cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6037979.v1
title: full data set for mcmcclmm models

description: full data set from mcmcclmm model of phylogenetic analysis of 45 species of drosophila, dataset includes; wing length, viral load, temperature treatment, full block effects, basal metabolic rate data, critical thermal maximum and minimum data.
DOI: 10.6084/m9.figshare.6035975
title: Propagation of nonstationary electronic and nuclear states: attosecond dynamics in LiF

description: Rapid optical excitation of a molecule produces a nonstationary state localised in the Franck–Condon region. To move out of that region, one needs to propagate both the electronic and the nuclear state. We formulate the motion on a grid of nuclear coordinate. The coupling to the electric field is fully included in the Hamiltonian used for propagation. We use perturbation theory to analyse the results of dynamics from one grid point to another. The nonadiabatic coupling terms arise from propagating the electronic states. We apply the formalism to the simple case of a diatomic molecule in an approximate but accurate scheme that allows performing computation on a limited number of grid points. As the coherent dynamics unfolds, we expand the grid in the direction of the wave packet motion with the quantum chemical calculations of the electronic structure performed ‘on the fly’. The LiF molecule excited by a one-cycle IR pulse is used as a computational example. The 30-fs propagation through the crossing of the ionic and covalent states is overall adiabatic. The role of electron–nuclear coherences is emphasised.
DOI: 10.6084/m9.figshare.6035975.v1
title: Propagation of nonstationary electronic and nuclear states: attosecond dynamics in LiF

description: Rapid optical excitation of a molecule produces a nonstationary state localised in the Franck–Condon region. To move out of that region, one needs to propagate both the electronic and the nuclear state. We formulate the motion on a grid of nuclear coordinate. The coupling to the electric field is fully included in the Hamiltonian used for propagation. We use perturbation theory to analyse the results of dynamics from one grid point to another. The nonadiabatic coupling terms arise from propagating the electronic states. We apply the formalism to the simple case of a diatomic molecule in an approximate but accurate scheme that allows performing computation on a limited number of grid points. As the coherent dynamics unfolds, we expand the grid in the direction of the wave packet motion with the quantum chemical calculations of the electronic structure performed ‘on the fly’. The LiF molecule excited by a one-cycle IR pulse is used as a computational example. The 30-fs propagation through the crossing of the ionic and covalent states is overall adiabatic. The role of electron–nuclear coherences is emphasised.
DOI: 10.6084/m9.figshare.6034766
title: FTIR synchrotron spectroscopy of the S–H stretching fundamental of the <sup>12</sup>CH<sub>3</sub><sup>32</sup>SH species of methyl mercaptan

description: The infrared Fourier transform spectrum of the S–H stretching fundamental band of <sup>12</sup>CH<sub>3</sub> <sup>32</sup>SH has been recorded using synchrotron radiation at the far-infrared beamline of the Canadian Light Source in Saskatoon. The S–H stretch is a hybrid band predominantly of perpendicular <i>b</i>-type with a small parallel <i>a</i>-component. With both Δ<i>K</i> = +1 and Δ<i>K</i> = −1 sub-bands present, the assignments are well determined from ground-state combination difference relations. The identified sub-bands access S–H stretching ground torsional substates from <i>K′</i> = 0–14 for <i>A</i> and <i>E</i> torsional species. The substate origins have been obtained by expanding the term values in <i>J</i>(<i>J</i> + 1) power series, and have been fitted to a simple 6-parameter Fourier Hamiltonian to deduce the torsional energies. The oscillation amplitude of the S–H stretching torsional curves is 0.547 cm<sup>−</sup> <sup>1</sup> compared to 0.653 cm<sup>−</sup> <sup>1</sup> for the ground state, implying an increase on the order of 6.9% in the torsional barrier height. The vibrational wavenumber for the S–H stretch mode is found to be 2603.5 cm<sup>−</sup> <sup>1</sup>.
DOI: 10.6084/m9.figshare.6034766.v1
title: FTIR synchrotron spectroscopy of the S–H stretching fundamental of the <sup>12</sup>CH<sub>3</sub><sup>32</sup>SH species of methyl mercaptan

description: The infrared Fourier transform spectrum of the S–H stretching fundamental band of <sup>12</sup>CH<sub>3</sub> <sup>32</sup>SH has been recorded using synchrotron radiation at the far-infrared beamline of the Canadian Light Source in Saskatoon. The S–H stretch is a hybrid band predominantly of perpendicular <i>b</i>-type with a small parallel <i>a</i>-component. With both Δ<i>K</i> = +1 and Δ<i>K</i> = −1 sub-bands present, the assignments are well determined from ground-state combination difference relations. The identified sub-bands access S–H stretching ground torsional substates from <i>K′</i> = 0–14 for <i>A</i> and <i>E</i> torsional species. The substate origins have been obtained by expanding the term values in <i>J</i>(<i>J</i> + 1) power series, and have been fitted to a simple 6-parameter Fourier Hamiltonian to deduce the torsional energies. The oscillation amplitude of the S–H stretching torsional curves is 0.547 cm<sup>−</sup> <sup>1</sup> compared to 0.653 cm<sup>−</sup> <sup>1</sup> for the ground state, implying an increase on the order of 6.9% in the torsional barrier height. The vibrational wavenumber for the S–H stretch mode is found to be 2603.5 cm<sup>−</sup> <sup>1</sup>.
DOI: 10.6084/m9.figshare.6034586
title: Table S1: Garnet–monazite rare earth element relationships in sub-solidus metapelites: a case study from Bhutan

description: Monazite trace element concentrations
DOI: 10.6084/m9.figshare.6034586.v1
title: Table S1: Garnet–monazite rare earth element relationships in sub-solidus metapelites: a case study from Bhutan

description: Monazite trace element concentrations
DOI: 10.6084/m9.figshare.6034577
title: Table S3: Garnet–monazite rare earth element relationships in sub-solidus metapelites: a case study from Bhutan

description: Titanium-in-biotite data
DOI: 10.6084/m9.figshare.6034577.v1
title: Table S3: Garnet–monazite rare earth element relationships in sub-solidus metapelites: a case study from Bhutan

description: Titanium-in-biotite data
DOI: 10.6084/m9.figshare.6034571
title: Table S2: Garnet–monazite rare earth element relationships in sub-solidus metapelites: a case study from Bhutan

description: Garnet trace element concentrations
DOI: 10.6084/m9.figshare.6034571.v1
title: Table S2: Garnet–monazite rare earth element relationships in sub-solidus metapelites: a case study from Bhutan

description: Garnet trace element concentrations
DOI: 10.6084/m9.figshare.6034559
title: Table S4: Garnet–monazite rare earth element relationships in sub-solidus metapelites: a case study from Bhutan

description: Monazite U–Th–Pb data
DOI: 10.6084/m9.figshare.6034559.v1
title: Table S4: Garnet–monazite rare earth element relationships in sub-solidus metapelites: a case study from Bhutan

description: Monazite U–Th–Pb data
DOI: 10.6084/m9.figshare.6034466
title: ctmax_min_data critical thermal data for drosophila species

description: 45 species of drosophila assayed for their critical thermal maximum and critical thermal minimum temperatures
DOI: 10.6084/m9.figshare.6034466.v1
title: ctmax_min_data critical thermal data for drosophila species

description: 45 species of drosophila assayed for their critical thermal maximum and critical thermal minimum temperatures
DOI: 10.6084/m9.figshare.6034160
title: Supplementary Material for: Impact of Chronic Kidney Disease on Cardiovascular and Renal Events in Patients Undergoing Percutaneous Coronary Intervention with Everolimus-Eluting Stent: Risk Stratification with C-Reactive Protein

description: <b><i>Background:</i></b> Chronic kidney disease (CKD) and inflammation play critical roles in atherosclerosis. There is limited evidence regarding the relationship between CKD and patients receiving second-generation drug-eluting stents for coronary artery disease. <b><i>Objective:</i></b> This study aimed to investigate the effect of CKD on cardiovascular and renal events in patients undergoing percutaneous coronary intervention (PCI) with everolimus-eluting stents (EES). <b><i>Methods:</i></b> We analyzed 504 consecutive patients with stable angina pectoris and significant coronary artery stenosis treated with EES. CKD was defined as an estimated glomerular filtration rate &lt; 60 mL/min/1.73 m<sup>2</sup> before coronary angiography. The primary outcome was the occurrence of major adverse renal and cardiovascular events (MARCE) including cardiac death, revascularization, heart failure, cerebral infarction, worsening renal function &gt; 25% from baseline, and renal replacement therapy at 1 year. <b><i>Results:</i></b> Patients were divided into the a MARCE (<i>n</i> = 126) and a non-MARCE (<i>n</i> = 378) group. The incidence of CKD was 51% in all subjects (including those on hemodialysis) and was significantly higher in the MARCE group than in the non-MARCE group (<i>p</i> = 0.00001). Multivariate logistic regression analysis identified that CKD was independently associated with MARCE (adjusted odds ratio 2.03, 95% confidence interval 1.21–3.39, <i>p</i> = 0.007). Patients were divided into four groups based on CKD and C-reactive protein (CRP) level prior to initial coronary angiography. Cox proportional hazards analysis revealed that patients with CKD and high CRP (≥0.3 mg/dL) had the worst prognosis (hazard ratio 4.371, 95% confidence interval 2.634–7.252, <i>p</i> = 0.00001) compared to patients without CKD and with low CRP. <b><i>Conclusion:</i></b> CKD combined with CRP predicted more clinical events in patients undergoing PCI with EES.
DOI: 10.6084/m9.figshare.6034067
title: Supplementary Material for: Whole-Genome Linkage Analysis with Whole-Exome Sequencing Identifies a Novel Frameshift Variant in <b><i>NEFH</i></b> in a Chinese Family with Charcot-Marie-Tooth 2: A Novel Variant in <b><i>NEFH</i></b> for Charcot-Marie-Tooth 2

description: <b><i>Background:</i></b> Charcot-Marie-Tooth disease (CMT) is the most common neurodegenerative disorder of the peripheral nervous system. More than 50 genes/loci were found associated with the disease. We found a family with autosomal-dominant CMT2. <b><i>Objective:</i></b> To reveal the pathogenic gene of the family and further investigate the function of the variant. <b><i>Methods:</i></b> DNA underwent whole-genome linkage analysis for all family members and whole-exome sequencing for 2 affected members. Neurofilament light polypeptide and wild-type or mutant neurofilament heavy polypeptide (NEFH) were co-transfected into SW13 (vim–) cells. The <i>nefh</i>-knockdown zebrafish model was produced by using morpholino antisense oligonucleotides. <b><i>Results:</i></b> We identified a novel insertion variant (c.3057insG) in <i>NEFH</i> in the family. The variant led to the loss of a stop codon and an extended 41 amino acids in the protein. Immunofluorescence results revealed that mutant <i>NEFH</i> disrupted the neurofilament network and induced aggregation of NEFH protein. Knockdown of<i> nefh</i> in zebrafish caused a slightly or severely curled tail. The motor ability of <i>nefh</i>-knockdown embryos was impaired or even absent, and the embryos showed developmental defects of axons in motor neurons. The abnormal phenotype and axonal developmental defects could be rescued by injection of human wild-type but not human mutant<i> NEFH</i> mRNA. <b><i>Conclusions:</i></b> We identified a novel stop loss variant in <i>NEFH</i> that is likely pathogenic for CMT2, and the results provide further evidence for the role of an aberrant assembly of neurofilament in CMT.
DOI: 10.6084/m9.figshare.6033893
title: Exercise and sleep in the course of aging

description: datasets from different groups for statistical analysis
DOI: 10.6084/m9.figshare.6033893.v2
title: Exercise and sleep in the course of aging

description: datasets from different groups for statistical analysis
DOI: 10.6084/m9.figshare.6033893.v1
title: Exercise and sleep in the course of aging

description: datasets from different groups for statistical analysis
DOI: 10.6084/m9.figshare.6033887
title: Supplementary Material for: Verbascoside Alleviates Atopic Dermatitis-Like Symptoms in Mice via Its Potent Anti-Inflammatory Effect

description: <b><i>Background:</i></b> Atopic dermatitis (AD) is a chronic inflammatory skin disease characterized by the interplay between multiple genetic and environmental factors. The pathogenesis of AD remains incompletely understood. Treatment with topical steroids for chronic AD symptoms has severe side effects and so a new treatment is required.<b><i></i></b> Verbascoside is a hydrophilic phenylethanoid glycoside with antioxidant, anti-inflammatory properties. <b><i>Methods:</i></b> Verbascoside was evaluated in AD-like lesions induced by the repetitive and alternative application of 2,4-dinitrochlorobenzene (DNCB) in BALB/c mice. Overall symptomatic score and serological and molecular changes of the skin lesions were investigated. <b><i>Results:</i></b> Verbascoside relieved the overall AD-like symptoms such as scratching behavior and skin lesion severity. At whole-body level, verbascoside significantly reduced DNCB-induced IgE and Th2 cytokines in the peripheral blood. At the skin lesion site, verbascoside also inhibited DNCB-induced production of proinflammatory cytokine TNF-α, IL-6, and IL-4 mRNA. In a human monocyte THP-1 model, verbascoside could suppress DNCB-induced upregulation of CD86 and CD54 at the cell surface, the secretion of the proinflammatory cytokines TNF-α and IL-6, and the activation of NFκB signaling in a dose-dependent manner. <b><i>Conclusion:</i></b> Our results demonstrate that verbascoside could be a potential therapeutic agent for the treatment of AD.
DOI: 10.6084/m9.figshare.6033761.v1
title: Supplemental data for "Pervasive influence of iron limitation in subsurface chlorophyll maximum layers of the California Current"

description: Dereived datasets presented here are licensed under the CC0 1.0 Universal license (see LICENSE.txt) and have been compiled from sources including:<br>1. Pacific Fisheries Environmental Laboratory (PFEL) [https://www.pfeg.noaa.gov/]2. The North Pacific Gyre Oscillation Index (NPGO) from Emanuele Di Lorenzo at Georgia Tech [http://www.o3d.org/npgo/enso.html]3. California Coopeative Fisheries Oceanic Fisheries Investigations (CalCOFI) [http://calcofi.org/]4. iMicrobe (Project ID: CAM_P_0001069) [https://imicrobe.us]5. UCSD Datazoo Research Project [http://oceaninformatics.ucsd.edu/datazoo/catalogs/ccelter/sources/1758]6. The authors' (SL Hogle et al.) own work<br>If using these original and/or derived datasets in your work pleaseconsider citing the original sources.<br>S.L Hogle - March 27, 2018
DOI: 10.6084/m9.figshare.6033722.v1
title: IDL code for fitting methods for heliospheric imagers (FPF, HMF, SSEF) observed with the STEREO mission

description: This is an IDL code that fits height-time observations of solar coronal mass ejections (CME) that were made with heliospheric imagers on the STEREO spacecraft, to produce speeds, directions and arrival times of CMEs. These codes may also be helpful in interpreting the wide-angle imager observations by Solar Orbiter and Parker Solar Probe.<br>The main program calling all others is "fitall_sse_out.pro" which needs a file with height-time observations as input (.ht from SATPLOT) but it can easily be rewritten for other input formats.<br>If this code is used to produce results for a peer-reviewed scientific publication, please contact me for a mandatory check on the results and for a possible co-authorship:<br>christian.moestl [at] oeaw.ac.at<br>twitter: @chrisoutofspace<br>An extensive discussion of the methods is given here:https://arxiv.org/abs/1404.3579<br>Möstl et al. (2014)<br>An application to over 1000 CMEs observed by STEREO is presented here:Möstl et al. (2017)https://arxiv.org/abs/1703.00705<br><br><br>
DOI: 10.6084/m9.figshare.6031958
title: Computational study of solution behavior of magainin 2 monomers

description: Antimicrobial peptides (AMPs) play crucial role as mediators of the primary host defense against microbial invasion. They are considered a promising alternative to antibiotics for multidrug resistant bacterial strains. For complete understanding of the antimicrobial defense mechanism, a detailed knowledge of the dynamics of peptide-membrane interactions, including atomistic studies on AMPs geometry and both peptide and membrane structural changes during the whole process is a prerequisite. We aim at clarifying the conformation dynamics of small linear AMPs in solution as a first step of <i>in silico</i> protocol for establishing a correspondence between certain amino-acid sequence motifs, secondary-structure elements, conformational dynamics in solution and the intensity and mode of interaction with the bacterial membrane. To this end, we use molecular dynamics simulations augmented by well-tempered metadynamics to study the free-energy landscape of two AMPs with close primary structure and different antibacterial activity – the native magainin 2 (MG2) and an analog (MG2m, with substitutions F5Y and F16W) in aqueous solution. We observe that upon solvation, the initial α-helical structures change differently. The native form remains structured, with three shorter α-helical motifs, connected by random coils, while the synthetic analog tends predominantly to a disordered conformation. Our results indicate the importance of the side-chains at positions 5 and 16 for maintaining the solvated peptide conformation. They also provide a modeling background for recent experimental observations, relating the higher α-helical content in solution (peptide pre-folding) in the case of small linear AMPs to a lower antibacterial activity.
DOI: 10.6084/m9.figshare.6031958.v1
title: Computational study of solution behavior of magainin 2 monomers

description: Antimicrobial peptides (AMPs) play crucial role as mediators of the primary host defense against microbial invasion. They are considered a promising alternative to antibiotics for multidrug resistant bacterial strains. For complete understanding of the antimicrobial defense mechanism, a detailed knowledge of the dynamics of peptide-membrane interactions, including atomistic studies on AMPs geometry and both peptide and membrane structural changes during the whole process is a prerequisite. We aim at clarifying the conformation dynamics of small linear AMPs in solution as a first step of <i>in silico</i> protocol for establishing a correspondence between certain amino-acid sequence motifs, secondary-structure elements, conformational dynamics in solution and the intensity and mode of interaction with the bacterial membrane. To this end, we use molecular dynamics simulations augmented by well-tempered metadynamics to study the free-energy landscape of two AMPs with close primary structure and different antibacterial activity – the native magainin 2 (MG2) and an analog (MG2m, with substitutions F5Y and F16W) in aqueous solution. We observe that upon solvation, the initial α-helical structures change differently. The native form remains structured, with three shorter α-helical motifs, connected by random coils, while the synthetic analog tends predominantly to a disordered conformation. Our results indicate the importance of the side-chains at positions 5 and 16 for maintaining the solvated peptide conformation. They also provide a modeling background for recent experimental observations, relating the higher α-helical content in solution (peptide pre-folding) in the case of small linear AMPs to a lower antibacterial activity.
DOI: 10.6084/m9.figshare.6031925
title: <i>Axelrodichthys araripensis</i> Maisey, 1986 revisited

description: <i>Axelrodichtys</i> is a genus of fossil coelacanth of the family Mawsoniidae with a wide spatial and temporal range, spanning from the Aptian/Albian of Brazil to the Campanian of France. In light of new discoveries in recent years a renewed interest in <i>Axelrodichthys</i> has emerged. Here we offer new insights on the type species – <i>A. araripensis</i> – based on a complete new description of all its morphological characters and a comparative study of several other Mawsoniidae. A relatively large sample composed of 113 specimens of <i>A. araripensis</i> and associated Mawsoniidae species was observed. Among the newly observed features are the broad aspect of premaxillae supporting the anterior opening of the rostral organ; a unique pattern of skull roof ornamentation; the basioccipital; a passage of nerves in the prootic; the passage for the superior ophthalmic nerve; the anocleithrum; and ossified zygal plates. Observation of two juvenile specimens in different growth stages allowed for the inference of negative allometric growth in the epicaudal lobe. Morphological comparisons pointed out that <i>M. lavocati</i> is more closely associated with the <i>Axelrodichthys</i> than with <i>Mawsonia</i>, therefore we included it in the <i>Axelrodichthys</i> genus as <i>A. lavocati.</i>
DOI: 10.6084/m9.figshare.6031916
title: Beyond Sequencing: Re-visiting Annotations for PJL as a Test Case

description: This is the PJL's annotated VCF file used in this study.
DOI: 10.6084/m9.figshare.6031916.v3
title: Beyond Sequencing: Re-visiting Annotations for PJL as a Test Case

description: This is the PJL's annotated VCF file used in this study.
DOI: 10.6084/m9.figshare.6031892
title: Supplementary Material for: Activation of Adenylyl Cyclase Causes Stimulation of Adenosine Receptors

description: <b><i>Background/Aims:</i></b> Signaling of G<sub>s</sub> protein-coupled receptors (GsPCRs) is accomplished by stimulation of adenylyl cyclase, causing an increase of the intracellular cAMP concentration, activation of the intracellular cAMP effectors protein kinase A (PKA) and Epac, and an efflux of cAMP, the function of which is still unclear. <b><i>Methods:</i></b> Activation of adenylyl cyclase by GsPCR agonists or cholera toxin was monitored by measurement of the intracellular cAMP concentration by ELISA, anti-phospho-PKA substrate motif phosphorylation by immunoblotting, and an Epac-FRET assay in the presence and absence of adenosine receptor antagonists or ecto-nucleotide phosphodiesterase/pyrophosphatase2 (eNPP2) inhibitors. The production of AMP from cAMP by recombinant eNPP2 was measured by HPLC. Extracellular adenosine was determined by LC-MS/MS, extracellular ATP by luciferase and LC-MS/MS. The expression of eNPP isoenzymes 1-3 was examined by RT-PCR. The expression of multidrug resistance protein 4 was suppressed by siRNA. <b><i>Results:</i></b> Here we show that the activation of GsPCRs and the GsPCRs-independent activation of G<sub>s</sub> proteins and adenylyl cyclase by cholera toxin induce stimulation of cell surface adenosine receptors (A<sub>2A</sub> or A<sub>2B</sub> adenosine receptors). In PC12 cells stimulation of adenylyl cyclase by GsPCR or cholera toxin caused activation of A<sub>2A</sub> adenosine receptors by an autocrine signaling pathway involving cAMP efflux through multidrug resistance protein 4 and hydrolysis of released cAMP to AMP by eNPP2. In contrast, in PC3 cells cholera toxin- and GsPCR-induced stimulation of adenylyl cyclase resulted in the activation of A<sub>2B</sub> adenosine receptors. <b><i>Conclusion:</i></b> Our findings show that stimulation of adenylyl cyclase causes a remarkable activation of cell surface adenosine receptors.