cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5293705
title: SQSTM1/p62-mediated autophagy compensates for loss of proteasome polyubiquitin recruiting capacity

description: Protein homeostasis in eukaryotic cells is regulated by 2 highly conserved degradative pathways, the ubiquitin-proteasome system (UPS) and macroautophagy/autophagy. Recent studies revealed a coordinated and complementary crosstalk between these systems that becomes critical under proteostatic stress. Under physiological conditions, however, the molecular crosstalk between these 2 pathways is still far from clear. Here we describe a cellular model of proteasomal substrate accumulation due to the combined knockdown of PSMD4/S5a and ADRM1, the 2 proteasomal ubiquitin receptors. This model reveals a compensatory autophagic pathway, mediated by a SQSTM1/p62-dependent clearance of accumulated polyubiquitinated proteins. In addition to mediating the sequestration of ubiquitinated cargos into phagophores, the precursors to autophagosomes, SQSTM1 is also important for polyubiquitinated aggregate formation upon proteasomal inhibition. Finally, we demonstrate that the concomitant stabilization of steady-state levels of ATF4, a rapidly degraded transcription factor, mediates SQSTM1 upregulation. These findings provide new insight into the molecular mechanisms by which selective autophagy is regulated in response to proteasomal overflow.
DOI: 10.6084/m9.figshare.5293759.v1
title: Is Use of Homeopathy a Proxy Indicator for Poor Prescribing in English Primary Care

description: Data (.csv) and analysis, using Python and Stata, to determine associations between homeopathy prescribing and prescribing measures on OpenPrescribing.net
DOI: 10.6084/m9.figshare.5293756.v1
title: Preferred, voluntary and critical temperatures from all individuals tested in ecophysiological experiments.

description: Supporting Information from the manuscript "Thermal physiology of Amazonian lizards (Reptilia: Squamata)".<br>
DOI: 10.6084/m9.figshare.5293696
title: A check list of non-lichenised fungi occurring on <i>Fagus crenata</i>, a tree endemic to Japan

description: Non-lichenised fungi from <i>Fagus crenata</i>, an endemic and major temperate tree species, were enumerated based on three approaches: fungarium specimens at the National Museum of Nature and Science; isolates obtained mainly from leaves and roots, and their molecular identification by barcoding region; and literature. In total, 209, 49, and 232 taxa were recognised from the fungarium specimens, isolates, and literature, respectively. Only three taxa were commonly observed using all three approaches. Moreover, the results demonstrate the diversity of fungi occurring on a single host plant species, and provide the basis for comparisons between fungi from <i>Fagus</i> spp. in other regions of the world.
DOI: 10.6084/m9.figshare.5293705.v1
title: SQSTM1/p62-mediated autophagy compensates for loss of proteasome polyubiquitin recruiting capacity

description: Protein homeostasis in eukaryotic cells is regulated by 2 highly conserved degradative pathways, the ubiquitin-proteasome system (UPS) and macroautophagy/autophagy. Recent studies revealed a coordinated and complementary crosstalk between these systems that becomes critical under proteostatic stress. Under physiological conditions, however, the molecular crosstalk between these 2 pathways is still far from clear. Here we describe a cellular model of proteasomal substrate accumulation due to the combined knockdown of PSMD4/S5a and ADRM1, the 2 proteasomal ubiquitin receptors. This model reveals a compensatory autophagic pathway, mediated by a SQSTM1/p62-dependent clearance of accumulated polyubiquitinated proteins. In addition to mediating the sequestration of ubiquitinated cargos into phagophores, the precursors to autophagosomes, SQSTM1 is also important for polyubiquitinated aggregate formation upon proteasomal inhibition. Finally, we demonstrate that the concomitant stabilization of steady-state levels of ATF4, a rapidly degraded transcription factor, mediates SQSTM1 upregulation. These findings provide new insight into the molecular mechanisms by which selective autophagy is regulated in response to proteasomal overflow.
DOI: 10.6084/m9.figshare.5293699
title: Flame Inhibition by Potassium-Containing Compounds

description: A kinetic model of inhibition by the potassium-containing compound potassium bicarbonate is suggested. The model is based on the previous work concerning kinetic studies of suppression of secondary flashes, inhibition by alkali metals, and the emission of sulfates and chlorides during biomass combustion. The kinetic model includes reactions with the following gas-phase potassium-containing species: K, KO, KO<sub>2</sub>, KO<sub>3</sub>, KH, KOH, K<sub>2</sub>O, K<sub>2</sub>O<sub>2</sub>, (KOH)<sub>2</sub>, K<sub>2</sub>CO<sub>3</sub>, KHCO<sub>3</sub>, and KCO<sub>3</sub>. Flame equilibrium calculations demonstrate that the main potassium-containing species in the combustion products are K and KOH. The main inhibition reactions, which comprise the radical termination inhibition cycle are KOH + H=K + H<sub>2</sub>O and K + OH + M=KOH + M with the overall termination effect: H + OH=H<sub>2</sub>O. Numerically predicted burning velocities for stoichiometric methane/air flames with added KHCO<sub>3</sub> demonstrate reasonable agreement with available experimental data. A strong saturation effect is observed for potassium compounds: approximately 0.1% volume fraction of KHCO<sub>3</sub> is required to decrease burning velocity by a factor of 2; however, an additional 0.6% volume fraction is required to reach a burning velocity of 5 cm/s. Analysis of the calculation results indicates that addition of the potassium compound quickly reduces the radical super-equilibrium down to equilibrium levels, so that further addition of the potassium compound has little effect on the flame radicals.
DOI: 10.6084/m9.figshare.5293696.v1
title: A check list of non-lichenised fungi occurring on <i>Fagus crenata</i>, a tree endemic to Japan

description: Non-lichenised fungi from <i>Fagus crenata</i>, an endemic and major temperate tree species, were enumerated based on three approaches: fungarium specimens at the National Museum of Nature and Science; isolates obtained mainly from leaves and roots, and their molecular identification by barcoding region; and literature. In total, 209, 49, and 232 taxa were recognised from the fungarium specimens, isolates, and literature, respectively. Only three taxa were commonly observed using all three approaches. Moreover, the results demonstrate the diversity of fungi occurring on a single host plant species, and provide the basis for comparisons between fungi from <i>Fagus</i> spp. in other regions of the world.
DOI: 10.6084/m9.figshare.5293699.v1
title: Flame Inhibition by Potassium-Containing Compounds

description: A kinetic model of inhibition by the potassium-containing compound potassium bicarbonate is suggested. The model is based on the previous work concerning kinetic studies of suppression of secondary flashes, inhibition by alkali metals, and the emission of sulfates and chlorides during biomass combustion. The kinetic model includes reactions with the following gas-phase potassium-containing species: K, KO, KO<sub>2</sub>, KO<sub>3</sub>, KH, KOH, K<sub>2</sub>O, K<sub>2</sub>O<sub>2</sub>, (KOH)<sub>2</sub>, K<sub>2</sub>CO<sub>3</sub>, KHCO<sub>3</sub>, and KCO<sub>3</sub>. Flame equilibrium calculations demonstrate that the main potassium-containing species in the combustion products are K and KOH. The main inhibition reactions, which comprise the radical termination inhibition cycle are KOH + H=K + H<sub>2</sub>O and K + OH + M=KOH + M with the overall termination effect: H + OH=H<sub>2</sub>O. Numerically predicted burning velocities for stoichiometric methane/air flames with added KHCO<sub>3</sub> demonstrate reasonable agreement with available experimental data. A strong saturation effect is observed for potassium compounds: approximately 0.1% volume fraction of KHCO<sub>3</sub> is required to decrease burning velocity by a factor of 2; however, an additional 0.6% volume fraction is required to reach a burning velocity of 5 cm/s. Analysis of the calculation results indicates that addition of the potassium compound quickly reduces the radical super-equilibrium down to equilibrium levels, so that further addition of the potassium compound has little effect on the flame radicals.
DOI: 10.6084/m9.figshare.5293672
title: Hypothermia increases aquaporin 4 (AQP4) plasma membrane abundance in human primary cortical astrocytes via a calcium/ transient receptor potential vanilloid 4 (TRPV4)- and calmodulin-mediated mechanism

description: Human aquaporin 4 (AQP4) is the primary water channel protein in brain astrocytes. Hypothermia is known to cause astrocyte swelling in culture, but the precise role of AQP4 in this process is unknown. This work shows that hypothermia led to an increase in surface localization of AQP4 in human astrocytes through a mechanism likely dependent on the TRPV4 calcium channel and calmodulin activation.
DOI: 10.6084/m9.figshare.5293672.v2
title: Hypothermia increases aquaporin 4 (AQP4) plasma membrane abundance in human primary cortical astrocytes via a calcium/ transient receptor potential vanilloid 4 (TRPV4)- and calmodulin-mediated mechanism

description: Human aquaporin 4 (AQP4) is the primary water channel protein in brain astrocytes. Hypothermia is known to cause astrocyte swelling in culture, but the precise role of AQP4 in this process is unknown. This work shows that hypothermia led to an increase in surface localization of AQP4 in human astrocytes through a mechanism likely dependent on the TRPV4 calcium channel and calmodulin activation.
DOI: 10.6084/m9.figshare.5293624
title: Eugenol exhibits anti-virulence properties by competitively binding to quorum sensing receptors

description: The primary objective of this study was to ascertain the anti-biofilm and anti-virulence properties of sub-minimum inhibitory concentration (MIC) levels of eugenol against the standard strain PAO1 and two multi-drug resistant <i>P. aeruginosa</i> clinical isolates utilizing quorum sensing inhibition (QSI). Eugenol at 400 μM significantly reduced biofilm formation on urinary catheters and the virulence factors (VF) including extracellular polysaccharides, rhamnolipid, elastase, protease, pyocyanin, and pyoverdine (<i>p</i> &lt; 0.001). Further, eugenol exhibited a marked effect on the production of QS signals (AIs) (<i>p</i> &lt; 0.001) without affecting their chemical integrity. <i>In silico</i> docking studies demonstrated a stable molecular binding between eugenol and QS receptor(s) in comparison with respective AIs. Investigation on reporter strains confirmed the competitive binding of eugenol to a QS receptor (LasR) as the possible QSI mechanism leading to significant repression of QS associated genes besides the VF genes (<i>p</i> &lt; 0.001). This study provides insights, for the first time, into the mechanism of the anti-virulence properties of eugenol.
DOI: 10.6084/m9.figshare.5293627
title: Application of methyl jasmonate to grey willow (Salix cinerea) attracts insectivorous birds in nature

description: Primary data for paper: Application of methyl jasmonate to grey willow (<i>Salix cinerea</i>) attracts insectivorous birds in nature.
DOI: 10.6084/m9.figshare.5293627.v1
title: Application of methyl jasmonate to grey willow (Salix cinerea) attracts insectivorous birds in nature

description: Primary data for paper: Application of methyl jasmonate to grey willow (<i>Salix cinerea</i>) attracts insectivorous birds in nature.
DOI: 10.6084/m9.figshare.5291110
title: A new flow-through bioassay for testing low-emission antifouling coatings

description: Current antifouling (AF) technologies are based on the continuous release of biocides into the water, and consequently discharge into the environment. Major efforts to develop more environmentally friendly coatings require efficient testing in laboratory assays, followed by field studies. Barnacles are important fouling organisms worldwide, increasing hydrodynamic drag on ships and damaging coatings on underwater surfaces, and thus are extensively used as models in AF research, mostly in static, laboratory-based systems. Reliable flow-through test assays for the screening of biocide-containing AF paints, however, are rare. Herein, a flow-through bioassay was developed to screen for diverse low-release biocide paints, and to evaluate their effects on pre- and post-settlement traits in barnacles. The assay distinguishes between the effects from direct surface contact and bulk-water effects, which are crucial when developing low-emission AF coatings. This flow-through bioassay adds a new tool for rapid laboratory-based first-stage screening of candidate compounds and novel AF formulations.
DOI: 10.6084/m9.figshare.5293624.v1
title: Eugenol exhibits anti-virulence properties by competitively binding to quorum sensing receptors

description: The primary objective of this study was to ascertain the anti-biofilm and anti-virulence properties of sub-minimum inhibitory concentration (MIC) levels of eugenol against the standard strain PAO1 and two multi-drug resistant <i>P. aeruginosa</i> clinical isolates utilizing quorum sensing inhibition (QSI). Eugenol at 400 μM significantly reduced biofilm formation on urinary catheters and the virulence factors (VF) including extracellular polysaccharides, rhamnolipid, elastase, protease, pyocyanin, and pyoverdine (<i>p</i> &lt; 0.001). Further, eugenol exhibited a marked effect on the production of QS signals (AIs) (<i>p</i> &lt; 0.001) without affecting their chemical integrity. <i>In silico</i> docking studies demonstrated a stable molecular binding between eugenol and QS receptor(s) in comparison with respective AIs. Investigation on reporter strains confirmed the competitive binding of eugenol to a QS receptor (LasR) as the possible QSI mechanism leading to significant repression of QS associated genes besides the VF genes (<i>p</i> &lt; 0.001). This study provides insights, for the first time, into the mechanism of the anti-virulence properties of eugenol.
DOI: 10.6084/m9.figshare.5290348
title: <i>In vitro</i> biofilm models to study dental caries: a systematic review

description: The aim of this systematic review is to characterize and discuss key methodological aspects of <i>in vitro</i> biofilm models for caries-related research and to verify the reproducibility and dose-response of models considering the response to anti-caries and/or antimicrobial substances. Inclusion criteria were divided into Part I (PI): an <i>in vitro</i> biofilm model that produces a cariogenic biofilm and/or caries-like lesions and allows pH fluctuations; and Part II (PII): models showing an effect of anti-caries and/or antimicrobial substances. Within PI, 72.9% consisted of dynamic biofilm models, while 27.1% consisted of batch models. Within PII, 75.5% corresponded to dynamic models, whereas 24.5% corresponded to batch models. Respectively, 20.4 and 14.3% of the studies reported dose-response validations and reproducibility, and 32.7% were classified as having a high risk of bias. Several <i>in vitro</i> biofilm models are available for caries-related research; however, most models lack validation by dose-response and reproducibility experiments for each proposed protocol.
DOI: 10.6084/m9.figshare.5290090
title: Supplementary Material for: Frontal Cortex Myo-Inositol Is Associated with Sleep and Depression in Adolescents: A Proton Magnetic Resonance Spectroscopy Study

description: <b><i>Aim:</i></b> This study used proton magnetic resonance spectroscopy (<sup>1</sup>H MRS) to evaluate the neurochemistry of the frontal cortex in adolescents with symptoms of sleep and depression. <b><i>Methods:</i></b> Nineteen non-medicated adolescent boys (mean age 16.0 years; 9 clinical cases with depression/sleep symptoms and 10 healthy controls) underwent <sup>1</sup>H MRS at 3 T. MR spectra were acquired from the anterior cingulate cortex (ACC), the dorsolateral prefrontal cortex, and frontal white matter. Concentrations of N-acetyl aspartate, total creatine, choline-containing compounds, total glutamine plus glutamate, and myo-inositol (mI) were compared in the 2 subgroups, and correlated with sleep and clinical measures in the total sample. Sleep was assessed with self-report questionnaires and ambulatory polysomnography recordings. <b><i>Results:</i></b> Concentrations of mI were lower in both frontal cortical regions among the depressed adolescents than in controls. No statistically significant differences in other metabolite concentrations were observed between the subgroups. Frontal cortex mI concentrations correlated negatively with depression severity, subjective daytime sleepiness, insomnia symptoms, and the level of anxiety, and correlated positively with total sleep time and overall psychosocial functioning. The correlations between mI in the ACC and total sleep time as well as daytime sleepiness remained statistically significant when depression severity was controlled in the analyses. <b><i>Conclusion:</i></b> Lower frontal cortex mI may indicate a disturbed second messenger system. Frontal cortical mI may thus be linked to the pathophysiology of depression and concomitant sleep symptoms among maturing adolescents. Short sleep and daytime sleepiness may be associated with frontal cortex mI independently from depression.
DOI: 10.6084/m9.figshare.5290348.v1
title: <i>In vitro</i> biofilm models to study dental caries: a systematic review

description: The aim of this systematic review is to characterize and discuss key methodological aspects of <i>in vitro</i> biofilm models for caries-related research and to verify the reproducibility and dose-response of models considering the response to anti-caries and/or antimicrobial substances. Inclusion criteria were divided into Part I (PI): an <i>in vitro</i> biofilm model that produces a cariogenic biofilm and/or caries-like lesions and allows pH fluctuations; and Part II (PII): models showing an effect of anti-caries and/or antimicrobial substances. Within PI, 72.9% consisted of dynamic biofilm models, while 27.1% consisted of batch models. Within PII, 75.5% corresponded to dynamic models, whereas 24.5% corresponded to batch models. Respectively, 20.4 and 14.3% of the studies reported dose-response validations and reproducibility, and 32.7% were classified as having a high risk of bias. Several <i>in vitro</i> biofilm models are available for caries-related research; however, most models lack validation by dose-response and reproducibility experiments for each proposed protocol.
DOI: 10.6084/m9.figshare.5291110.v1
title: A new flow-through bioassay for testing low-emission antifouling coatings

description: Current antifouling (AF) technologies are based on the continuous release of biocides into the water, and consequently discharge into the environment. Major efforts to develop more environmentally friendly coatings require efficient testing in laboratory assays, followed by field studies. Barnacles are important fouling organisms worldwide, increasing hydrodynamic drag on ships and damaging coatings on underwater surfaces, and thus are extensively used as models in AF research, mostly in static, laboratory-based systems. Reliable flow-through test assays for the screening of biocide-containing AF paints, however, are rare. Herein, a flow-through bioassay was developed to screen for diverse low-release biocide paints, and to evaluate their effects on pre- and post-settlement traits in barnacles. The assay distinguishes between the effects from direct surface contact and bulk-water effects, which are crucial when developing low-emission AF coatings. This flow-through bioassay adds a new tool for rapid laboratory-based first-stage screening of candidate compounds and novel AF formulations.
DOI: 10.6084/m9.figshare.5290009
title: Histological Sequences of Long Bone Development in the New Zealand White Rabbits

description: Long bone development occurred through endochondral ossification. The current study investigated the main histological changes associated with the development of humerus from the New Zealand white rabbits. The upper limb or humerus during embryonic (12, 14, 15, 16, 18, 21, 24 and 27 days) and neonatal (3 and 7 days) development was processed for light microscopy. Three stages preceded endochondral ossification; limb bud (mesenchymal cells), cartilage primordia (mesenchymal condensation and differentiation into chondrocytes) and cartilage template (organization of chondrocytes into proliferative and hypertrophic zones) by 12, 14 and 15 days, respectively. At day 16, cartilage template elongated forming a cartilaginous diaphysis of the prospective humerus. At day 18, cartilaginous epiphyses were formed. Medullary cavity was established by day 21 with no signs of calcification in the bone collar. Primary ossification center appeared within the diaphysis at day 24 of embryonic development. Secondary ossification centers were seen within the epiphyses by day 3 of neonatal development. Two types of cartilage canals were investigated; short epiphyseal canals appeared from day 21 and long transphyseal canals appeared from day 27. At day 7 of neonatal development, the cartilage of the humerus was limited in two places; articular epiphyseal growth cartilage between articular surface and secondary ossification center, epiphyseal physeal growth cartilage between the secondary and primary ossification centers. The current study summarized the main histological stages of development of rabbit humerus. These results should be considered in molecular studies of endochondral bone formation <br><br>
DOI: 10.6084/m9.figshare.5290015
title: Morphological and Biochemical Adaptive Changes Associated.pdf

description: Background The morphological and biochemical impact of a short-period of starvation on Japanese quail was investigated. Materials and methods Ten adult male Japanese quail were divided into two groups; control fed and starved. The control-fed group was offered food and water ad libitum and the starved group was subjected to a short-period of food deprivation. After 2.5 days, the serum was obtained and different parameters including the total protein, AST, ALT, triglyceride, HDL, LDL, creatinine and urea were assessed. Gastrointestinal tract, stomach and liver were excised and their masses were estimated. Paraffin and resin embedded sections from the proventriculus, gizzard, liver, duodenum, kidney and pancreas were examined with a light microscopy. Results Significant decreases in the masses of body, gastrointestinal tract, stomach and liver of the starved group were recorded. The liver and duodenum were the most affected organs. The liver showed depletion of glycogen, vacuolation, hyperemia and cellular infiltrations. Duodenal villi showed degenerative changes in lamina epithelialis and cellular infiltrations in the lamina propria. Biochemical analysis revealed a decreased level of total protein, AST and ALT, increased cholesterol, triglycerides and LDL, and unchanged HDL, urea and creatinine by starvation. Conclusion The current study described in details the effect of short time starvation on quail organs. Time-point adaptive responses of male quail to starvation and refeeding on quail organs will be investigated in future studies <br><br>
DOI: 10.6084/m9.figshare.5290045
title: Mathematica notebook with simulation methods

description: This notebook includes the simulation model for the paper "Introgression makes waves in inferred histories of effectivepopulation size". In the present state, the key elements of the simulations are expressed in functions, with the simulation of population structure with gene flow or introgression in the function "funkycoalescence". <br> These functions are insufficiently commented as they stand, and comments need to be added. The function incorporates the coalescence approach as described by Hudson (1990), with mutation (added as "rate") and migration (or instantaneous separation into subpopulations).