cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3202051.v1
title: 20 September 2014 VID00043 Discussion

description: Discussion notes on video VID00043 taken on 20 September 2014. This video is notable for documenting an eye-to-eye observation of an anomalous large non-human primate.<br>Original and two versions of adjusted frames for the entire VID00043 are posted in separate folders. For convenience, additional processed images are made available in this folder.<br>The original video is located in the 20 September 2014 Field Notes folder. For convenience, it is also included here along with two enhanced versions of the video. These are described in the Discussion document.<br>See also 20 September 2014 Field Notes for additional details on the data collection.<br>
DOI: 10.6084/m9.figshare.3202072.v2
title: Maize RefGen_v3 GO Annotations

description: These are the GO Annotations downloaded from Gramene and Phytozome for Maize REfGen_v3.<br><br><b>Please cite Gramene and Phytozome projects if you use these datasets</b><br>
DOI: 10.6084/m9.figshare.3202072.v1
title: gramene - maize_v3_go.zip

description: These are the GO Annotations downloaded from Gramene and Phytozome for Maize REfGen_v3
DOI: 10.6084/m9.figshare.3201934
title: Switching of deformation modes in soft mechanical metamaterials

description: Mechanical metamaterials have attracted tremendous interests, owing to their fruitfulness of underlying physics and mechanics as well as diverse potential applications. Conventional soft mechanical metamaterials contain periodic distribution of holes having identical sizes, which can only display one mechanical function. Periodically dispersing a regular pattern of through-holes with two sizes into an elastomer results in metamaterials with more mechanical functions and deformation scenarios. We numerically investigate the deformation behaviors of this type of metamaterials. Switching of modes from the buckling-dominated deformation to a loss-of-instability deformation is emphasized. Replacing the pattern of holes with the same sizes by a pattern of holes with two sizes imposes higher compliance and even loss of negative Poisson’s ratio of the material.
DOI: 10.6084/m9.figshare.3202051.v2
title: 20 September 2014 VID00043 Discussion

description: Discussion notes on video VID00043 taken on 20 September 2014. This video is notable for documenting an eye-to-eye observation of an anomalous large non-human primate.<br>Original and two versions of adjusted frames for the entire VID00043 are posted in separate folders. For convenience, additional processed images are made available in this folder.<br>The original video is located in the 20 September 2014 Field Notes folder. For convenience, it is also included here along with two enhanced versions of the video. These are described in the Discussion document.<br>See also 20 September 2014 Field Notes for additional details on the data collection.<br>
DOI: 10.6084/m9.figshare.3201934.v1
title: Switching of deformation modes in soft mechanical metamaterials

description: Mechanical metamaterials have attracted tremendous interests, owing to their fruitfulness of underlying physics and mechanics as well as diverse potential applications. Conventional soft mechanical metamaterials contain periodic distribution of holes having identical sizes, which can only display one mechanical function. Periodically dispersing a regular pattern of through-holes with two sizes into an elastomer results in metamaterials with more mechanical functions and deformation scenarios. We numerically investigate the deformation behaviors of this type of metamaterials. Switching of modes from the buckling-dominated deformation to a loss-of-instability deformation is emphasized. Replacing the pattern of holes with the same sizes by a pattern of holes with two sizes imposes higher compliance and even loss of negative Poisson’s ratio of the material.
DOI: 10.6084/m9.figshare.3201838
title: Efficiency of genome-wide association study in random cross populations

description: Compacted data files (.rar) used in the study "<b>Efficiency of genome-wide association study in random cross populations</b>". Details on the files content are in the Description of the data files.txt file.<br>
DOI: 10.6084/m9.figshare.3201811
title: Ultrastructural features of spermatozoa and their phylogenetic application in Zaprionus (Diptera, Drosophilidae)

description: The genus <i>Zaprionus</i> consists of approximately 60 species of drosophilids that are native to the Afrotropical region. The phylogenetic position of <i>Zaprionus</i> within the Drosophilidae family is still unresolved. In the present study, ultrastructural features of spermatozoa of 6 species of <i>Zaprionus</i> as well as the species <i>Drosophila willistoni</i> and <i>Scaptodrosophila latifasciaeformis</i> were analyzed. The ultrastructure revealed that the species have the same flagellar ultrastructure. Two mitochondrial derivatives, one larger than the other, close to the axoneme were present, primarily in <i>D. willistoni</i> (subgenus Sophophora). Except for <i>Z. davidi</i> and <i>Z. tuberculatus</i>, the analyzed species had paracrystalline material in both mitochondrial derivatives. Moreover, the testes showed 64 spermatozoa per bundle in all of the species. In the cluster analysis, 6 <i>Zaprionus</i> species were grouped closely, but there were some incongruent positions in the cladogram. The results indicated that sperm ultrastructure is an important tool for elucidating the phylogeny and taxonomy of insects.
DOI: 10.6084/m9.figshare.3201811.v1
title: Ultrastructural features of spermatozoa and their phylogenetic application in Zaprionus (Diptera, Drosophilidae)

description: The genus <i>Zaprionus</i> consists of approximately 60 species of drosophilids that are native to the Afrotropical region. The phylogenetic position of <i>Zaprionus</i> within the Drosophilidae family is still unresolved. In the present study, ultrastructural features of spermatozoa of 6 species of <i>Zaprionus</i> as well as the species <i>Drosophila willistoni</i> and <i>Scaptodrosophila latifasciaeformis</i> were analyzed. The ultrastructure revealed that the species have the same flagellar ultrastructure. Two mitochondrial derivatives, one larger than the other, close to the axoneme were present, primarily in <i>D. willistoni</i> (subgenus Sophophora). Except for <i>Z. davidi</i> and <i>Z. tuberculatus</i>, the analyzed species had paracrystalline material in both mitochondrial derivatives. Moreover, the testes showed 64 spermatozoa per bundle in all of the species. In the cluster analysis, 6 <i>Zaprionus</i> species were grouped closely, but there were some incongruent positions in the cladogram. The results indicated that sperm ultrastructure is an important tool for elucidating the phylogeny and taxonomy of insects.
DOI: 10.6084/m9.figshare.3201838.v1
title: Efficiency of genome-wide association study in open-pollinated populations

description: Compacted data files (.rar) used in the study "<b>Efficiency of genome-wide association study in open-pollinated populations</b>". Details on the files content are in the G3 Genes Genomes Genetics supplemental file S1.<br>
DOI: 10.6084/m9.figshare.3201838.v3
title: Efficiency of genome-wide association study in random cross populations

description: Compacted data files (.rar) used in the study "<b>Efficiency of genome-wide association study in random cross populations</b>". Details on the files content are in the Description of the data files.txt file.<br>
DOI: 10.6084/m9.figshare.3201838.v2
title: Efficiency of genome-wide association study in open-pollinated populations

description: Compacted data files (.rar) used in the study "<b>Efficiency of genome-wide association study in open-pollinated populations</b>". Details on the files content are in the Description of the data files.txt file.<br>
DOI: 10.6084/m9.figshare.3201802
title: Outcomes of follow-up care after an emergency department visit among pediatric asthmatics in the military health system

description: <i>Background and Objectives</i>: Asthma exacerbations frequently trigger emergency department (ED) visits. Guidelines recommend timely follow-up after an ED visit for asthma, however, other studies have questioned the quality of follow-up care and their effect on subsequent ED utilization. We evaluated follow-up care on asthma outcomes in pediatric asthmatics enrolled in the Military Health System (MHS) after an ED visit for asthma. <i>Methods</i>: This retrospective study utilized MHS data to evaluate 2–17-year-old persistent asthmatics with an ED visit for asthma between 2010–2012. Demographics, medication dispensing, and subsequent asthma related ED and hospital utilization were compared between those with or without a 28-day follow-up appointment. <i>Results</i>: 10,460 of 88,837 persistent asthmatics met inclusion criteria for an asthma ED visit. 4,964 (47.5%) had ≥ 1 follow-up visit. In the 29–365 days after their ED visit, 21.1% of the follow-up cohort required an ED re-visit compared to 24.0% of the patients without follow-up. Follow-up care was associated with a reduction in ED re-visits (adjusted hazard ratio 0.86; 95% confidence interval 0.79, 0.93). Controller medications were dispensed to 76.0% of the follow-up cohort within 90 days of their ED visit compared to 49.7% in the group without follow-up. <i>Conclusions</i>: Despite universal access to healthcare, less than half of pediatric MHS asthma patients had follow-up within 28 days of an ED visit. Those with follow-up were more likely to fill a controller medication within 90 days post-ED visit, and less likely to have an asthma ED re-visit in the subsequent year.
DOI: 10.6084/m9.figshare.3201814.v3
title: Development of marker genes for jasmonic acid signaling in shoots and roots of wheat

description: The jasmonic acid (JA) signaling pathway plays key roles in a diverse array of plant development, reproduction, and responses to biotic and abiotic stresses. Most of our understanding of the JA signaling pathway derives from the dicot model plant <i>Arabidopsis thaliana</i>, while corresponding knowledge in wheat is somewhat limited. In this study, the expression of 41 genes implicated in the JA signaling pathway has been assessed on 10 day-old bread wheat seedlings, 24 h, 48 h, and 72 h after methyl-jasmonate (MeJA) treatment using quantitative real-time PCR. The examined genes have been previously reported to be involved in JA biosynthesis and catabolism, JA perception and signaling, and pathogen defense in wheat shoots and roots. This study provides evidence to suggest that the effect of MeJA treatment is more prominent in shoots than roots of wheat seedlings, and substantial regulation of the JA pathway-dependent defense genes occurs at 72 h after MeJA treatment. Results show that the expression of 22 genes was significantly affected by MeJA treatment in wheat shoots. However, only <i>PR1.1</i> and <i>PR3</i> were significantly differentially expressed in wheat roots, both at 24 h post-MeJA treatment, with other genes showing large variation in their gene expression in roots. While providing marker genes on JA signaling in wheat, future work may focus on elucidating the regulatory function of JA-modulated transcription factors, some of which have well-studied potential orthologs in <i>Arabidopsis</i>.
DOI: 10.6084/m9.figshare.3201802.v2
title: Outcomes of follow-up care after an emergency department visit among pediatric asthmatics in the military health system

description: <i>Background and Objectives</i>: Asthma exacerbations frequently trigger emergency department (ED) visits. Guidelines recommend timely follow-up after an ED visit for asthma, however, other studies have questioned the quality of follow-up care and their effect on subsequent ED utilization. We evaluated follow-up care on asthma outcomes in pediatric asthmatics enrolled in the Military Health System (MHS) after an ED visit for asthma. <i>Methods</i>: This retrospective study utilized MHS data to evaluate 2–17-year-old persistent asthmatics with an ED visit for asthma between 2010–2012. Demographics, medication dispensing, and subsequent asthma related ED and hospital utilization were compared between those with or without a 28-day follow-up appointment. <i>Results</i>: 10,460 of 88,837 persistent asthmatics met inclusion criteria for an asthma ED visit. 4,964 (47.5%) had ≥ 1 follow-up visit. In the 29–365 days after their ED visit, 21.1% of the follow-up cohort required an ED re-visit compared to 24.0% of the patients without follow-up. Follow-up care was associated with a reduction in ED re-visits (adjusted hazard ratio 0.86; 95% confidence interval 0.79, 0.93). Controller medications were dispensed to 76.0% of the follow-up cohort within 90 days of their ED visit compared to 49.7% in the group without follow-up. <i>Conclusions</i>: Despite universal access to healthcare, less than half of pediatric MHS asthma patients had follow-up within 28 days of an ED visit. Those with follow-up were more likely to fill a controller medication within 90 days post-ED visit, and less likely to have an asthma ED re-visit in the subsequent year.
DOI: 10.6084/m9.figshare.3201802.v1
title: Outcomes of Follow-Up Care After an Emergency Department Visit Among Pediatric Asthmatics in the Military Health System

description: <b>Background and Objectives</b>: Asthma exacerbations frequently trigger emergency department (ED) visits. Guidelines recommend timely follow-up after an ED visit for asthma, however, other studies have questioned the quality of follow-up care and their effect on subsequent ED utilization. We evaluated follow-up care on asthma outcomes in pediatric asthmatics enrolled in the Military Health System (MHS) after an ED visit for asthma. <b>Methods</b>: This retrospective study utilized MHS data to evaluate 2–17 year old persistent asthmatics with an ED visit for asthma between 2010–2012. Demographics, medication dispensing, and subsequent asthma related ED and hospital utilization were compared between those with or without a 28 day follow-up appointment. <b>Results</b>: 10,460 of 88,837 persistent asthmatics met inclusion criteria for an asthma ED visit. 4,964 (47.5%) had ≥ 1 follow-up visit. In the 29–365 days after their ED visit, 21.1% of the follow-up cohort required an ED re-visit compared to 24.0% of the patients without follow-up. Follow-up care was associated with a reduction in ED re-visits (adjusted hazard ratio 0.86; 95% confidence interval 0.79, 0.93). Controller medications were dispensed to 76.0% of the follow-up cohort within 90 days of their ED visit compared to 49.7% in the group without follow-up. <b>Conclusions</b>: Despite universal access to healthcare, less than half of pediatric MHS asthma patients had follow-up within 28 days of an ED visit. Those with follow-up were more likely to fill a controller medication within 90 days post ED visit, and less likely to have an asthma ED re-visit in the subsequent year.
DOI: 10.6084/m9.figshare.3201814.v2
title: Development of marker genes for jasmonic acid signaling in shoots and roots of wheat

description: The jasmonic acid (JA) signaling pathway plays key roles in a diverse array of plant development, reproduction, and responses to biotic and abiotic stresses. Most of our understanding of the JA signaling pathway derives from the dicot model plant <i>Arabidopsis thaliana</i>, while corresponding knowledge in wheat is somewhat limited. In this study, the expression of 41 genes implicated in the JA signaling pathway has been assessed on 10 day-old bread wheat seedlings, 24 h, 48 h, and 72 h after methyl-jasmonate (MeJA) treatment using quantitative real-time PCR. The examined genes have been previously reported to be involved in JA biosynthesis and catabolism, JA perception and signaling, and pathogen defense in wheat shoots and roots. This study provides evidence to suggest that the effect of MeJA treatment is more prominent in shoots than roots of wheat seedlings, and substantial regulation of the JA pathway-dependent defense genes occurs at 72 h after MeJA treatment. Results show that the expression of 22 genes was significantly affected by MeJA treatment in wheat shoots. However, only <i>PR1.1</i> and <i>PR3</i> were significantly differentially expressed in wheat roots, both at 24 h post-MeJA treatment, with other genes showing large variation in their gene expression in roots. While providing marker genes on JA signaling in wheat, future work may focus on elucidating the regulatory function of JA-modulated transcription factors, some of which have well-studied potential orthologs in <i>Arabidopsis</i>.
DOI: 10.6084/m9.figshare.3201547
title: Correlation of Aqueous Humor Lysyl Oxidase Activity with TGF-ß Levels and LOXL1 Genotype in Pseudoexfoliation

description: <i>Purpose</i>: Pseudoexfoliation (PXF) is a microfibrillopathy involving disordered elastogenesis. Abnormal extracellular matrix (ECM) production underlies the pathophysiology of PXF. The enzyme Lysyl oxidase (LOX) and its isoforms are known to cross-link the elastin and collagen. Though the etiopathogensis of PXF is not well understood, studies report on the genetic risk involving <i>LOXL1</i> gene. This study aims to screen LOXL1 coding variants rs1048661 and rs3825942 in the South Indian population and the implication of the single nucleotide polymorphism (SNP) with LOX activity. The levels of transforming growth factor β (TGF-β) in aqueous humor and its correlation with the LOX activity were also examined.<i>Methods</i>: Blood, plasma, and aqueous aspirates were prospectively collected from PXF cases with and without glaucoma and cataract cases as controls. DNA was extracted from 48 PXF cases without glaucoma, 12 PXF cases with glaucoma, and 40 age-matched cataract-alone controls without PXF/glaucoma for analyzing LOX SNPs. LOX activity was measured in aqueous humor and plasma of 30 PXF cases without glaucoma, 24 age-matched cataract-alone controls without PXF/glaucoma, and 14 PXF cases with glaucoma. Protein levels of LOX, LOXL1, LOXL2, and total TGF-β were estimated in plasma and aqueous humor by ELISA.<i>Results</i>: The specific activity of LOX in aqueous humor was found to be significantly lowered in PXF cases compared with cataract-alone controls (<i>p</i> = 0.014). This decrease in LOX activity in PXF cases was associated with high-risk GG haplotype. However, this was not statistically significant and a larger sample size is warranted. TGF-β1 and TGF-β2 negatively correlated with LOX activity in aqueous humor (<i>p</i> = 0.028; <i>p</i> = 0.046, respectively).<i>Conclusions</i>: The LOXL1 SNPs, rs1048661 and rs3825942, are associated with PXF in the South Indian population correlating with lowered LOX activity in the aqueous humor. The increased level of total TGF-β in the aqueous humor of PXF cases is possibly associated with LOX regulation which needs further investigation.
DOI: 10.6084/m9.figshare.3201559
title: Functional Single Nucleotide Polymorphisms (SNPs) in the Genes Encoding the Human Deoxyribonuclease (DNase) Family Potentially Relevant to Autoimmunity

description: <b>Objective</b>: To continue our previous investigations, we have extensively investigated the function of the 61, 41, and 35 non-synonymous single nucleotide polymorphisms (SNPs) in the human genes encoding <i>DNASE1, DNASE1L3</i>, and <i>DNASE2</i>, respectively, potentially relevant to autoimmune diseases. <b>Methods</b>: The site-directed mutagenesis was employed to amino acid–substituted constructs corresponding to each SNP. The COS-7 cells were transfected with each vector and DNase activity was assayed by the single radial enzyme diffusion method. By using PolyPhen-2, changes in the DNase function of each non-synonymous SNP were predicted. Genotyping of all the non-synonymous SNPs was performed in 14 different populations including 3 ethnic groups using the polymerase chain reaction followed by the restriction fragment length polymorphism method. <b>Results</b>: Expression analysis demonstrated these SNPs to be classified into four categories with regard to the effect on DNase activity: SNPs not affecting the activity level, ones reducing it, ones abolishing it, and ones elevating it. In particular, 9, 5, and 4 SNPs producing a loss-of-function variant of the enzymes in <i>DNASE1, DNASE1L3</i>, and <i>DNASE2</i>, respectively, were confirmed. SNPs producing DNase loss of function can be estimated by PolyPhen-2 to be “probably damaging” with a high accuracy of prediction. Almost all of these functional SNPs producing a loss of function or substantially low activity-harboring forms exhibited a mono-allelic distribution in all of the populations. <b>Conclusion</b>: A minor allele of functional SNPs, despite the remarkably low genetic heterogeneity of the SNPs, might be a genetic risk factor for autoimmune diseases.
DOI: 10.6084/m9.figshare.3201547.v1
title: Correlation of Aqueous Humor Lysyl Oxidase Activity with TGF-ß Levels and LOXL1 Genotype in Pseudoexfoliation

description: <i>Purpose</i>: Pseudoexfoliation (PXF) is a microfibrillopathy involving disordered elastogenesis. Abnormal extracellular matrix (ECM) production underlies the pathophysiology of PXF. The enzyme Lysyl oxidase (LOX) and its isoforms are known to cross-link the elastin and collagen. Though the etiopathogensis of PXF is not well understood, studies report on the genetic risk involving <i>LOXL1</i> gene. This study aims to screen LOXL1 coding variants rs1048661 and rs3825942 in the South Indian population and the implication of the single nucleotide polymorphism (SNP) with LOX activity. The levels of transforming growth factor β (TGF-β) in aqueous humor and its correlation with the LOX activity were also examined.<i>Methods</i>: Blood, plasma, and aqueous aspirates were prospectively collected from PXF cases with and without glaucoma and cataract cases as controls. DNA was extracted from 48 PXF cases without glaucoma, 12 PXF cases with glaucoma, and 40 age-matched cataract-alone controls without PXF/glaucoma for analyzing LOX SNPs. LOX activity was measured in aqueous humor and plasma of 30 PXF cases without glaucoma, 24 age-matched cataract-alone controls without PXF/glaucoma, and 14 PXF cases with glaucoma. Protein levels of LOX, LOXL1, LOXL2, and total TGF-β were estimated in plasma and aqueous humor by ELISA.<i>Results</i>: The specific activity of LOX in aqueous humor was found to be significantly lowered in PXF cases compared with cataract-alone controls (<i>p</i> = 0.014). This decrease in LOX activity in PXF cases was associated with high-risk GG haplotype. However, this was not statistically significant and a larger sample size is warranted. TGF-β1 and TGF-β2 negatively correlated with LOX activity in aqueous humor (<i>p</i> = 0.028; <i>p</i> = 0.046, respectively).<i>Conclusions</i>: The LOXL1 SNPs, rs1048661 and rs3825942, are associated with PXF in the South Indian population correlating with lowered LOX activity in the aqueous humor. The increased level of total TGF-β in the aqueous humor of PXF cases is possibly associated with LOX regulation which needs further investigation.