cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7001081
title: Involvement of the SnRK1 subunit KIN10 in sucrose-induced hypocotyl elongation

description: A mechanism participating in energy sensing and signalling in plants involves the regulation of sucrose non-fermenting1 (Snf1)-related protein kinase 1 (SnRK1) activity in response to sugar availability. SnRK1 is thought to regulate the activity of both metabolic enzymes and transcription factors in response to changes in energy availability, with trehalose-6-phospate functioning as a signalling sugar that suppresses SnRK1 activity under sugar-replete conditions. Sucrose supplementation increases the elongation of hypocotyls of developing Arabidopsis seedlings, and this response to sucrose involves both the SnRK1 subunit KIN10 and also TREHALOSE-6-PHOSPHATE SYNTHASE1 (TPS1). Here, we measured sucrose-induced hypocotyl elongation in two insertional mutants of KIN10 (<i>akin10</i> and <i>akin10</i>-2). Under short photoperiods, sucrose supplementation caused great proportional hypocotyl elongation in these KIN10 mutants compared with the wild type, and these mutants had shorter hypocotyls than the wild type in the absence of sucrose supplementation. One interpretation is that SnRK1 activity might suppress hypocotyl elongation in the presence of sucrose, because KIN10 overexpression inhibits sucrose-induced hypocotyl elongation and <i>akin10</i> mutants enhance sucrose-induced hypocotyl elongation.
DOI: 10.6084/m9.figshare.7001096
title: Data.mat

description: · In deep ocean systems, sediment resuspension occurs even for mean velocities below the time-averaged critical velocity. · In the continental slope regions, sediment flux is largely controlled by ejection and sweep turbulent events. · Wavelet transform associates turbulent bursting sequences with intense sediment resuspension.
DOI: 10.6084/m9.figshare.7001081.v1
title: Involvement of the SnRK1 subunit KIN10 in sucrose-induced hypocotyl elongation

description: A mechanism participating in energy sensing and signalling in plants involves the regulation of sucrose non-fermenting1 (Snf1)-related protein kinase 1 (SnRK1) activity in response to sugar availability. SnRK1 is thought to regulate the activity of both metabolic enzymes and transcription factors in response to changes in energy availability, with trehalose-6-phospate functioning as a signalling sugar that suppresses SnRK1 activity under sugar-replete conditions. Sucrose supplementation increases the elongation of hypocotyls of developing Arabidopsis seedlings, and this response to sucrose involves both the SnRK1 subunit KIN10 and also TREHALOSE-6-PHOSPHATE SYNTHASE1 (TPS1). Here, we measured sucrose-induced hypocotyl elongation in two insertional mutants of KIN10 (<i>akin10</i> and <i>akin10</i>-2). Under short photoperiods, sucrose supplementation caused great proportional hypocotyl elongation in these KIN10 mutants compared with the wild type, and these mutants had shorter hypocotyls than the wild type in the absence of sucrose supplementation. One interpretation is that SnRK1 activity might suppress hypocotyl elongation in the presence of sucrose, because KIN10 overexpression inhibits sucrose-induced hypocotyl elongation and <i>akin10</i> mutants enhance sucrose-induced hypocotyl elongation.
DOI: 10.6084/m9.figshare.7001078
title: Exploring the metabolic variation between domesticated and wild tetraploid wheat genotypes in response to corn leaf aphid infestation

description: Infestation of <i>Triticum</i> (wheat) plants by their pest <i>Rhopalosiphum maidis</i> (corn leaf aphid) causes severe vegetative damage. Despite the agro-economic importance of wheat, the metabolic diversity of <i>Triticum turgidum</i> (tetraploid wheat) in response to aphid attack has not been sufficiently addressed. In this study, we compared the metabolic diversity of two tetraploid wheat genotypes, domesticated and wild emmer. The plants were grown in a control growth room and infested with aphids for 96 h. Our untargeted metabolic analysis performed on plants with and without aphids revealed massive differences between the two genotypes. The targeted metabolic analysis highlighted the differences in the biosynthesis of phytohormones. The aphid progeny was lower in the cultivated durum wheat than in the wild emmer wheat. Overall, these observations emphasize the potential of using the natural diversity of wheat species to better understand the metabolic responses to pest damage.
DOI: 10.6084/m9.figshare.7001096.v1
title: Data.mat

description: · In deep ocean systems, sediment resuspension occurs even for mean velocities below the time-averaged critical velocity. · In the continental slope regions, sediment flux is largely controlled by ejection and sweep turbulent events. · Wavelet transform associates turbulent bursting sequences with intense sediment resuspension.
DOI: 10.6084/m9.figshare.7001051
title: Effects of simulated visual acuity and ocular motility impairments on SSVEP brain-computer interface performance: an experiment with Shuffle Speller

description: Individuals with severe speech and physical impairments may have concomitant visual acuity impairments (VAI) or ocular motility impairments (OMI) impacting visual BCI use. We report on use of the Shuffle Speller typing interface for SSVEP BCI copy-spelling with simulated VAI, simulated OMI, and unimpaired vision. To mitigate the effects of visual impairments, we introduce a method that adaptively selects user-specific trial lengths to maximize expected information transfer rate (ITR), which is shown to closely approximate correct letter selection rate. All participants could type under the unimpaired and simulated VAI conditions, without significant differences in typing accuracy or speed. Most participants (31 of 37) could not type under the simulated OMI condition; some achieved high accuracy with slower typing speeds. Reported workload and discomfort were low, and satisfaction high, under the unimpaired and simulated VAI conditions. Implications and future directions for exploration of visual impairment in BCI use are discussed.
DOI: 10.6084/m9.figshare.7001078.v1
title: Exploring the metabolic variation between domesticated and wild tetraploid wheat genotypes in response to corn leaf aphid infestation

description: Infestation of <i>Triticum</i> (wheat) plants by their pest <i>Rhopalosiphum maidis</i> (corn leaf aphid) causes severe vegetative damage. Despite the agro-economic importance of wheat, the metabolic diversity of <i>Triticum turgidum</i> (tetraploid wheat) in response to aphid attack has not been sufficiently addressed. In this study, we compared the metabolic diversity of two tetraploid wheat genotypes, domesticated and wild emmer. The plants were grown in a control growth room and infested with aphids for 96 h. Our untargeted metabolic analysis performed on plants with and without aphids revealed massive differences between the two genotypes. The targeted metabolic analysis highlighted the differences in the biosynthesis of phytohormones. The aphid progeny was lower in the cultivated durum wheat than in the wild emmer wheat. Overall, these observations emphasize the potential of using the natural diversity of wheat species to better understand the metabolic responses to pest damage.
DOI: 10.6084/m9.figshare.7001051.v1
title: Effects of simulated visual acuity and ocular motility impairments on SSVEP brain-computer interface performance: an experiment with Shuffle Speller

description: Individuals with severe speech and physical impairments may have concomitant visual acuity impairments (VAI) or ocular motility impairments (OMI) impacting visual BCI use. We report on use of the Shuffle Speller typing interface for SSVEP BCI copy-spelling with simulated VAI, simulated OMI, and unimpaired vision. To mitigate the effects of visual impairments, we introduce a method that adaptively selects user-specific trial lengths to maximize expected information transfer rate (ITR), which is shown to closely approximate correct letter selection rate. All participants could type under the unimpaired and simulated VAI conditions, without significant differences in typing accuracy or speed. Most participants (31 of 37) could not type under the simulated OMI condition; some achieved high accuracy with slower typing speeds. Reported workload and discomfort were low, and satisfaction high, under the unimpaired and simulated VAI conditions. Implications and future directions for exploration of visual impairment in BCI use are discussed.
DOI: 10.6084/m9.figshare.7000859
title: Supplementary Material for: Genetic Evaluation of 114 Chinese Short Stature Children in the Next Generation Era: a Single Center Study

description: <b><i>Background/Aims:</i></b> The genetics of human height is a frequently studied and complex issue. However, there is limited genetic research of short stature. To uncover the subgroup of patients to have higher yield and to propose a simplified diagnostic algorithm in the next generation era. <b><i>Methods:</i></b> This study included 114 Chinese children with height SDS ≤ -2.5 and unknown etiology from 2014 to 2015. Target/whole exome sequencing (referred as NGS) and chromosomal microarray analysis (CMA) were performed on the enrolled patients sequentially to identify potential genetic etiologies. The samples solved by NGS and CMA were retrospectively studied to evaluate the clinical pathway of the patients following a standard diagnostic algorithm. <b><i>Results:</i></b> In total, a potential genetic etiology was identified in 41 (36%) patients: 38 by NGS (33.3%), two by CMA (1.8%), and an additional one by both (0.9%). There were 46 different variants in 29 genes and 2 pathogenic CNVs identified. The diagnostic yield was significantly higher in patients with facial dysmorphism or skeletal abnormalities than those without the corresponding phenotype (<i>P</i>=0.006 and <i>P</i>=0.009, respectively, Pearson’s χ<sup>2</sup> test). Retrospectively study the cohort indicate 83.3% patients eventually would be evaluated by NGS/CMA. <b><i>Conclusion:</i></b> This study confirms the utility of high-throughput molecular detection techniques for the etiological diagnosis of undiagnosed short stature and suggests that NGS could be used as a primary diagnostic strategy. Patients with facial dysmorphism and/or skeletal abnormalities are more likely to have a known genetic etiology. Moving NGS forward would simplified the diagnostic algorithm.
DOI: 10.6084/m9.figshare.7000769
title: Soil pH and phosphorus drive species composition and richness in semi-natural heathlands and grasslands unaffected by twentieth-century agricultural intensification

description: <b><i>Background</i></b>: Increased soil phosphorus (P) caused by agricultural intensification has been associated with decreased plant species richness (SR) in central Europe. How plant communities and soil P gradients are related in unimproved open habitats remains unclear. <b><i>Aims</i></b>: The aim of this article was to characterise the relationship between soil chemical parameters and plant species composition and richness in unimproved open habitats. <b><i>Methods</i></b>: The influence of soil chemical parameters (pH, P, K, Mg) on species composition was assessed, using data from 40 heathland and 54 grassland plots, by non-metric multidimensional scaling and permutational multivariate analysis of variance. The relationship between soil chemical parameters and SR was tested by linear mixed effects models. <b><i>Results</i></b>: A direct relationship between heathland community composition and pH was observed, explaining 10% of variation in species composition, while P, Mg and pH together explained 17% of variation in grassland composition. In heathlands, SR increased with increasing pH, whereas in grasslands, SR decreased with increasing soil P. <b><i>Conclusions</i></b>: Soil chemical parameters were substantially related to plant community composition and richness. In an area spared from a century of agricultural intensification, reduced pH appeared to constrain SR in heathlands, while even slight P increases (&lt;10 mg kg<sup>−1</sup>) depressed plant SR in semi-natural grasslands.
DOI: 10.6084/m9.figshare.7000769.v1
title: Soil pH and phosphorus drive species composition and richness in semi-natural heathlands and grasslands unaffected by twentieth-century agricultural intensification

description: <b><i>Background</i></b>: Increased soil phosphorus (P) caused by agricultural intensification has been associated with decreased plant species richness (SR) in central Europe. How plant communities and soil P gradients are related in unimproved open habitats remains unclear. <b><i>Aims</i></b>: The aim of this article was to characterise the relationship between soil chemical parameters and plant species composition and richness in unimproved open habitats. <b><i>Methods</i></b>: The influence of soil chemical parameters (pH, P, K, Mg) on species composition was assessed, using data from 40 heathland and 54 grassland plots, by non-metric multidimensional scaling and permutational multivariate analysis of variance. The relationship between soil chemical parameters and SR was tested by linear mixed effects models. <b><i>Results</i></b>: A direct relationship between heathland community composition and pH was observed, explaining 10% of variation in species composition, while P, Mg and pH together explained 17% of variation in grassland composition. In heathlands, SR increased with increasing pH, whereas in grasslands, SR decreased with increasing soil P. <b><i>Conclusions</i></b>: Soil chemical parameters were substantially related to plant community composition and richness. In an area spared from a century of agricultural intensification, reduced pH appeared to constrain SR in heathlands, while even slight P increases (&lt;10 mg kg<sup>−1</sup>) depressed plant SR in semi-natural grasslands.
DOI: 10.6084/m9.figshare.7000766
title: Spatial patterns of species diversity in sand dune plant communities in Yucatan, Mexico: importance of invasive species for species dominance patterns

description: <b><i>Background</i></b>: Coastal ecosystems in Mexico remain understudied in spite of their ecological, economic and conservation value and are being impacted by human activities along the coast. Knowledge on spatial patterns of plant species distribution that helps preserve these fragile ecosystems is crucial. <b><i>Aims</i></b>: We evaluated differences in species richness, species diversity and species dominance patterns in 16 plant communities as well as the degree to which differences were driven by climatic conditions in sandy dunes in Yucatán. We evaluated the importance of invasive species in mediating patterns of species diversity and species dominance patterns. <b><i>Results</i></b>: We found wide variation in plant species richness, species diversity and species dominance patterns among communities that stems from broad climatic differences along dune systems. Invasive plants represent almost one-third of total species richness and seem to be drastically changing the species dominance patterns in these communities. <b><i>Conclusions</i></b>: Regional climatic differences along the Yucatán north coast seems to be a major driver of plant diversity and species composition. Our findings suggest that invasive plants have successfully colonised and spread along the coast over the past 30 years. Even though invasive species do not alter spatial patterns of species diversity, they are becoming more dominant with potential detrimental consequences for native plants.
DOI: 10.6084/m9.figshare.7000766.v1
title: Spatial patterns of species diversity in sand dune plant communities in Yucatan, Mexico: importance of invasive species for species dominance patterns

description: <b><i>Background</i></b>: Coastal ecosystems in Mexico remain understudied in spite of their ecological, economic and conservation value and are being impacted by human activities along the coast. Knowledge on spatial patterns of plant species distribution that helps preserve these fragile ecosystems is crucial. <b><i>Aims</i></b>: We evaluated differences in species richness, species diversity and species dominance patterns in 16 plant communities as well as the degree to which differences were driven by climatic conditions in sandy dunes in Yucatán. We evaluated the importance of invasive species in mediating patterns of species diversity and species dominance patterns. <b><i>Results</i></b>: We found wide variation in plant species richness, species diversity and species dominance patterns among communities that stems from broad climatic differences along dune systems. Invasive plants represent almost one-third of total species richness and seem to be drastically changing the species dominance patterns in these communities. <b><i>Conclusions</i></b>: Regional climatic differences along the Yucatán north coast seems to be a major driver of plant diversity and species composition. Our findings suggest that invasive plants have successfully colonised and spread along the coast over the past 30 years. Even though invasive species do not alter spatial patterns of species diversity, they are becoming more dominant with potential detrimental consequences for native plants.
DOI: 10.6084/m9.figshare.7000751
title: Supplementary Material for: Targeting Peroxisome Proliferator Activated Receptor α (PPAR α) for the Prevention of Mitochondrial Impairment and Hypertrophy in Cardiomyocytes

description: <b><i>Background/Aims:</i></b> Morphological and biochemical maladaptation of cardiomyocytes are associated with mitochondrial dysfunction and dysregulation in hypertrophic conditions. Peroxisome proliferator activated receptor α (PPARα), a drug target for dyslipidemia, is known to be downregulated in cardiomyocytes in response to hypertrophic stimuli. The current study was undertaken to investigate the role of PPARα signaling in mitochondrial remodeling and thereby dysregulation of cardiomyocytes due to hypertrophy <i>in vitro</i>. <b><i>Methods:</i></b> Rat cardiomyocytes H9c2 (2-1) and neonatal rat ventricular myocytes (NRVMs) were cultured and treated with α<sub>1</sub>-adrenergic agonist phenylephrine (PE, 100 µM, 24 hours) in the presence or absence of 10 µM fenofibrate or bezafibrate. Cellular hypertrophy was observed by atomic force microscopy and immunofluorescence with F-actin antibody. mRNA levels of hypertrophic marker genes and other genes were examined by quantitative real time PCR. Structural as well as functional remodeling of the mitochondria were evaluated by immunofluorescence (F-actin and COX-I), live cell imaging microscopy (JC-I, mitotracker), mitochondrial complex V activity, MPTP activity and ATP assay. Oxidative stress was measured by using sensitive fluorescent indicator probes. Cellular and mitochondrial calcium were measured by using fluorescent indicator probes Rhod-2 AM and X-rhod-1 AM, respectively. Targetscan prediction analysis was performed to find out miRNAs as putative regulators of VDAC. Luciferase assay was conducted to confirm binding of miR28 with VDAC. <b><i>Results:</i></b> Co-treatment of H9c2(2-1) cells with PE and fenofibrate restricted increase in cell size and expression of marker genes such as atrial-natriuretic peptide (ANP), brain-natriuretic peptide (BNP) and β-myosin heavy chain (β-MHC) compared to those with PE alone. Fenofibrate prevented PE-induced down regulation of PPARα-target genes like CPT-I and MCAD. Mitochondrial trans-membrane potential (Δψ<sub>m</sub>) and motility were reduced by PE which were significantly checked by fenofibrate. Increased ROS production and calcium level in PE-treated cells were ameliorated by fenofibrate. Mitochondrial activity and ATP generation were reduced by PE which was rescued by fenofibrate. Fenofibrate also prevented PE-induced down regulation of mitochondrial genes like VDAC-I and COX-IV. Expression of several miRNAs was altered in hypertrophic cardiomyocytes which were restored when co-treated with fenofibrate. miR28 was found to target 3’ untranslated region of VDAC-I. <b><i>Conclusion:</i></b> Overall, the results demonstrate that PPARα signaling is critically involved in mitochondrial dysfunction in hypertrophic cardiomyocytes in which miR28 plays a pivotal role.
DOI: 10.7284/108879
title: Multiplexed data collected during research cruise HRS100819JP using a Delaware SMS instrument system onboard the platform RV Hugh R. Sharp
DOI: 10.6084/m9.figshare.7000586
title: Bedaquiline- versus injectable-containing drug-resistant tuberculosis regimens: a cost-effectiveness analysis

description: <b>Background</b>: Drug-resistant tuberculosis (DR-TB) continues to be a major public health challenge with suboptimal treatment outcomes including well-documented treatment-related toxicities. We compared the cost-effectiveness of bedaquiline (BDQ) containing regimens with injectable containing regimens (short-course regimen [SCR] and long-course regimen [LCR]) in India, Russia, and South Africa. <b>Methods</b>: The analysis evaluated the direct costs of DR-TB treatment which included drugs, hospitalization, injectable-related adverse event costs, and other costs. Scenarios altered regimen costs, SCR/LCR ratio, and substitution rate between regimens (whether BDQ or injectable containing). <b>Results</b>: BDQ containing regimens are more cost effective based on cost per treatment success compared with injectable containing regimens, reducing these in SCR by 18–20% and in LCR by 49–54%. Average cost effectiveness ratios (ACERs) of BDQ containing regimens are lower. The incremental cost effectiveness ratio (ICER) is negative. Exclusive use of BDQ containing regimens results in approximately 61,000 more patients treated successfully over 5 years. <b>Conclusions</b>: Across all countries, BDQ containing regimens are dominant compared to injectable containing regimens, entailing lower treatment costs to achieve better clinical outcomes. This analysis can provide insight and support to local and global decision-makers and public health organizations to allocate efficiently resources improving patient and public health outcomes.
DOI: 10.6084/m9.figshare.7000598
title: Nanoviscosity effect on the spin chemistry of an electron donor/Pt-complex /electron acceptor triad - classical and quantum kinetics interpretation

description: The magnetic-field dependent charge recombination kinetics upon ns-laser flash photolysis of a novel triarylamine/cyclometalated platinum complex/napthalenediimide triad (<b>DPtA</b>) have been measured in tetrahydrofuran (THF) and polytetrahydrofuran (pTHF) to study the spinchemical effect of a large increase of the macroviscosity of the solvent by a factor of about 1000. The magnetic-field dependence of the decay kinetics of the charge separated state has been accurately reproduced by a classical kinetic model, wherein the rate constants of transitions between spin substates of different Zeeman energy are represented by a single magnetic-field dependent rate constant <i>k</i><sub>±</sub>. In THF, the magnetic-field dependence of <i>k</i><sub>±</sub> is given by a double Lorentzian function which, in a double log plot, shows two characteristic steps that can be consistently assigned to the magnetic field inhibition of the coherent and incoherent i.e. relaxational spin mixing mechanism. In pTHF, the magnetic field effect on <i>k</i><sub>±</sub> is a single step function decreasing to its limiting value at about 5 times lower fields than in THF. As shown by a quantum theoretical simulation, in this solvent coherent and incoherent processes are contributing equally at all fields. The nanoviscosity of pTHF appears to be much smaller than its macroviscosity.