and clearance of Borrelia burgdorferi elicits MyD88-dependent and -independent phagosomal signals that contribute to phagocytosis and inflammation

description: Additional file 1: Supplemental File 1. Gene ontology analysis of differentially expressed genes.
DOI: 10.6084/m9.figshare.14609466
title: Annex supplement

description: Phylogenetic tree construction using maximum likelihood based on the complete chloroplast genome sequences of Rohdea wattii and other 1820 species within Asparagaceae and two outgroup species (Lycoris anhuiensis and Lycoris chinensis).
DOI: 10.6084/m9.figshare.14609466.v2
title: Annex supplement

description: Phylogenetic tree construction using maximum likelihood based on the complete chloroplast genome sequences of Rohdea wattii and other 1820 species within Asparagaceae and two outgroup species (Lycoris anhuiensis and Lycoris chinensis).
DOI: 10.6084/m9.figshare.14608973
title: Additional file 1 of Prognostic value of noggin protein expression in patients with resected gastric cancer

description: Additional file 1: Supplementary Figure 1. The molecular function of Noggin and RBPMS2. Gene set enrichment analysis (GSEA) of positively correlated genes with Noggin and RBPMS2 in GSE62254, GSE15459, and GSE15460 datasets showed “Focal adhesion” and “ECM receptor interaction” signatures, which were enriched and positively correlated with both Noggin and RBPMS2 expression, respectively (A). KEGG pathway analysis of positively correlated genes with Noggin and RBPMS2 associated with the GO terms shown on the left side (B). Normalized Enrichment Scores are represented by the bars, where the adjusted p-values (familywise error rate, FWER) ≤ 0.05 are presented with a green bar or FWER &gt; 0.05 with a red bar. Supplementary Figure 2. Immunohistochemical staining of noggin (A, original magnification × 1 200; scale bar, 100 μm) and RBPMS2 (B, original magnification × 200; scale bar, 100 μm) in normal gastric mucosa. Foveolar cells are negative for noggin and RBPMS2, while both proteins are weakly expressed in parietal cells. Supplementary Figure 3. Kaplan-Meier survival curves for disease-free survival were plotted according to Noggin and RBPMS2 protein expression. Noggin protein expression at the invasive front (A) and tumor center (B); RBPMS2 expression in the invasive front (C) and tumor center (D). DFS, disease-free survival; RBMPS2, RNA-binding protein for multiple splicing 2; IF, invasive front; TC, tumor center.
DOI: 10.6084/m9.figshare.14608943
title: Additional file 16 of Characterization of the dynamics and variability of neuronal subtype responses during growth, degrowth, and regeneration of Nematostella vectensis

description: Additional file 16. Data collected for this study.
DOI: 10.6084/m9.figshare.13176855
title: Effect of crystal orientation on the size effects of nano-scale fcc metals

description: The present work investigates the dominant mechanisms in the plasticity of nano-sized fcc metallic samples. Molecular dynamics simulations of nanopillar compression show that plasticity always starts with the nucleation of dislocations at the free surface, and the crystal orientation affects the subsequent microstructural evolution. The Schmid factor of leading and trailing partials plays a decisive role in leading to the twinning, or slip deformation. A significant difference is observed in the strength of pillars of the same size with different orientations. The power-law equation exponent is completely dependent on the crystal orientations, and a weak or no size effect is observed in the compression of [100]- and [110]-oriented nanopillars. The observed orientation based behaviour decreases by confining the free surface.
DOI: 10.6084/m9.figshare.13176855.v1
title: Effect of crystal orientation on the size effects of nano-scale fcc metals

description: The present work investigates the dominant mechanisms in the plasticity of nano-sized fcc metallic samples. Molecular dynamics simulations of nanopillar compression show that plasticity always starts with the nucleation of dislocations at the free surface, and the crystal orientation affects the subsequent microstructural evolution. The Schmid factor of leading and trailing partials plays a decisive role in leading to the twinning, or slip deformation. A significant difference is observed in the strength of pillars of the same size with different orientations. The power-law equation exponent is completely dependent on the crystal orientations, and a weak or no size effect is observed in the compression of [100]- and [110]-oriented nanopillars. The observed orientation based behaviour decreases by confining the free surface.
DOI: 10.5281/zenodo.4750734
title: Deep learning generates custom-made logistic regression models for explaining how breast cancer subtypes are classified

description: Breast cancer is the most frequently found cancer in women and the one most often subjected to genetic analysis. Nonetheless, it has been causing the largest number of women's cancer-related deaths. PAM50, the intrinsic subtype assay for breast cancer, is beneficial for diagnosis and stratified treatment but does not explain each subtype's mechanism. Nowadays, deep learning can predict the subtypes from genetic information more accurately than conventional statistical methods. However, the previous studies did not directly use deep learning to examine which genes associate with the subtypes. Ours is the first study on a deep-learning approach to reveal the mechanisms embedded in the PAM50-classified subtypes. We developed an explainable deep learning model called a point-wise linear model, which uses a meta-learning approach to generate a custom-made logistic regression model for each sample. Logistic regression is familiar to physicians and medical informatics researchers, and we can use it to analyze which genes are important for subtype prediction. The custom-made logistic regression models generated by the point-wise linear model for each subtype used the specific genes selected in other subtypes compared to the conventional logistic regression model: the overlap ratio is less than twenty percent. And analyzing the point-wise linear model's inner state, we found that the point-wise linear model used genes relevant to the cell cycle-related pathways. The results of this study suggest the potential of our explainable deep learning to play a vital role in cancer treatment.
DOI: 10.5281/zenodo.4769028
title: Deep learning generates custom-made logistic regression models for explaining how breast cancer subtypes are classified

description: Breast cancer is the most frequently found cancer in women and the one most often subjected to genetic analysis. Nonetheless, it has been causing the largest number of women's cancer-related deaths. PAM50, the intrinsic subtype assay for breast cancer, is beneficial for diagnosis and stratified treatment but does not explain each subtype's mechanism. Nowadays, deep learning can predict the subtypes from genetic information more accurately than conventional statistical methods. However, the previous studies did not directly use deep learning to examine which genes associate with the subtypes. Ours is the first study on a deep-learning approach to reveal the mechanisms embedded in the PAM50-classified subtypes. We developed an explainable deep learning model called a point-wise linear model, which uses a meta-learning approach to generate a custom-made logistic regression model for each sample. Logistic regression is familiar to physicians and medical informatics researchers, and we can use it to analyze which genes are important for subtype prediction. The custom-made logistic regression models generated by the point-wise linear model for each subtype used the specific genes selected in other subtypes compared to the conventional logistic regression model: the overlap ratio is less than twenty percent. And analyzing the point-wise linear model's inner state, we found that the point-wise linear model used genes relevant to the cell cycle-related pathways. The results of this study suggest the potential of our explainable deep learning to play a vital role in cancer treatment.
DOI: 10.21227/326q-bf39
title: Three Benchmark Datasets for Scholarly Article Layout Analysis

description: This dataset contains three benchmark datasets as part of the scholarly output of and ICDAR 2021 paper: Meng Ling, Jian Chen, Torsten Moller, Petra Isenberg, Tobias Isenberg, Michael Sedlmair, Robert S. Laramee, Han-Wei Shen, Jian Wu, and C. Lee Giles, Document Domain Randomization for Deep Learning Document Layout Extraction, 16th International Conference on Document Analysis and Recognition (ICDAR) 2021. September 5-10, Lausanne, Switzerland. This dataset contains nine class lables: abstract, algorithm, author, body text, caption, equation, figure, table, and title. * Dataset 1: CS-150x, is an extension of the classical benchmark dataset CS-150 from three classes (figure, table, and caption) to nine classes, 1176 pages, Clark, C., Divvala, S.: Looking beyond text: Extracting figures, tables and captions from com- puter science papers. In: Workshops at the 29th AAAI Conference on Artificial Intelligence (2015), https://aaai.org/ocs/index.php/WS/AAAIW15/paper/view/10092.* Dataset 2: ACL300, has 300 randomly sampled articles (or 2508 pages) from the 55,759 papers scraped from the ACL anthology website; https://www.aclweb.org/anthology/.* Dataset 3: VIS300, has about 10% (or 2619 pages) of the document pages in randomly partitioned articles from 26,350 VIS paper pages, . Chen, J., Ling, M., Li, R., Isenberg, P., Isenberg, T., Sedlmair, M., Möller, T., Laramee, R.S., Shen, H.W., Wünsche, K., Wang, Q.: VIS30K: A collection of figures and tables from IEEE visualization conference publications. IEEE Trans. Vis. Comput. Graph. 27 (2021), to appear doi: 10.1109/TVCG.2021.3054916 This dataset is also available online at https://web.cse.ohio-state.edu/~chen.8028/ICDAR2021Benchmark/.
DOI: 10.6084/m9.figshare.13048746
title: Functional outcome after critical illness in older patients: a population-based study

description: To determine the prevalence of disability among ICU survivors one year after admission, and which factors influence functional outcome. We examined consecutive patients enrolled in the population-based Mayo Clinic Olmsted Study of Aging and then admitted to medical or surgical adult ICUs at Mayo Clinic, Rochester between January 1, 2006, and December 31, 2014 to determine one-year functional outcomes. 831cases were included. Mean age was 84 years (IQR 79–88). 569 (68.5%) patients were alive one year after ICU admission. Of them, 546 patients had functional assessment at one year and 367 (67.2%) had good functional outcome. On multivariable analysis, poor one-year functional outcome (death or disability) was more common among women, older patients, and patients with baseline cognitive impairment (mild cognitive impairment or dementia), higher Carlson scores, and longer ICU stay (all P On a population-based cohort of older, predominantly elderly patients, approximately two-thirds of survivors maintained or regained good functional status 1 year after ICU hospitalization. However, older age, female sex, greater comorbidities, abnormal baseline cognition, and longer ICU stay were associated with poor functional recovery and cognitive decline was common.
DOI: 10.6084/m9.figshare.13048746.v1
title: Functional outcome after critical illness in older patients: a population-based study

description: To determine the prevalence of disability among ICU survivors one year after admission, and which factors influence functional outcome. We examined consecutive patients enrolled in the population-based Mayo Clinic Olmsted Study of Aging and then admitted to medical or surgical adult ICUs at Mayo Clinic, Rochester between January 1, 2006, and December 31, 2014 to determine one-year functional outcomes. 831cases were included. Mean age was 84 years (IQR 79–88). 569 (68.5%) patients were alive one year after ICU admission. Of them, 546 patients had functional assessment at one year and 367 (67.2%) had good functional outcome. On multivariable analysis, poor one-year functional outcome (death or disability) was more common among women, older patients, and patients with baseline cognitive impairment (mild cognitive impairment or dementia), higher Carlson scores, and longer ICU stay (all P On a population-based cohort of older, predominantly elderly patients, approximately two-thirds of survivors maintained or regained good functional status 1 year after ICU hospitalization. However, older age, female sex, greater comorbidities, abnormal baseline cognition, and longer ICU stay were associated with poor functional recovery and cognitive decline was common.
DOI: 10.6084/m9.figshare.12848099.v2
title: Nicotine does not affect stem cell properties requisite for suicide gene therapy against glioma

description: Glioblastoma is one of the most lethal tumors in adult central nervous system with a median survival of a year and half and effective therapeutic strategy is urgently needed. For that reason, stem cell-based suicide gene therapies have attracted much interest because of potent tumor tropism of stem cells and bystander effect. In this current clinical situation, stem cells are promising delivery tool of suicide genes for glioma therapy. Since habitual cigarette smoking still prevails worldwide, we investigated the effect of nicotine on stem cell tropism toward glioma and gap junctional intercellular communication (GJIC) function between glioma and stem cells, both of which are important for suicide gene therapies. <b>Methods: </b>Mouse induced pluripotent stem cell-derived neural stem cells (iPS-NSCs) and human dental pulp mesenchymal stem cells (DPSCs) were used. The effect of nicotine on tumor tropism to glioma-conditioned medium (CM) at a non-cytotoxic concentration was assessed with Matrigel invasion assay. Nicotine effect on GJIC was assessed with the scrape loading/dye transfer (SL/DT) assay for co-culture of glioma and stem cells and the parachute assay among glioma cells using high-content analysis. <b>Results: </b>Tumor tropism of iPS-NSCs toward GL261-CM and DPSCs toward U251-CM was not affected by nicotine (0.1 and 1 µM). Nicotine at the concentrations equivalent to habitual smoking (1 µM) did not affect GJIC of iPS-NSC/GL261 and DPSC/U251 and GJIC among each glioma cells. <b>Conclusions: </b>The study demonstrated that non-cytotoxic concentrations of nicotine did not significantly change the stem cell properties requisite for stem cell-based suicide gene therapy.
DOI: 10.6084/m9.figshare.12848099
title: Nicotine does not affect stem cell properties requisite for suicide gene therapy against glioma

description: Glioblastoma is one of the most lethal tumors in adult central nervous system with a median survival of a year and half and effective therapeutic strategy is urgently needed. For that reason, stem cell-based suicide gene therapies have attracted much interest because of potent tumor tropism of stem cells and bystander effect. In this current clinical situation, stem cells are promising delivery tool of suicide genes for glioma therapy. Since habitual cigarette smoking still prevails worldwide, we investigated the effect of nicotine on stem cell tropism toward glioma and gap junctional intercellular communication (GJIC) function between glioma and stem cells, both of which are important for suicide gene therapies. <b>Methods: </b>Mouse induced pluripotent stem cell-derived neural stem cells (iPS-NSCs) and human dental pulp mesenchymal stem cells (DPSCs) were used. The effect of nicotine on tumor tropism to glioma-conditioned medium (CM) at a non-cytotoxic concentration was assessed with Matrigel invasion assay. Nicotine effect on GJIC was assessed with the scrape loading/dye transfer (SL/DT) assay for co-culture of glioma and stem cells and the parachute assay among glioma cells using high-content analysis. <b>Results: </b>Tumor tropism of iPS-NSCs toward GL261-CM and DPSCs toward U251-CM was not affected by nicotine (0.1 and 1 µM). Nicotine at the concentrations equivalent to habitual smoking (1 µM) did not affect GJIC of iPS-NSC/GL261 and DPSC/U251 and GJIC among each glioma cells. <b>Conclusions: </b>The study demonstrated that non-cytotoxic concentrations of nicotine did not significantly change the stem cell properties requisite for stem cell-based suicide gene therapy.