cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3113017
title: New roles for the <i>GLUTAMATE RECEPTOR-LIKE 3.3, 3.5</i>, and <i>3.6</i> genes as on/off switches of wound-induced systemic electrical signals

description: Wounding induces systemic potentials in <i>Arabidopsis thaliana</i> that can be abolished by concomitant suppression of the <i>GLUTAMATE RECEPTOR-LIKE GLR3.3</i> and <i>GLR3.6 g</i>enes. However, the roles of specific GLR channels to these potentials remain unclear. Here I applied the Electrical Penetration Graph (EPG) to study the contribution of three GLR channels to wound-induced, systemically propagated electrical potentials in <i>Arabidopsis thaliana</i>. In contrast to recordings made with conventional rigs for whole-plant electrophysiology, the EPG allows for the unambiguous distinction of the phloem-propagated action potential (AP) from the electrical activity outside of the phloem. The data reported here suggest that: (a) the transmission of wound-induced, phloem-propagated AP to neighbor leaves, requires expression of <i>GLR3.3</i> or <i>GLR3.6</i>, whereas <i>GLR3.5</i> prevents its transmission to non-neighbor leaves; (b) the generation of wound-induced electrical signals outside the phloem network depends on <i>GLR3.6</i> expression; and (c) wound-induced systemic potentials initiated in the shoot are transmitted to the root in the adult plant, which suggests a role for these electrical signals in coordinating the plant defenses in the shoot and in the root. Here, I propose a model for wound-induced systemic electrical signals at the molecular, cellular and anatomical level. In this model, <i>GLR3.3</i> and <i>GLR3.6</i> function as on switches for the propagation of wound-induced potentials beyond the wounded leaf, while <i>GLR3.5</i> functions as an off switch that prevents the propagation of wound-induced electrical potentials to distal, non-neighbor leaves.
DOI: 10.6084/m9.figshare.3113020.v2
title: The DNA methylation profile of activated human natural killer cells

description: Natural killer (NK) cells are now recognized to exhibit characteristics akin to cells of the adaptive immune system. The generation of adaptive memory is linked to epigenetic reprogramming including alterations in DNA methylation. The study herein found reproducible genome wide DNA methylation changes associated with human NK cell activation. Activation led predominately to CpG hypomethylation (81% of significant loci). Bioinformatics analysis confirmed that non-coding and gene-associated differentially methylated sites (DMS) are enriched for immune related functions (i.e., immune cell activation). Known DNA methylation-regulated immune loci were also identified in activated NK cells (e.g., <i>TNFA, LTA, IL13, CSF2</i>). Twenty-one loci were designated high priority and further investigated as potential markers of NK activation. <i>BHLHE40</i> was identified as a viable candidate for which a droplet digital PCR assay for demethylation was developed. The assay revealed high demethylation in activated NK cells and low demethylation in naïve NK, T- and B-cells. We conclude the NK cell methylome is plastic with potential for remodeling. The differentially methylated region signature of activated NKs revealed similarities with T cell activation, but also provided unique biomarker candidates of NK activation, which could be useful in epigenome-wide association studies to interrogate the role of NK subtypes in global methylation changes associated with exposures and/or disease states.
DOI: 10.6084/m9.figshare.3113008.v1
title: Involvement of an SRF-MADS protein McmA in regulation of extracellular enzyme production and asexual/sexual development in <i>Aspergillus nidulans</i>

description: SRF-MADS proteins are transcription factors conserved among eukaryotes that regulate a variety of cellular functions; however, their physiological roles are still not well understood in filamentous fungi. Effects of a mutation in <i>mcmA</i> gene that encodes the sole SRF-MADS protein in the fungus <i>Aspergillus nidulans</i> were examined by RNA sequencing. Sequencing data revealed that expression levels of cellulase genes were significantly decreased by the mutation as reported previously. However, expression levels of various hemicellulolytic enzyme genes, several extracellular protease genes, the <i>nosA</i> and <i>rosA</i> genes involved in sexual development, and AN4394 encoding an ortholog of EcdR involved in <i>Aspergillus oryzae</i> conidiation<i>,</i> were also significantly decreased by the mutation. As expected from the RNA sequencing data, the <i>mcmA</i> mutant had reduced protease production, cleistothecial development, and conidiation. This is the first report describing the involvement of SRF-MADS proteins in protease production in fungi, and asexual and sexual development in <i>Aspergillus</i>. McmA regulated cellulase/protease production and asexual/sexual development. The figure shows impaired development of fruiting bodies (cleistothecia) in the <i>mcmA</i> mutant.
DOI: 10.6084/m9.figshare.3112990
title: Purification and characterization of 2S albumin from <i>Nelumbo nucifera</i>

description: The 2S albumins are a group of seed storage proteins that have recently attracted considerable attention in the field of allergen science due to their allergenic potential. A new 2S albumin from seeds of <i>Nelumbo nucifera</i> (Nn-2S alb) was purified to electrophoretic homogeneity by the combination of ammonium sulfate fractionation, gel filtration, and ion exchange chromatography. The protein has a molecular mass of about 12 kDa estimated by SDS–PAGE, in good agreement with 12.5 ± 0.01 kDa determined by ESI–MS. Circular dichroism data showed that protein contained about 66% α-helices as estimated by K2D3, indicating that the protein was predominantly helical. The sedimentation coefficient (<i>s°</i><sub>20,w</sub>) of the predicted model was 1.72 ± 0.21 S. The predicted 3-dimensional structure of the Nn-2S alb revealed that the protein has a region of 12 amino acids which largely corresponds to the conserved immuno-dominant epitope of 2S allergens. Surface and ribbon representations of Nn-2S albumin model, showing hydrophobic cavity in gray (A), and hypervariable region (yellow in B) and the amino acids residues (sticks) that constitute hydrophobic cavity (B).
DOI: 10.6084/m9.figshare.3113020.v1
title: The dna methylation profile of activated human natural killer cells

description: Natural killer (NK) cells are now recognized to exhibit characteristics akin to cells of the adaptive immune system. The generation of adaptive memory is linked to epigenetic reprogramming including alterations in DNA methylation. The study herein found reproducible genome wide DNA methylation changes associated with human NK cell activation. Activation led predominately to CpG hypomethylation (81% of significant loci). Bioinformatics analysis confirmed that non-coding and gene-associated differentially methylated sites (DMS) are enriched for immune related functions (i.e., immune cell activation). Known DNA methylation-regulated immune loci were also identified in activated NK cells (e.g., <i>TNFA, LTA, IL13, CSF2</i>). Twenty-one loci were designated high priority and further investigated as potential markers of NK activation. <i>BHLHE40</i> was identified as a viable candidate for which a droplet digital PCR assay for demethylation was developed. The assay revealed high demethylation in activated NK cells and low demethylation in naïve NK, T- and B-cells. We conclude the NK cell methylome is plastic with potential for remodeling. The differentially methylated region signature of activated NKs revealed similarities with T cell activation, but also provided unique biomarker candidates of NK activation, which could be useful in epigenome-wide association studies to interrogate the role of NK subtypes in global methylation changes associated with exposures and/or disease states.
DOI: 10.6084/m9.figshare.3112990.v1
title: Purification and characterization of 2S albumin from <i>Nelumbo nucifera</i>

description: The 2S albumins are a group of seed storage proteins that have recently attracted considerable attention in the field of allergen science due to their allergenic potential. A new 2S albumin from seeds of <i>Nelumbo nucifera</i> (Nn-2S alb) was purified to electrophoretic homogeneity by the combination of ammonium sulfate fractionation, gel filtration, and ion exchange chromatography. The protein has a molecular mass of about 12 kDa estimated by SDS–PAGE, in good agreement with 12.5 ± 0.01 kDa determined by ESI–MS. Circular dichroism data showed that protein contained about 66% α-helices as estimated by K2D3, indicating that the protein was predominantly helical. The sedimentation coefficient (<i>s°</i><sub>20,w</sub>) of the predicted model was 1.72 ± 0.21 S. The predicted 3-dimensional structure of the Nn-2S alb revealed that the protein has a region of 12 amino acids which largely corresponds to the conserved immuno-dominant epitope of 2S allergens. Surface and ribbon representations of Nn-2S albumin model, showing hydrophobic cavity in gray (A), and hypervariable region (yellow in B) and the amino acids residues (sticks) that constitute hydrophobic cavity (B).
DOI: 10.6084/m9.figshare.3113017.v1
title: New roles for the <i>GLUTAMATE RECEPTOR-LIKE 3.3, 3.5</i>, and <i>3.6</i> genes as on/off switches of wound-induced systemic electrical signals

description: Wounding induces systemic potentials in <i>Arabidopsis thaliana</i> that can be abolished by concomitant suppression of the <i>GLUTAMATE RECEPTOR-LIKE GLR3.3</i> and <i>GLR3.6</i> genes. However, the roles of specific GLR channels to these potentials remain unclear. Here I applied the Electrical Penetration Graph (EPG) to study the contribution of three GLR channels to wound-induced, systemically propagated electrical potentials in <i>Arabidopsis thaliana</i>. In contrast to recordings made with conventional rigs for whole-plant electrophysiology, the EPG allows for the unambiguous distinction of the phloem-propagated action potential (AP) from the electrical activity outside of the phloem. The data reported here suggest that: (a) the transmission of wound-induced, phloem-propagated AP to neighbor leaves, requires expression of <i>GLR3.3</i> or <i>GLR3.6</i>, whereas <i>GLR3.5</i> prevents its transmission to non-neighbor leaves; (b) the generation of wound-induced electrical signals outside the phloem network depends on <i>GLR3.6</i> expression; and (c) wound-induced systemic potentials initiated in the shoot are transmitted to the root in the adult plant, which suggests a role for these electrical signals in coordinating the plant defenses in the shoot and in the root. Here, I propose a model for wound-induced systemic electrical signals at the molecular, cellular and anatomical level. In this model, <i>GLR3.3</i> and <i>GLR3.6</i> function as on switches for the propagation of wound-induced potentials beyond the wounded leaf, while <i>GLR3.5</i> functions as an off switch that prevents the propagation of wound-induced electrical potentials to distal, non-neighbor leaves.
DOI: 10.6084/m9.figshare.3112900
title: IREN, a novel EF-hand motif-containing nuclease, functions in the degradation of nuclear DNA during the hypersensitive response cell death in rice

description: The hypersensitive response (HR), a type of programmed cell death that is accompanied by DNA degradation and loss of plasma membrane integrity, is a common feature of plant immune responses. We previously reported that transcription of <i>IREN</i> which encodes a novel EF-hand containing plant nuclease is controlled by OsNAC4, a key positive regulator of HR cell death. Transient overexpression of IREN in rice protoplasts also led to rapid DNA fragmentation, while suppression of IREN using RNA interference showed remarkable decrease of DNA fragmentation during HR cell death. Maximum DNA degradation associated with the recombinant IREN was observed in the presence of Ca<sup>2+</sup> and Mg<sup>2+</sup> or Ca<sup>2+</sup> and Mn<sup>2+</sup>. Interestingly, DNA degradation mediated by the recombinant IREN was completely abolished by Zn<sup>2+</sup>, even when Ca<sup>2+</sup>, Mg<sup>2+</sup>, or Mn<sup>2+</sup> were present in the reaction buffer. These data indicate that IREN functions in the degradation of nuclear DNA during HR cell death. IREN, novel EF-hand containing plant nuclease, functions in the degradation of nuclear DNA during immune-related hypersensitive cell death.
DOI: 10.6084/m9.figshare.3112900.v1
title: IREN, a novel EF-hand motif-containing nuclease, functions in the degradation of nuclear DNA during the hypersensitive response cell death in rice

description: The hypersensitive response (HR), a type of programmed cell death that is accompanied by DNA degradation and loss of plasma membrane integrity, is a common feature of plant immune responses. We previously reported that transcription of <i>IREN</i> which encodes a novel EF-hand containing plant nuclease is controlled by OsNAC4, a key positive regulator of HR cell death. Transient overexpression of IREN in rice protoplasts also led to rapid DNA fragmentation, while suppression of IREN using RNA interference showed remarkable decrease of DNA fragmentation during HR cell death. Maximum DNA degradation associated with the recombinant IREN was observed in the presence of Ca<sup>2+</sup> and Mg<sup>2+</sup> or Ca<sup>2+</sup> and Mn<sup>2+</sup>. Interestingly, DNA degradation mediated by the recombinant IREN was completely abolished by Zn<sup>2+</sup>, even when Ca<sup>2+</sup>, Mg<sup>2+</sup>, or Mn<sup>2+</sup> were present in the reaction buffer. These data indicate that IREN functions in the degradation of nuclear DNA during HR cell death. IREN, novel EF-hand containing plant nuclease, functions in the degradation of nuclear DNA during immune-related hypersensitive cell death.
DOI: 10.6084/m9.figshare.3112843
title: Automatic classification model for Volunteered Geographic Information, applied to birds observer credibility

description: Data and code used in the research of automatic classification model for Volunteered Geographic Information, applied to birds observer credibility.<br><br>original data comes from http://ebird.org, here is the data used as imput and the R code.<br><br>GPL licence is only for the R code.<br>
DOI: 10.6084/m9.figshare.3112864.v2
title: Designing an evaluation framework for WFME basic standards for medical education

description: <b>Purpose</b>: To create an evaluation plan for the World Federation for Medical Education (WFME) accreditation standards for basic medical education. <b>Methods</b>: We conceptualized the 100 basic standards from “Basic Medical Education: WFME Global Standards for Quality Improvement: The 2012 Revision” as medical education program objectives. Standards were simplified into evaluable items, which were then categorized as inputs, processes, outputs and/or outcomes to generate a logic model and corresponding plan for data collection. <b>Results</b>: WFME standards posed significant challenges to evaluation due to complex wording, inconsistent formatting and lack of existing assessment tools. Our resulting logic model contained 244 items. Standard B 5.1.1 separated into 24 items, the most for any single standard. A large proportion of items (40%) required evaluation of more than one input, process, output and/or outcome. Only one standard (B 3.2.2) was interpreted as requiring evaluation of a program outcome. <b>Conclusions</b>: Current WFME standards are difficult to use for evaluation planning. Our analysis may guide adaptation and revision of standards to make them more evaluable. Our logic model and data collection plan may be useful to medical schools planning an institutional self-review and to accrediting authorities wanting to provide guidance to schools under their purview.
DOI: 10.6084/m9.figshare.3112840
title: Evaluation of SAMe-TT<sub>2</sub>R<sub>2</sub> score and other clinical factors influencing the quality of anticoagulation therapy in non-valvular atrial fibrillation: a nationwide study in Spain

description: <b>Objective</b>: To assess the major clinical factors affecting the quality of anticoagulation and evaluate the predictive value of the SAMe-TT<sub>2</sub>R<sub>2</sub> score to identify patients who will achieve a high average time in therapeutic range (T.T.R.) with vitamin K antagonist (V.K.A.) treatment. <b>Research design and methods</b>: This observational, cross-sectional, retrospective and nationwide multicenter study included 1524 patients from the primary care setting with non-valvular atrial fibrillation receiving V.K.A. (≥12 months). We performed a bivariate analysis to identify factors individually associated with the T.T.R. and a multiple regression analysis to identify the independent predictive factors. For the validation of the SAMe-TT<sub>2</sub>R<sub>2</sub> score, the receiver operating characteristic (R.O.C.) curve was calculated and the Hosmer–Lemeshow test was used to test calibration. <b>Results</b>: A total of 94.8% of patients received acenocumarol (4.8% warfarin). A progressive decrease in mean T.T.R. was found when the SAMe-TT<sub>2</sub>R<sub>2</sub> score increased from 0 points (72.1 ± 17.1%) to 4 points (64.1 ± 23.2%), <i>p</i> 2 and CHA<sub>2</sub>DS<sub>2</sub>-VASc, HAS-BLED) were also associated with the mean T.T.R. We found a significant association between low T.T.R. and the following clinical factors: female sex, three or more comorbidities, amiodarone treatment, dietary habits, bleeding history and the intake of ≥7 tablets per day besides V.K.A. (<i>p</i> 2R<sub>2</sub> score validation, the R.O.C. curve showed significant capability, although not high, of discriminating good anticoagulation control (T.T.R. ≥65%) with an area under the curve of 0.562 (95% C.I. 0.533–0.592, <i>p</i> p 2R<sub>2</sub> score were added. <b>Conclusion</b>: In this cohort, the SAMe-TT<sub>2</sub>R<sub>2</sub> score had a significant, although modest, ability to assess the likelihood of good international normalized ration (I.N.R.) control, and its predictive value might slightly improve by adding other simple clinical factors. Further research is needed to refine the predictive scales.
DOI: 10.6084/m9.figshare.3112864
title: Designing an evaluation framework for WFME basic standards for medical education

description: <b>Purpose</b>: To create an evaluation plan for the World Federation for Medical Education (WFME) accreditation standards for basic medical education. <b>Methods</b>: We conceptualized the 100 basic standards from “Basic Medical Education: WFME Global Standards for Quality Improvement: The 2012 Revision” as medical education program objectives. Standards were simplified into evaluable items, which were then categorized as inputs, processes, outputs and/or outcomes to generate a logic model and corresponding plan for data collection. <b>Results</b>: WFME standards posed significant challenges to evaluation due to complex wording, inconsistent formatting and lack of existing assessment tools. Our resulting logic model contained 244 items. Standard B 5.1.1 separated into 24 items, the most for any single standard. A large proportion of items (40%) required evaluation of more than one input, process, output and/or outcome. Only one standard (B 3.2.2) was interpreted as requiring evaluation of a program outcome. <b>Conclusions</b>: Current WFME standards are difficult to use for evaluation planning. Our analysis may guide adaptation and revision of standards to make them more evaluable. Our logic model and data collection plan may be useful to medical schools planning an institutional self-review and to accrediting authorities wanting to provide guidance to schools under their purview.
DOI: 10.6084/m9.figshare.3112840.v1
title: Evaluation of SAMe-TT<sub>2</sub>R<sub>2</sub> score and other clinical factors influencing the quality of anticoagulation therapy in non-valvular atrial fibrillation: a nationwide study in Spain

description: <b>Objective</b>: To assess the major clinical factors affecting the quality of anticoagulation and evaluate the predictive value of the SAMe-TT<sub>2</sub>R<sub>2</sub> score to identify patients who will achieve a high average time in therapeutic range (T.T.R.) with vitamin K antagonist (V.K.A.) treatment. <b>Research design and methods</b>: This observational, cross-sectional, retrospective and nationwide multicenter study included 1524 patients from the primary care setting with non-valvular atrial fibrillation receiving V.K.A. (≥12 months). We performed a bivariate analysis to identify factors individually associated with the T.T.R. and a multiple regression analysis to identify the independent predictive factors. For the validation of the SAMe-TT<sub>2</sub>R<sub>2</sub> score, the receiver operating characteristic (R.O.C.) curve was calculated and the Hosmer–Lemeshow test was used to test calibration. <b>Results</b>: A total of 94.8% of patients received acenocumarol (4.8% warfarin). A progressive decrease in mean T.T.R. was found when the SAMe-TT<sub>2</sub>R<sub>2</sub> score increased from 0 points (72.1 ± 17.1%) to 4 points (64.1 ± 23.2%), <i>p</i> 2 and CHA<sub>2</sub>DS<sub>2</sub>-VASc, HAS-BLED) were also associated with the mean T.T.R. We found a significant association between low T.T.R. and the following clinical factors: female sex, three or more comorbidities, amiodarone treatment, dietary habits, bleeding history and the intake of ≥7 tablets per day besides V.K.A. (<i>p</i> 2R<sub>2</sub> score validation, the R.O.C. curve showed significant capability, although not high, of discriminating good anticoagulation control (T.T.R. ≥65%) with an area under the curve of 0.562 (95% C.I. 0.533–0.592, <i>p</i> p 2R<sub>2</sub> score were added. <b>Conclusion</b>: In this cohort, the SAMe-TT<sub>2</sub>R<sub>2</sub> score had a significant, although modest, ability to assess the likelihood of good international normalized ration (I.N.R.) control, and its predictive value might slightly improve by adding other simple clinical factors. Further research is needed to refine the predictive scales.
DOI: 10.6084/m9.figshare.3112843.v1
title: Automatic classification model for Volunteered Geographic Information, applied to birds observer credibility

description: Data and code used in the research of automatic classification model for Volunteered Geographic Information, applied to birds observer credibility.<br><br>original data comes from http://ebird.org, here is the data used as imput and the R code.<br><br>GPL licence is only for the R code.<br>
DOI: 10.6084/m9.figshare.3112687
title: Identification of novel putative adipomyokines by a cross-species annotation of secretomes and expression profiles

description: Adipose tissue and skeletal muscle are organs that respond strongly to obesity and physical activity exhibiting high secretory activity. To identify novel putative adipomyokines, comparative expression studies of skeletal muscle and adipose tissue of lean (C57BL/6J) and obese (C57BL/6J on a high-fat diet and NZO) mice, of sedentary and endurance trained C57BL/6J mice and of cattle characterized by different amounts of intramuscular fat were combined with human secretome data and scored. In highly regulated transcripts, we identified 119 myokines, 79 adipokines and 22 adipomyokines. Network analysis of these candidates revealed remodelling of extracellular matrix and tissue fibrosis as relevant functions of several of these candidates. Given the pathophysiogical relevance of fibrosis for adipose-muscle-cross-talk in obesity and type 2 diabetes and its physiological role in exercise adaptation and meat quality of farm animals, they represent interesting candidates for further investigations in different research areas and species.