cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24787254
title: Plate-curving cell culture as a model for assessing curvature-induced cellular responses during neural tube morphogenesis

description: Neurulation is an important shape-transforming event during embryonic development where a flat neural plate is converted into a neural tube. Failure in this morphogenetic process accounts for one of the most common birth defects. Mechanical biology has provided key insights into neural tube formation and curvature among many physical properties that are eliciting attention. However, the lack of a proper model to study the effect of curvature has limited the potential to reveal its role in neurulation. In this study, we introduce a novel cell culture method called plate-curving cell culture where a polydimethylsiloxane (PDMS) plate of desired physical properties is curved in either a concave or convex form while the human pluripotent stem cell culture induced to have early neural plate identity is placed on top of its surface. With this method, we observed the elongation of cell colony morphology, as well as the perpendicular alignment of the cell division axis in the concave surface; the oriented cell division does not seem to explain the colony elongation. Transcriptome comparison in search of alternate possibilities suggested selectively altered pathways in the concave surface culture. Our new method is widely available, easy-to-use and culture-friendly, facilitating future mechanobiological studies of neurulation.
DOI: 10.6084/m9.figshare.24787254.v1
title: Plate-curving cell culture as a model for assessing curvature-induced cellular responses during neural tube morphogenesis

description: Neurulation is an important shape-transforming event during embryonic development where a flat neural plate is converted into a neural tube. Failure in this morphogenetic process accounts for one of the most common birth defects. Mechanical biology has provided key insights into neural tube formation and curvature among many physical properties that are eliciting attention. However, the lack of a proper model to study the effect of curvature has limited the potential to reveal its role in neurulation. In this study, we introduce a novel cell culture method called plate-curving cell culture where a polydimethylsiloxane (PDMS) plate of desired physical properties is curved in either a concave or convex form while the human pluripotent stem cell culture induced to have early neural plate identity is placed on top of its surface. With this method, we observed the elongation of cell colony morphology, as well as the perpendicular alignment of the cell division axis in the concave surface; the oriented cell division does not seem to explain the colony elongation. Transcriptome comparison in search of alternate possibilities suggested selectively altered pathways in the concave surface culture. Our new method is widely available, easy-to-use and culture-friendly, facilitating future mechanobiological studies of neurulation.
DOI: 10.6084/m9.figshare.24243993
title: The RNA ligation method using modified splint DNAs significantly improves the efficiency of circular RNA synthesis

description: Circular RNA (circRNA) is a non-coding RNA with a covalently closed loop structure and usually more stable than messenger RNA (mRNA). However, coding sequences (CDSs) following an internal ribosome entry site (IRES) in circRNAs can be translated, and this property has been recently utilized to produce proteins as novel therapeutic tools. However, it is difficult to produce large proteins from circRNAs because of the low circularization efficiency of lengthy RNAs. In this study, we report that we successfully synthesized circRNAs with the splint DNA ligation method using RNA ligase 1 and the splint DNAs, which contain complementary sequences to both ends of precursor linear RNAs. This method results in more efficient circularization than the conventional enzymatic method that does not use the splint DNAs, easily generating circRNAs that express relatively large proteins, including IgG heavy and light chains. Longer splint DNA (42 nucleotide) is more effective in circularization. Also, the use of splint DNAs with an adenine analog, 2,6-diaminopurine (DAP), increase the circularization efficiency presumably by strengthening the interaction between the splint DNAs and the precursor RNAs. The splint DNA ligation method requires 5 times more splint DNA than the precursor RNA to efficiently produce circRNAs, but our modified splint DNA ligation method can produce circRNAs using the amount of splint DNA which is equal to that of the precursor RNA. Our modified splint DNA ligation method will help develop novel therapeutic tools using circRNAs, to treat various diseases and to develop human and veterinary vaccines.
DOI: 10.6084/m9.figshare.24243993.v1
title: The RNA ligation method using modified splint DNAs significantly improves the efficiency of circular RNA synthesis

description: Circular RNA (circRNA) is a non-coding RNA with a covalently closed loop structure and usually more stable than messenger RNA (mRNA). However, coding sequences (CDSs) following an internal ribosome entry site (IRES) in circRNAs can be translated, and this property has been recently utilized to produce proteins as novel therapeutic tools. However, it is difficult to produce large proteins from circRNAs because of the low circularization efficiency of lengthy RNAs. In this study, we report that we successfully synthesized circRNAs with the splint DNA ligation method using RNA ligase 1 and the splint DNAs, which contain complementary sequences to both ends of precursor linear RNAs. This method results in more efficient circularization than the conventional enzymatic method that does not use the splint DNAs, easily generating circRNAs that express relatively large proteins, including IgG heavy and light chains. Longer splint DNA (42 nucleotide) is more effective in circularization. Also, the use of splint DNAs with an adenine analog, 2,6-diaminopurine (DAP), increase the circularization efficiency presumably by strengthening the interaction between the splint DNAs and the precursor RNAs. The splint DNA ligation method requires 5 times more splint DNA than the precursor RNA to efficiently produce circRNAs, but our modified splint DNA ligation method can produce circRNAs using the amount of splint DNA which is equal to that of the precursor RNA. Our modified splint DNA ligation method will help develop novel therapeutic tools using circRNAs, to treat various diseases and to develop human and veterinary vaccines.
DOI: 10.6084/m9.figshare.24448471
title: A push–pull strategy for controlling <i>Riptortus pedestris</i> (Hemiptera: Alydidae) using host plant semiochemicals

description: <i>Riptortus pedestris</i> is a major pest of soybean in East Asia that feeds on maturing seeds, reducing nutritional quality and causing seed abortion. Aggregation pheromone of the bean bug has been conventionally used as a lure for mass-trapping, but the control practices, used by farmers and recommended by the manufacturer can increase infestation in soybean fields. Here we investigated the efficacy of soybean semiochemical blend as a repellent incorporated with an attractant blend to develop a push–pull strategy. The efficacy of potential repellents was tested in a soybean field by evaluating three control strategies: a potential repellent (push), an attractant based on the synergistic effect of synthetic host plant volatiles and the aggregation pheromone (pull), and a combination of the attractant and the potential repellent. We adopted two different monitoring systems, sticky traps and camera traps, to assess the spatial distribution of the bean bugs. The attractant and repellents were strategically deployed, by putting the repellent in the center of soybean plot while the attractants were placed at the edge of the plot. In soybean plots treated with only attractants at the edge, the number of bean bugs was significantly higher in both soybean and edge areas than those of control plots. In contrast, the number of attracted bean bugs to soybean area significantly decreased in the push–pull treated plot, verified by both sticky trap and camera trap methods. This strategy could prevent colonization and population establishment of the bean bugs in soybean fields as part of an integrated pest management.
DOI: 10.6084/m9.figshare.24448471.v1
title: A push–pull strategy for controlling <i>Riptortus pedestris</i> (Hemiptera: Alydidae) using host plant semiochemicals

description: <i>Riptortus pedestris</i> is a major pest of soybean in East Asia that feeds on maturing seeds, reducing nutritional quality and causing seed abortion. Aggregation pheromone of the bean bug has been conventionally used as a lure for mass-trapping, but the control practices, used by farmers and recommended by the manufacturer can increase infestation in soybean fields. Here we investigated the efficacy of soybean semiochemical blend as a repellent incorporated with an attractant blend to develop a push–pull strategy. The efficacy of potential repellents was tested in a soybean field by evaluating three control strategies: a potential repellent (push), an attractant based on the synergistic effect of synthetic host plant volatiles and the aggregation pheromone (pull), and a combination of the attractant and the potential repellent. We adopted two different monitoring systems, sticky traps and camera traps, to assess the spatial distribution of the bean bugs. The attractant and repellents were strategically deployed, by putting the repellent in the center of soybean plot while the attractants were placed at the edge of the plot. In soybean plots treated with only attractants at the edge, the number of bean bugs was significantly higher in both soybean and edge areas than those of control plots. In contrast, the number of attracted bean bugs to soybean area significantly decreased in the push–pull treated plot, verified by both sticky trap and camera trap methods. This strategy could prevent colonization and population establishment of the bean bugs in soybean fields as part of an integrated pest management.
DOI: 10.6084/m9.figshare.24638878
title: Mitochondrial genome-based synthesis and timeline of Eurasian otter (<i>Lutra lutra</i>) phylogeography

description: Eurasian otters (<i>Lutra lutra</i>) have a broad distribution across Eurasia, but biogeographic data outside of western Europe is limited to disconnected pockets. Based on current subspecies designations, Asia appears to harbour a large proportion of the species’ diversity, with 10 of 12 Eurasian otter subspecies found in Asia. Here we provide a range-wide synthesis of mitochondrial data, inferring a timeline and pattern of phylogeographic signals. Whole mitochondrial genomes of 27 Eurasian otters across 4 subspecies are presented from newly generated data (<i>n</i> = 6; 4 from Korea, 1 from Hong Kong and 2 from UK), assembled from the Sequence Read Archive (<i>n</i> = 4), and sourced from GenBank (<i>n</i> = 17). We then combined whole mitochondrial genome results with cytochrome <i>b</i> data to increase the sample size and contextualise our results with prior studies. We identified five distinct lineages that were discordant with current subspecies classification. Phylogenetic dating revealed that the earliest diverging lineage was the Japanese lineage, with remaining lineages diverging ≥0.08 million years ago. Mitochondrial diversity calculated by sample locations seemed mainly driven by the presence of multiple lineages. When grouping samples by lineage, genetic diversity was highest in Lineage 1 (primarily found in China and Laos), followed by Lineage 2 (primarily found in Korea), and lowest diversity identified in Lineage 3 (primarily found in Europe). Our findings highlight previously undetected lineage diversity within Eurasian otters, but also the need for further taxonomic and genomic evaluation of the species in Asia. The identified unique, distinct lineages of Eurasian otters also warrant urgent conservation attention.
DOI: 10.6084/m9.figshare.24962454
title: Supplementary materials: Discharges against medical advice and 30-day healthcare costs: an analysis of commercially insured adult

description: <b>These are peer-reviewed supplementary material for the article 'Discharges against medical advice and 30-day healthcare costs: an analysis of commercially insured adults' published in the </b><b><i>Journal of Comparative Effectiveness Research</i></b><b>.</b><b>Appendix Table 1.</b> A comparison of standardized mean differences for baseline covariates between matched and unmatched samples.<b>Figure S1. </b>Histogram of 30-day healthcare costs for the total matched sample.<b>Figure S2.</b> Histogram of 30-day inpatient readmission costs for the total matched sample.<b>Figure S3. </b>Histogram of 30-day emergency department visit costs for the total matched sample.<b>Figure S4.</b> Histogram of 30-day physician office visit costs for the total matched sample.<b>Figure S5.</b> Histogram of 30-day non-physician outpatient encounter costs for the total matched sample.<b>Figure S6. </b>Histogram of 30-day prescription drug fill costs for the total matched sample.<b>Figure S7.</b> Consort diagram displaying study inclusion and exclusion criteria for the study sample.<b>Summary: </b><b>Aim:</b> Prior literature detailing the consequences of a discharge against medical advice (DAMA) has not focused on costs. We examine costs following a DAMA. <b>Materials & methods:</b> This retrospective cohort study utilized the IQVIA PharMetrics<sup>®</sup> Plus database to identify adults hospitalized during 2007–2015. We compared 30-day postdischarge healthcare costs between matched DAMA and routinely discharged groups. <b>Results:</b> Thirty-day healthcare costs for the DAMA group were US$1078 (95% CI: US$434–1730) higher, driven by inpatient readmissions (US$979; 95% CI: US$415–1543) and emergency department visits (US$79; 95% CI: US$56–102). Costs due to prescription drug fills were lower in the DAMA group. <b>Conclusion:</b> A DAMA was associated with higher 30-day postdischarge healthcare costs compared with routine discharges.
DOI: 10.6084/m9.figshare.24962454.v1
title: Supplementary materials: Discharges against medical advice and 30-day healthcare costs: an analysis of commercially insured adult

description: <b>These are peer-reviewed supplementary material for the article 'Discharges against medical advice and 30-day healthcare costs: an analysis of commercially insured adults' published in the </b><b><i>Journal of Comparative Effectiveness Research</i></b><b>.</b><b>Appendix Table 1.</b> A comparison of standardized mean differences for baseline covariates between matched and unmatched samples.<b>Figure S1. </b>Histogram of 30-day healthcare costs for the total matched sample.<b>Figure S2.</b> Histogram of 30-day inpatient readmission costs for the total matched sample.<b>Figure S3. </b>Histogram of 30-day emergency department visit costs for the total matched sample.<b>Figure S4.</b> Histogram of 30-day physician office visit costs for the total matched sample.<b>Figure S5.</b> Histogram of 30-day non-physician outpatient encounter costs for the total matched sample.<b>Figure S6. </b>Histogram of 30-day prescription drug fill costs for the total matched sample.<b>Figure S7.</b> Consort diagram displaying study inclusion and exclusion criteria for the study sample.<b>Summary: </b><b>Aim:</b> Prior literature detailing the consequences of a discharge against medical advice (DAMA) has not focused on costs. We examine costs following a DAMA. <b>Materials & methods:</b> This retrospective cohort study utilized the IQVIA PharMetrics<sup>®</sup> Plus database to identify adults hospitalized during 2007–2015. We compared 30-day postdischarge healthcare costs between matched DAMA and routinely discharged groups. <b>Results:</b> Thirty-day healthcare costs for the DAMA group were US$1078 (95% CI: US$434–1730) higher, driven by inpatient readmissions (US$979; 95% CI: US$415–1543) and emergency department visits (US$79; 95% CI: US$56–102). Costs due to prescription drug fills were lower in the DAMA group. <b>Conclusion:</b> A DAMA was associated with higher 30-day postdischarge healthcare costs compared with routine discharges.
DOI: 10.6084/m9.figshare.24961974
title: Supplement, data and code: "Guiltily indebted? How a word is linked to individual borrowing"

description: This fileset contains the supplement, the data and the replication code for the paper "Guiltily indebted? How a word is linked to individual borrowing" Abstract: Using data from the World Values Survey, we show that individuals who speak a language in which the same word is used for both (financial) debt and (moral) guilt have a statistically significant and economically meaningful lower likelihood of borrowing money. This relationship holds even after controlling for a range of covariates, fixed effects, grammatical future tense reference, and the Germanic language family. Our results suggest that the synonymity of debt and guilt may be a hitherto overlooked aspect in explaining borrowing behaviour.
DOI: 10.5517/ccdc.csd.cc2dmrd6
title: CCDC 2223518: Experimental Crystal Structure Determination

description: Related Article: Yu-Qing Wang, Yan Luo, Guan-Cheng Xu|2023|Cryst.Growth Des.|24|532|doi:10.1021/acs.cgd.3c01214
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2dmsrl
title: CCDC 2223560: Experimental Crystal Structure Determination

description: Related Article: Yu-Qing Wang, Yan Luo, Guan-Cheng Xu|2023|Cryst.Growth Des.|24|532|doi:10.1021/acs.cgd.3c01214
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2c5m7f
title: CCDC 2180144: Experimental Crystal Structure Determination

description: Related Article: Hai-Ling Wang, Qiu-Xiang Yu, Zhong-Hong Zhu, Xing-Lin Lu, Yun-Lan Li, Fu-Pei Liang, Hua-Hong Zou|2023|Inorg.Chem.|62|5863|doi:10.1021/acs.inorgchem.3c00743
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2c5m9h
title: CCDC 2180146: Experimental Crystal Structure Determination

description: Related Article: Hai-Ling Wang, Qiu-Xiang Yu, Zhong-Hong Zhu, Xing-Lin Lu, Yun-Lan Li, Fu-Pei Liang, Hua-Hong Zou|2023|Inorg.Chem.|62|5863|doi:10.1021/acs.inorgchem.3c00743
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2gkct7
title: CCDC 2280819: Experimental Crystal Structure Determination

description: Related Article: Dionisio Poveda, Ángela Vivancos, Delia Bautista, Pablo González-Herrero|2023|Inorg.Chem.|62|20987|doi:10.1021/acs.inorgchem.3c02399
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2gkcv8
title: CCDC 2280820: Experimental Crystal Structure Determination

description: Related Article: Dionisio Poveda, Ángela Vivancos, Delia Bautista, Pablo González-Herrero|2023|Inorg.Chem.|62|20987|doi:10.1021/acs.inorgchem.3c02399
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2gkcw9
title: CCDC 2280821: Experimental Crystal Structure Determination

description: Related Article: Dionisio Poveda, Ángela Vivancos, Delia Bautista, Pablo González-Herrero|2023|Inorg.Chem.|62|20987|doi:10.1021/acs.inorgchem.3c02399
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.35090/gatech/72958
title: Data for the publication "Pressure control of magnetic order and excitations in the pyrochlore antiferromagnet MgCr2O4"
DOI: 10.6084/m9.figshare.24570361
title: Fast Matrix-Free Methods for Model-Based Personalized Synthetic MR Imaging

description: Synthetic Magnetic Resonance (MR) imaging predicts images at new design parameter settings from a few observed MR scans. Model-based methods, that use both the physical and statistical properties underlying the MR signal and its acquisition, can predict images at any setting from as few as three scans, allowing it to be used in individualized patient- and anatomy-specific contexts. However, the estimation problem in model-based synthetic MR imaging is ill-posed and so regularization, in the form of correlated Gaussian markov random fields, is imposed on the voxel-wise spin-lattice relaxation time, spin-spin relaxation time and the proton density underlying the MR image. We develop theoretically sound but computationally practical matrix-free estimation methods for synthetic MR imaging. Our evaluations demonstrate superior performance of our methods in currently-used clinical settings when compared to existing model-based and deep learning methods. Moreover, unlike deep learning approaches, our fast methodology can synthesize needed images during patient visits, with good estimation and prediction accuracy and consistency. An added strength of our model-based approach, also developed and illustrated here, is the accurate estimation of standard errors of regional contrasts in the synthesized images. A R package symr implements our methodology. Supplementary materials for this article are available online.