cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4252193.v2
title: Supplemental Data Files for "Benthic Biofilm Controls on Fine Particle Dynamics in Streams". Water Resources Research

description: Benthic (streambed) biofilms metabolize a substantial fraction of particulate organic matter and nutrient inputs to streams. These microbial communities comprise a significant proportion of overall biomass in headwater streams, and they present a primary control on the transformation and export of labile organic carbon. Biofilm growth has been linked to enhanced fine particle deposition and retention, a feedback that confers a distinct advantage for the acquisition and utilization of energy sources. We quantified the influence of biofilm structure on fine particle deposition and resuspension in experimental stream mesocosms. Biofilms were grown in identical 3-m recirculating flumes over periods of 18-47 days to obtain a range of biofilm characteristics. Fluorescent, 8-mm particles were introduced to each flume, and their concentrations in the water column were monitored over a 30-minute period. We measured particle concentrations using a flow cytometer and mesoscale (10 μm to 1 cm) biofilm structure using optical coherence tomography. Particle deposition-resuspension dynamics were determined by fitting results to a stochastic mobile-immobile model, which showed retention timescales for particles within the biofilm-covered streambeds followed a power-law residence time distribution. Particle retention timescales increased with biofilm areal coverage, biofilm roughness, and mean biofilm height. Our findings suggest that biofilm structural parameters are key predictors of particle retention in streams and rivers.
DOI: 10.6084/m9.figshare.4252025
title: Dataset for: Effect of preceding stimulation on sound localization and its representation in the auditory midbrain

description: Prior stimulation can influence the perception of sound source location. Some psychophysical sound localization procedures differ in the amount of prior stimulation, which may affect measures of localization accuracy. If and how particularly the number of preceding stimuli affects sound localization and the neural representation of sound source position has not been investigated so far and will be the focus of the present report. We trained Mongolian gerbils in a left/right discrimination task where the target stimulus was preceded by silence or followed a number of reference stimuli. Localization thresholds decreased with the number of references presented before the target stimulus. The smallest thresholds were found after the presentation of a train of five reference stimuli and after silence. We recorded from units in the inferior colliculus (IC) of anaesthetised gerbils using virtual-acoustic space stimuli mimicking the ones used in the behavioral task and applied signal detection theory to compare behavioral and neurometric thresholds. We found that neurometric thresholds based on spike rate information of single units covered a wide range of threshold values but only neurometric thresholds based on responses of small populations of IC units reached consistently thresholds we also observed in the behavioral experiment. Unlike behavioral thresholds, however, neurometric thresholds were independent of the number of reference stimuli suggesting that processing stages downstream from the IC might better reflect the effect of prior stimulation.
DOI: 10.6084/m9.figshare.4252025.v1
title: Dataset for: Effect of preceding stimulation on sound localization and its representation in the auditory midbrain

description: Prior stimulation can influence the perception of sound source location. Some psychophysical sound localization procedures differ in the amount of prior stimulation, which may affect measures of localization accuracy. If and how particularly the number of preceding stimuli affects sound localization and the neural representation of sound source position has not been investigated so far and will be the focus of the present report. We trained Mongolian gerbils in a left/right discrimination task where the target stimulus was preceded by silence or followed a number of reference stimuli. Localization thresholds decreased with the number of references presented before the target stimulus. The smallest thresholds were found after the presentation of a train of five reference stimuli and after silence. We recorded from units in the inferior colliculus (IC) of anaesthetised gerbils using virtual-acoustic space stimuli mimicking the ones used in the behavioral task and applied signal detection theory to compare behavioral and neurometric thresholds. We found that neurometric thresholds based on spike rate information of single units covered a wide range of threshold values but only neurometric thresholds based on responses of small populations of IC units reached consistently thresholds we also observed in the behavioral experiment. Unlike behavioral thresholds, however, neurometric thresholds were independent of the number of reference stimuli suggesting that processing stages downstream from the IC might better reflect the effect of prior stimulation.
DOI: 10.6084/m9.figshare.4251899
title: Rebounding hygroscopic inorganic aerosol particles: Liquids, gels, and hydrates

description: Particle rebound was studied for ten atmospherically relevant inorganics. Experiments were conducted with submicron particles in aerosol form to a relative humidity (RH) of &lt;5% followed by progressive exposure to RH up to 95% for 2 s. At low RH, particles of MgCl<sub>2</sub>, NaCl, NH<sub>4</sub>Cl, KCl, (NH<sub>4</sub>)<sub>2</sub>SO<sub>4</sub>, and Na<sub>2</sub>SO<sub>4</sub> crystallized. As RH increased, these particles completed the transition from rebounding to adhering close to their deliquescence RH (DRH). The onset of decreased rebound, however, was below the DRH. Rebound curves for particles of MgCl<sub>2</sub>, NH<sub>4</sub>NO<sub>3</sub>, MgSO<sub>4</sub>, and NaNO<sub>3</sub> had different features than explained by water adsorption and deliquescence. Particles of MgCl<sub>2</sub> had rebound curves characterized by two domains, corresponding to its two hydrates. At low RH, particles of MgSO<sub>4</sub> and NaNO<sub>3</sub> did not crystallize but rebound occurred, suggesting a glassy or high-viscosity though noncrystalline state. Gel formation for MgSO<sub>4</sub> can increase viscosity, affecting rebound behavior. Particles of NH<sub>4</sub>NO<sub>3</sub> adhered even to &lt;5% RH, suggesting a low-viscosity state even to low RH. Particles of NH<sub>4</sub>HSO<sub>4</sub> were investigated as a special case by exposure to 5 ppm ammonia at 10% and 90% RH. At low RH, these particles still had sufficient molecular diffusivity to maintain active heterogeneous chemistry, although with some kinetic limitations. The different behaviors between nitrates and sulfates suggest different roles of heterogeneous chemistry in regions affected by NO<sub>x</sub> compared to SO<sub>2</sub> emissions. The results of this study could have implications for the use of different wet and dry seed particles in chamber experiments. Copyright © 2017 American Association for Aerosol Research
DOI: 10.6084/m9.figshare.12369335
title: C8S3 molecular geometry and charge distributions

description: The geometry was optimized at the B3LYP/6-31G(d,p) DFT level.<br>CHELPG charges were computed at the wB97XD/6-31G(d,p) DFT level and constrained to reproduce the dipole moment of either the ground state (<b>gs</b>) or (brightest) excited state (<b>es</b>).<br>For more details, see:A.S. Bondarenko, I. Patmanidis, R. Alessandri, P.C.T. Souza, A.H. de Vries, S.J. Marrink, T.L.C. Jansen, & J. Knoester, <i>Multiscale Modeling of Molecular Structure and Optical Properties of Complex Supramolecular Aggregates</i>, Chemrxiv <b>2020</b>, doi: 10.26434/chemrxiv.12279956<br><br>
DOI: 10.6084/m9.figshare.4251899.v2
title: Rebounding hygroscopic inorganic aerosol particles: Liquids, gels, and hydrates

description: Particle rebound was studied for ten atmospherically relevant inorganics. Experiments were conducted with submicron particles in aerosol form to a relative humidity (RH) of &lt;5% followed by progressive exposure to RH up to 95% for 2 s. At low RH, particles of MgCl<sub>2</sub>, NaCl, NH<sub>4</sub>Cl, KCl, (NH<sub>4</sub>)<sub>2</sub>SO<sub>4</sub>, and Na<sub>2</sub>SO<sub>4</sub> crystallized. As RH increased, these particles completed the transition from rebounding to adhering close to their deliquescence RH (DRH). The onset of decreased rebound, however, was below the DRH. Rebound curves for particles of MgCl<sub>2</sub>, NH<sub>4</sub>NO<sub>3</sub>, MgSO<sub>4</sub>, and NaNO<sub>3</sub> had different features than explained by water adsorption and deliquescence. Particles of MgCl<sub>2</sub> had rebound curves characterized by two domains, corresponding to its two hydrates. At low RH, particles of MgSO<sub>4</sub> and NaNO<sub>3</sub> did not crystallize but rebound occurred, suggesting a glassy or high-viscosity though noncrystalline state. Gel formation for MgSO<sub>4</sub> can increase viscosity, affecting rebound behavior. Particles of NH<sub>4</sub>NO<sub>3</sub> adhered even to &lt;5% RH, suggesting a low-viscosity state even to low RH. Particles of NH<sub>4</sub>HSO<sub>4</sub> were investigated as a special case by exposure to 5 ppm ammonia at 10% and 90% RH. At low RH, these particles still had sufficient molecular diffusivity to maintain active heterogeneous chemistry, although with some kinetic limitations. The different behaviors between nitrates and sulfates suggest different roles of heterogeneous chemistry in regions affected by NO<sub>x</sub> compared to SO<sub>2</sub> emissions. The results of this study could have implications for the use of different wet and dry seed particles in chamber experiments. Copyright © 2017 American Association for Aerosol Research
DOI: 10.6084/m9.figshare.4251890
title: Interplay of <i>cis</i>- and <i>trans</i>-regulatory mechanisms in the spliceosomal RNA helicase Brr2

description: RNA helicase Brr2 is implicated in multiple phases of pre-mRNA splicing and thus requires tight regulation. Brr2 can be auto-inhibited <i>via</i> a large N-terminal region folding back onto its helicase core and auto-activated by a catalytically inactive C-terminal helicase cassette. Furthermore, it can be regulated in <i>trans</i> by the Jab1 domain of the Prp8 protein, which can inhibit Brr2 by intermittently inserting a C-terminal tail in the enzyme's RNA-binding tunnel or activate the helicase after removal of this tail. Presently it is unclear, whether these regulatory mechanisms functionally interact and to which extent they are evolutionarily conserved. Here, we report crystal structures of <i>Saccharomyces cerevisiae</i> and <i>Chaetomium thermophilum</i> Brr2-Jab1 complexes, demonstrating that Jab1-based inhibition of Brr2 presumably takes effect in all eukaryotes but is implemented <i>via</i> organism-specific molecular contacts. Moreover, the structures show that Brr2 auto-inhibition can act in concert with Jab1-mediated inhibition, and suggest that the N-terminal region influences how the Jab1 C-terminal tail interacts at the RNA-binding tunnel. Systematic RNA binding and unwinding studies revealed that the N-terminal region and the Jab1 C-terminal tail specifically interfere with accommodation of double-stranded and single-stranded regions of an RNA substrate, respectively, mutually reinforcing each other. Additionally, such analyses show that regulation based on the N-terminal region requires the presence of the inactive C-terminal helicase cassette. Together, our results outline an intricate system of regulatory mechanisms, which control Brr2 activities during snRNP assembly and splicing.
DOI: 10.6084/m9.figshare.4251890.v1
title: Interplay of <i>cis</i>- and <i>trans</i>-regulatory mechanisms in the spliceosomal RNA helicase Brr2

description: RNA helicase Brr2 is implicated in multiple phases of pre-mRNA splicing and thus requires tight regulation. Brr2 can be auto-inhibited <i>via</i> a large N-terminal region folding back onto its helicase core and auto-activated by a catalytically inactive C-terminal helicase cassette. Furthermore, it can be regulated in <i>trans</i> by the Jab1 domain of the Prp8 protein, which can inhibit Brr2 by intermittently inserting a C-terminal tail in the enzyme's RNA-binding tunnel or activate the helicase after removal of this tail. Presently it is unclear, whether these regulatory mechanisms functionally interact and to which extent they are evolutionarily conserved. Here, we report crystal structures of <i>Saccharomyces cerevisiae</i> and <i>Chaetomium thermophilum</i> Brr2-Jab1 complexes, demonstrating that Jab1-based inhibition of Brr2 presumably takes effect in all eukaryotes but is implemented <i>via</i> organism-specific molecular contacts. Moreover, the structures show that Brr2 auto-inhibition can act in concert with Jab1-mediated inhibition, and suggest that the N-terminal region influences how the Jab1 C-terminal tail interacts at the RNA-binding tunnel. Systematic RNA binding and unwinding studies revealed that the N-terminal region and the Jab1 C-terminal tail specifically interfere with accommodation of double-stranded and single-stranded regions of an RNA substrate, respectively, mutually reinforcing each other. Additionally, such analyses show that regulation based on the N-terminal region requires the presence of the inactive C-terminal helicase cassette. Together, our results outline an intricate system of regulatory mechanisms, which control Brr2 activities during snRNP assembly and splicing.
DOI: 10.6084/m9.figshare.4251833
title: MMP-8, MMP-9 and Neutrophil Elastase in Peripheral Blood and Exhaled Breath Condensate in COPD

description: Chronic obstructive pulmonary disease (COPD) is characterised by progressive and irreversible airflow limitation associated with chronic inflammation involving cytokines and metalloproteinases (MMPs). MMP-8, MMP-9 and neutrophil elastase (NE) are known to be implicated in COPD but the factors influencing activation and suppression remain unclear. This study aimed to compare MMP-8, MMP-9 and NE in the peripheral blood of COPD patients and controls and to likewise assess exhaled breath condensate (EBC) for these MMPs. Peripheral blood micro(mi)RNA139-5p levels, which may regulate MMPs in COPD, were also measured. Blood and EBC were collected from COPD patients (stable and during exacerbations) and healthy controls. Expression of mRNA for MMP-8, MMP-9, NE and miRNA-139-5p expression in peripheral blood mononuclear cells (PBMCs) was measured using qRT-PCR. MMP-8, MMP-9 and NE protein in plasma as well as MMP-8 and MMP-9 protein in EBC were analysed by enzyme-linked immunoassays. PBMCs from COPD patients showed greater expression of mRNA for MMP-8 (<i>p</i> = 0.0004), MMP-9 (<i>p</i> = 0.0023) and NE (<i>p</i> = 0.0019). PBMC expression of mRNA for NE was significantly higher in COPD exacerbations compared to stable cases (<i>p</i> &lt; 0.05). Expression of mRNA for MMP-9 and NE correlated negatively with spirometry in patients (<i>p</i> &lt; 0.05). Plasma from COPD patients showed greater levels of protein for MMP-8 (<i>p</i> = 0.003), MMP-9 (<i>p</i> = 0.046) and NE (<i>p</i> = 0.018). MMP-8 protein levels were lower in the EBC of COPD patients (<i>p</i> &lt; 0.0001). In PBMCs, enhanced expression of mRNA for MMP-9 and NE is associated with COPD and may correlate with disease severity and exacerbations.
DOI: 10.6084/m9.figshare.4251833.v1
title: MMP-8, MMP-9 and Neutrophil Elastase in Peripheral Blood and Exhaled Breath Condensate in COPD

description: Chronic obstructive pulmonary disease (COPD) is characterised by progressive and irreversible airflow limitation associated with chronic inflammation involving cytokines and metalloproteinases (MMPs). MMP-8, MMP-9 and neutrophil elastase (NE) are known to be implicated in COPD but the factors influencing activation and suppression remain unclear. This study aimed to compare MMP-8, MMP-9 and NE in the peripheral blood of COPD patients and controls and to likewise assess exhaled breath condensate (EBC) for these MMPs. Peripheral blood micro(mi)RNA139-5p levels, which may regulate MMPs in COPD, were also measured. Blood and EBC were collected from COPD patients (stable and during exacerbations) and healthy controls. Expression of mRNA for MMP-8, MMP-9, NE and miRNA-139-5p expression in peripheral blood mononuclear cells (PBMCs) was measured using qRT-PCR. MMP-8, MMP-9 and NE protein in plasma as well as MMP-8 and MMP-9 protein in EBC were analysed by enzyme-linked immunoassays. PBMCs from COPD patients showed greater expression of mRNA for MMP-8 (<i>p</i> = 0.0004), MMP-9 (<i>p</i> = 0.0023) and NE (<i>p</i> = 0.0019). PBMC expression of mRNA for NE was significantly higher in COPD exacerbations compared to stable cases (<i>p</i> &lt; 0.05). Expression of mRNA for MMP-9 and NE correlated negatively with spirometry in patients (<i>p</i> &lt; 0.05). Plasma from COPD patients showed greater levels of protein for MMP-8 (<i>p</i> = 0.003), MMP-9 (<i>p</i> = 0.046) and NE (<i>p</i> = 0.018). MMP-8 protein levels were lower in the EBC of COPD patients (<i>p</i> &lt; 0.0001). In PBMCs, enhanced expression of mRNA for MMP-9 and NE is associated with COPD and may correlate with disease severity and exacerbations.
DOI: 10.6084/m9.figshare.4249964
title: Supplementary Material for: Epigenetic Dysregulation in the Prefrontal Cortex of Suicide Completers

description: The epigenome is thought to mediate between genes and the environment, particularly in response to adverse life experiences. Similar to other psychiatric diseases, the suicide liability of an individual appears to be influenced by many genetic factors of small effect size as well as by environmental stressors. To identify epigenetic marks associated with suicide, which is considered the endpoint of complex gene-environment interactions, we compared the cortex DNA methylation patterns of 6 suicide completers versus 6 non-psychiatric sudden-death controls, using Illumina 450K methylation arrays. Consistent with a multifactorial disease model, we found DNA methylation changes in a large number of genes, but no changes with large effects reaching genome-wide significance. Global methylation of all analyzed CpG sites was significantly (0.25 percentage point) lower in suicide than in control brains, whereas the vast majority (97%) of the top 1,000 differentially methylated regions (DMRs) were higher methylated (0.6 percentage point) in suicide brains. Annotation analysis of the top 1,000 DMRs revealed an enrichment of differentially methylated promoters in functional categories associated with transcription and expression in the brain. In addition, we performed a comprehensive literature research to identify suicide genes that have been replicated in independent genetic association, brain methylation and/or expression studies. Although, in general, there was no significant overlap between different published data sets or between our top 1,000 DMRs and published data sets, our methylation screen strengthens a number of candidate genes <i>(APLP2</i>, <i>BDNF</i>, <i>HTR1A</i>, <i>NUAK1</i>, <i>PHACTR3</i>, <i>MSMP</i>, <i>SLC6A4</i>, <i>SYN2</i>, and <i>SYNE2)</i> and supports a role for epigenetics in the pathophysiology of suicide.
DOI: 10.6084/m9.figshare.4249982.v1
title: Supplementary Material for: Investigation of Lung Involvement in Connective Tissue Disorders

description: Lung involvement in connective tissue disorders (CTDs) may present as pleomorphic since any lung compartment may be involved such as airways, exocrine secretory and alveolar epithelia, interstitial lung structure, pulmonary vasculature and pleura as well as, in specific disorders, several tissues of the thoracoabdominal ventilator pump. Any combination of the above anatomic structures may be involved concomitantly although some specific combinations may include a determinant of rheumatic disorders. The diagnosis of a specific CTD requires the fulfilment of clearly defined clinical and laboratory criteria including in most cases positivity for autoantibodies, mostly specific serologic combinations. In this setting, serologic investigation targets mainly, although not exclusively, the detection of antinuclear antibodies. A specific serologic positivity or a combination of autoantibodies constitutes not only a diagnostic criterion for a specific CTD, but may also characterize the pattern of respiratory manifestation in a determinant rheumatic disorder. Therefore, the investigation of lung involvement in CTDs requires adequate skills in the ambit of a multidisciplinary approach and an extended spectrum of diagnostic tools and modalities able to detect both early clinical clues and serologic conversion as well as any pathophysiologic alteration that regards the complexity of respiratory functional status. Although many patients with CTDs suffer from a ‘vicious' combination of lung involvement, lung drug toxicity and infections related to the above two as well as to the ‘mater' disease, for space reasons this review will focus on the established lung manifestations that regard the 7 major CTDs.
DOI: 10.6084/m9.figshare.4249940
title: Supplementary Material for: Off-Hour Admission and Outcomes in Patients with Acute Intracerebral Hemorrhage in the INTERACT2 Trial

description: <b><i>Background:</i></b> Conflicting data exist of an association between off-hour (weekend, holiday, or night-time) hospital admission and adverse outcome in intracerebral hemorrhage (ICH). We determined the association between off-hour admissions and poor clinical outcome, and of any differential effect of early intensive blood pressure (BP) lowering treatment between off- and on-hour admissions, among participants of the Intensive BP Reduction in Acute Cerebral Hemorrhage Trial (INTERACT2). <b><i>Methods:</i></b> Subsidiary analysis of INTERACT2, a multinational, multicenter, clinical trial of patients with spontaneous ICH with elevated systolic BP, randomly assigned to intensive (target systolic BP &lt;140 mm Hg) or guideline-based (&lt;180 mm Hg) BP management. Primary outcome was death or major disability (modified Rankin scale of 3-6) at 90 days. Off-hour admission was defined as night-time (4:30 p.m. to 8:30 a.m.) on weekdays, weekends (Saturday and Sunday), and public holidays in each participating country. <b><i>Results:</i></b> Of 2,794 patients with information on the primary outcome, 1,770 (63%) were admitted to study centers during off-hours. Off-hour admission was not associated with risk of poor outcome at 90 days (53% off-hour vs. 55% on-hour; p = 0.49), even after adjustment for comorbid risk factors (odds ratio 0.92; 95% CI 0.76-1.12). Consistency exists in the effects of intensive BP lowering between off- and on-hour admission (p = 0.85 for homogeneity). <b><i>Conclusions:</i></b> Off-hour admission was not associated with increased risks of death or major disability among trial protocol participants with acute ICH. Intensive BP lowering can provide similar treatment effect irrespective of admission hours.